Starting phenix.real_space_refine on Sat Aug 8 04:27:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szw_40922/08_2026/8szw_40922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szw_40922/08_2026/8szw_40922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8szw_40922/08_2026/8szw_40922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szw_40922/08_2026/8szw_40922.map" model { file = "/net/cci-nas-00/data/ceres_data/8szw_40922/08_2026/8szw_40922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szw_40922/08_2026/8szw_40922.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.063 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 51 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 16105 2.51 5 N 4579 2.21 5 O 5087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25930 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1714 Classifications: {'peptide': 223} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "I" Number of atoms: 10424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1322, 10424 Classifications: {'peptide': 1322} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1266} Chain breaks: 1 Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10386 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 55, 'TRANS': 1280} Chain breaks: 2 Chain: "K" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 555 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "A" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 567 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 480 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14388 SG CYS J 70 95.723 108.214 98.833 1.00 99.82 S ATOM 14402 SG CYS J 72 97.651 109.596 99.617 1.00101.62 S ATOM 14510 SG CYS J 85 96.276 109.950 97.197 1.00 93.93 S ATOM 14534 SG CYS J 88 99.575 107.024 96.108 1.00100.58 S ATOM 20222 SG CYS J 814 55.175 72.379 59.658 1.00 58.61 S ATOM 20787 SG CYS J 888 58.455 71.809 62.194 1.00 49.96 S ATOM 20838 SG CYS J 895 56.245 71.860 62.314 1.00 48.36 S ATOM 20859 SG CYS J 898 56.474 70.111 61.649 1.00 42.69 S Time building chain proxies: 4.84, per 1000 atoms: 0.19 Number of scatterers: 25930 At special positions: 0 Unit cell: (164.628, 123.74, 166.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 105 16.00 P 51 15.00 Mg 1 11.99 O 5087 8.00 N 4579 7.00 C 16105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 769.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5872 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 51 sheets defined 38.7% alpha, 14.3% beta 20 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.790A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.721A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 228 through 233 removed outlier: 3.815A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 4.038A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.944A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.570A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 198 through 201 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.918A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.887A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.041A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE I 390 " --> pdb=" O GLU I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 451 removed outlier: 3.923A pdb=" N ARG I 451 " --> pdb=" O LEU I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.611A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.710A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 539 through 543 Processing helix chain 'I' and resid 551 through 555 removed outlier: 4.010A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 614 removed outlier: 4.272A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 609 through 614' Processing helix chain 'I' and resid 656 through 661 removed outlier: 4.216A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 705 through 712 Processing helix chain 'I' and resid 713 through 716 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.516A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 859 through 864 removed outlier: 4.191A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 981 removed outlier: 4.197A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU I 967 " --> pdb=" O GLU I 963 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 999 removed outlier: 4.230A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU I 999 " --> pdb=" O ARG I 996 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1009 removed outlier: 3.826A pdb=" N ASN I1009 " --> pdb=" O GLU I1006 " (cutoff:3.500A) Processing helix chain 'I' and resid 1010 through 1038 Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.292A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.731A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1150 Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.858A pdb=" N LYS I1196 " --> pdb=" O GLU I1192 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.551A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1261 through 1265 removed outlier: 3.640A pdb=" N GLN I1264 " --> pdb=" O GLY I1261 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1280 removed outlier: 3.854A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.702A pdb=" N ARG I1301 " --> pdb=" O ASP I1297 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.585A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.535A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.561A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.506A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.730A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 removed outlier: 4.147A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 406 through 417 removed outlier: 4.506A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE J 411 " --> pdb=" O VAL J 407 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 452 through 458 removed outlier: 4.238A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 588 through 593 Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.743A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.902A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 768 through 775 Processing helix chain 'J' and resid 776 through 804 removed outlier: 4.022A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.977A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.555A pdb=" N TYR J 899 " --> pdb=" O CYS J 895 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 895 through 900' Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.927A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1068 through 1073 removed outlier: 3.937A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 3.563A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 4.193A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1325 removed outlier: 3.927A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.729A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1348 through 1354 Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 71 Processing sheet with id=AA1, first strand: chain 'G' and resid 23 through 25 removed outlier: 4.281A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 105 removed outlier: 6.088A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.715A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 13 through 17 removed outlier: 3.756A pdb=" N LEU H 201 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 13 through 17 removed outlier: 3.756A pdb=" N LEU H 201 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.569A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AB1, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'H' and resid 110 through 111 removed outlier: 3.671A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 152 through 153 removed outlier: 3.560A pdb=" N ALA H 175 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.563A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.775A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB7, first strand: chain 'I' and resid 147 through 148 removed outlier: 6.324A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.598A pdb=" N ASP I 185 " --> pdb=" O ARG I 197 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG I 197 " --> pdb=" O ASP I 185 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 227 through 230 Processing sheet with id=AC1, first strand: chain 'I' and resid 238 through 240 Processing sheet with id=AC2, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.127A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC4, first strand: chain 'I' and resid 599 through 606 removed outlier: 5.554A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 633 through 637 Processing sheet with id=AC6, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.995A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'I' and resid 798 through 803 Processing sheet with id=AD2, first strand: chain 'I' and resid 1065 through 1067 removed outlier: 7.416A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.845A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.780A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD6, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD8, first strand: chain 'I' and resid 1268 through 1269 removed outlier: 3.688A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AE1, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.306A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.963A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE3, first strand: chain 'J' and resid 254 through 255 Processing sheet with id=AE4, first strand: chain 'J' and resid 355 through 356 removed outlier: 3.703A pdb=" N THR J 356 " --> pdb=" O ILE J 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'J' and resid 367 through 369 removed outlier: 5.841A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE7, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE8, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE9, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.146A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 991 through 996 removed outlier: 4.343A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 965 through 967 removed outlier: 3.871A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1080 through 1081 Processing sheet with id=AF4, first strand: chain 'J' and resid 1049 through 1050 removed outlier: 3.785A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.745A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 5.88 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4466 1.32 - 1.44: 6480 1.44 - 1.57: 15192 1.57 - 1.69: 100 1.69 - 1.82: 182 Bond restraints: 26420 Sorted by residual: bond pdb=" N LEU I 397 " pdb=" CA LEU I 397 " ideal model delta sigma weight residual 1.459 1.389 0.071 1.19e-02 7.06e+03 3.53e+01 bond pdb=" CA SER I 398 " pdb=" CB SER I 398 " ideal model delta sigma weight residual 1.530 1.452 0.078 1.69e-02 3.50e+03 2.15e+01 bond pdb=" CA ALA I 399 " pdb=" CB ALA I 399 " ideal model delta sigma weight residual 1.530 1.454 0.077 1.69e-02 3.50e+03 2.05e+01 bond pdb=" C1' DT B 127 " pdb=" N1 DT B 127 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" C1' DT B 105 " pdb=" N1 DT B 105 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.70e+01 ... (remaining 26415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.13: 35868 6.13 - 12.27: 25 12.27 - 18.40: 2 18.40 - 24.54: 1 24.54 - 30.67: 2 Bond angle restraints: 35898 Sorted by residual: angle pdb=" N ILE H 168 " pdb=" CA ILE H 168 " pdb=" CB ILE H 168 " ideal model delta sigma weight residual 111.23 141.90 -30.67 1.65e+00 3.67e-01 3.46e+02 angle pdb=" C PRO H 167 " pdb=" CA PRO H 167 " pdb=" CB PRO H 167 " ideal model delta sigma weight residual 110.10 90.03 20.07 1.90e+00 2.77e-01 1.12e+02 angle pdb=" N PRO H 167 " pdb=" CA PRO H 167 " pdb=" C PRO H 167 " ideal model delta sigma weight residual 112.10 86.03 26.07 2.50e+00 1.60e-01 1.09e+02 angle pdb=" N VAL I 400 " pdb=" CA VAL I 400 " pdb=" C VAL I 400 " ideal model delta sigma weight residual 111.05 99.39 11.66 1.25e+00 6.40e-01 8.70e+01 angle pdb=" N LEU I 397 " pdb=" CA LEU I 397 " pdb=" C LEU I 397 " ideal model delta sigma weight residual 111.07 102.58 8.49 1.07e+00 8.73e-01 6.29e+01 ... (remaining 35893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.88: 14944 26.88 - 53.76: 1070 53.76 - 80.64: 148 80.64 - 107.51: 17 107.51 - 134.39: 1 Dihedral angle restraints: 16180 sinusoidal: 7049 harmonic: 9131 Sorted by residual: dihedral pdb=" C PRO H 167 " pdb=" N PRO H 167 " pdb=" CA PRO H 167 " pdb=" CB PRO H 167 " ideal model delta harmonic sigma weight residual -120.70 -89.11 -31.59 0 2.50e+00 1.60e-01 1.60e+02 dihedral pdb=" N ILE H 168 " pdb=" C ILE H 168 " pdb=" CA ILE H 168 " pdb=" CB ILE H 168 " ideal model delta harmonic sigma weight residual 123.40 150.80 -27.40 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" C SER I 398 " pdb=" N SER I 398 " pdb=" CA SER I 398 " pdb=" CB SER I 398 " ideal model delta harmonic sigma weight residual -122.60 -101.23 -21.37 0 2.50e+00 1.60e-01 7.31e+01 ... (remaining 16177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 4087 0.176 - 0.351: 7 0.351 - 0.527: 2 0.527 - 0.702: 1 0.702 - 0.878: 1 Chirality restraints: 4098 Sorted by residual: chirality pdb=" CA ILE H 168 " pdb=" N ILE H 168 " pdb=" C ILE H 168 " pdb=" CB ILE H 168 " both_signs ideal model delta sigma weight residual False 2.43 1.56 0.88 2.00e-01 2.50e+01 1.93e+01 chirality pdb=" CA PRO H 167 " pdb=" N PRO H 167 " pdb=" C PRO H 167 " pdb=" CB PRO H 167 " both_signs ideal model delta sigma weight residual False 2.72 3.33 -0.61 2.00e-01 2.50e+01 9.38e+00 chirality pdb=" CA SER I 398 " pdb=" N SER I 398 " pdb=" C SER I 398 " pdb=" CB SER I 398 " both_signs ideal model delta sigma weight residual False 2.51 3.01 -0.50 2.00e-01 2.50e+01 6.36e+00 ... (remaining 4095 not shown) Planarity restraints: 4527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 53 " -0.643 9.50e-02 1.11e+02 2.88e-01 5.08e+01 pdb=" NE ARG J 53 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG J 53 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG J 53 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG J 53 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 479 " -0.026 2.00e-02 2.50e+03 5.24e-02 2.74e+01 pdb=" C LEU I 479 " 0.091 2.00e-02 2.50e+03 pdb=" O LEU I 479 " -0.035 2.00e-02 2.50e+03 pdb=" N SER I 480 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 26 " 0.020 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C VAL H 26 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL H 26 " 0.025 2.00e-02 2.50e+03 pdb=" N THR H 27 " 0.023 2.00e-02 2.50e+03 ... (remaining 4524 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 15 2.12 - 2.81: 7371 2.81 - 3.51: 36882 3.51 - 4.20: 58191 4.20 - 4.90: 104352 Nonbonded interactions: 206811 Sorted by model distance: nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1501 " model vdw 1.420 2.170 nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG J1501 " model vdw 1.988 2.170 nonbonded pdb=" OH TYR I 555 " pdb=" OD2 ASP I 654 " model vdw 1.991 3.040 nonbonded pdb=" OE1 GLU J 811 " pdb=" OG1 THR J 890 " model vdw 2.001 3.040 nonbonded pdb=" OG1 THR I 131 " pdb=" O THR I 135 " model vdw 2.007 3.040 ... (remaining 206806 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 'G' and (resid 6 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 6 through 233) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 26.430 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 0.264 26428 Z= 0.238 Angle : 1.043 61.725 35910 Z= 0.462 Chirality : 0.050 0.878 4098 Planarity : 0.006 0.288 4527 Dihedral : 17.491 134.393 10308 Min Nonbonded Distance : 1.420 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.69 % Favored : 93.97 % Rotamer: Outliers : 1.51 % Allowed : 19.86 % Favored : 78.63 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.15), residues: 3165 helix: 1.18 (0.17), residues: 1047 sheet: -1.39 (0.24), residues: 422 loop : -1.51 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 25 TYR 0.030 0.001 TYR I 395 PHE 0.016 0.001 PHE J1325 TRP 0.018 0.001 TRP I 807 HIS 0.007 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.23 (26420) covalent geometry : angle 0.73876 / 0.44 (35898) hydrogen bonds : bond 0.14996 / 10.28 ( 1044) hydrogen bonds : angle 6.08182 / 4.20 ( 2885) metal coordination : bond 0.11573 / 5.75 ( 8) metal coordination : angle 40.30062 / 22.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 597 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 170 ARG cc_start: 0.6427 (ttm170) cc_final: 0.6033 (ttm170) REVERT: H 15 ASP cc_start: 0.8052 (p0) cc_final: 0.7760 (p0) REVERT: H 50 SER cc_start: 0.8628 (p) cc_final: 0.8253 (t) REVERT: H 145 LYS cc_start: 0.6638 (tttp) cc_final: 0.5619 (tttp) REVERT: I 5 TYR cc_start: 0.5508 (t80) cc_final: 0.4858 (t80) REVERT: I 80 PHE cc_start: 0.6999 (m-10) cc_final: 0.6746 (m-10) REVERT: I 161 LYS cc_start: 0.8555 (mmtp) cc_final: 0.8303 (mtpt) REVERT: I 367 TYR cc_start: 0.8173 (t80) cc_final: 0.7739 (t80) REVERT: I 674 ASP cc_start: 0.8491 (m-30) cc_final: 0.8025 (m-30) REVERT: I 766 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8013 (p0) REVERT: I 870 ILE cc_start: 0.8255 (mt) cc_final: 0.7501 (mt) REVERT: I 1131 MET cc_start: 0.7506 (mtp) cc_final: 0.7044 (tpp) REVERT: I 1140 LYS cc_start: 0.7355 (mtmt) cc_final: 0.7057 (mtmm) REVERT: I 1211 ARG cc_start: 0.7551 (ttm110) cc_final: 0.7324 (ttp-110) REVERT: I 1214 ASP cc_start: 0.8680 (t0) cc_final: 0.8406 (t0) REVERT: I 1229 TYR cc_start: 0.8275 (m-80) cc_final: 0.7983 (m-80) REVERT: J 229 GLN cc_start: 0.8110 (mt0) cc_final: 0.7860 (mt0) REVERT: J 382 TYR cc_start: 0.7754 (m-10) cc_final: 0.7016 (m-10) REVERT: J 405 GLU cc_start: 0.7807 (tt0) cc_final: 0.7576 (tt0) REVERT: J 537 TYR cc_start: 0.8666 (t80) cc_final: 0.8453 (t80) REVERT: J 718 SER cc_start: 0.8581 (t) cc_final: 0.8156 (p) REVERT: J 743 MET cc_start: 0.8547 (ptp) cc_final: 0.8064 (ptm) REVERT: J 811 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6295 (mt-10) REVERT: J 979 ASN cc_start: 0.8056 (p0) cc_final: 0.7781 (p0) REVERT: K 43 ASN cc_start: 0.6723 (OUTLIER) cc_final: 0.6386 (t0) outliers start: 41 outliers final: 21 residues processed: 621 average time/residue: 0.1778 time to fit residues: 165.3367 Evaluate side-chains 482 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 459 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 43 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN G 147 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS I 387 ASN I 513 GLN I 725 GLN I 832 HIS I 856 ASN I1072 ASN I1146 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1268 GLN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 495 ASN J 921 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.239946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.178140 restraints weight = 30190.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.173618 restraints weight = 36736.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.165674 restraints weight = 23677.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.164337 restraints weight = 26218.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.165726 restraints weight = 23790.430| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 26428 Z= 0.394 Angle : 0.923 34.595 35910 Z= 0.452 Chirality : 0.050 0.236 4098 Planarity : 0.007 0.107 4527 Dihedral : 13.774 130.937 4140 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.52 % Favored : 92.29 % Rotamer: Outliers : 6.05 % Allowed : 20.01 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.15), residues: 3165 helix: 0.80 (0.16), residues: 1073 sheet: -1.42 (0.24), residues: 439 loop : -1.62 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 101 TYR 0.032 0.003 TYR H 68 PHE 0.030 0.002 PHE J 35 TRP 0.014 0.002 TRP I 183 HIS 0.008 0.002 HIS I 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00935 / 0.39 (26420) covalent geometry : angle 0.86118 / 0.45 (35898) hydrogen bonds : bond 0.05386 / 3.69 ( 1044) hydrogen bonds : angle 5.36937 / 3.69 ( 2885) metal coordination : bond 0.02438 / 1.33 ( 8) metal coordination : angle 18.24075 / 10.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 455 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7807 (mppt) REVERT: G 104 LYS cc_start: 0.8567 (tppt) cc_final: 0.8140 (tppp) REVERT: G 114 ASP cc_start: 0.7622 (m-30) cc_final: 0.7148 (m-30) REVERT: G 206 GLU cc_start: 0.7764 (tp30) cc_final: 0.7555 (tp30) REVERT: H 14 VAL cc_start: 0.6572 (OUTLIER) cc_final: 0.6323 (m) REVERT: H 15 ASP cc_start: 0.8206 (p0) cc_final: 0.7994 (p0) REVERT: H 147 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7969 (mm-40) REVERT: I 74 ARG cc_start: 0.7129 (mtp-110) cc_final: 0.6632 (mtm110) REVERT: I 161 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8596 (mtpt) REVERT: I 367 TYR cc_start: 0.8876 (t80) cc_final: 0.8107 (t80) REVERT: I 766 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8465 (p0) REVERT: I 870 ILE cc_start: 0.8389 (mt) cc_final: 0.7896 (mt) REVERT: I 1092 THR cc_start: 0.9223 (m) cc_final: 0.8990 (p) REVERT: I 1131 MET cc_start: 0.7712 (mtp) cc_final: 0.7319 (tpp) REVERT: I 1151 LEU cc_start: 0.7460 (tp) cc_final: 0.7005 (tp) REVERT: I 1303 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8319 (mttp) REVERT: J 229 GLN cc_start: 0.8535 (mt0) cc_final: 0.8113 (mt0) REVERT: J 382 TYR cc_start: 0.7793 (m-10) cc_final: 0.7010 (m-10) REVERT: J 702 GLN cc_start: 0.8151 (pp30) cc_final: 0.7800 (pp30) REVERT: J 802 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7633 (t70) REVERT: J 811 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: J 913 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6599 (mt-10) REVERT: J 979 ASN cc_start: 0.8943 (p0) cc_final: 0.8702 (p0) REVERT: J 1019 ASN cc_start: 0.8165 (t0) cc_final: 0.7656 (m110) REVERT: J 1040 MET cc_start: 0.5198 (ttm) cc_final: 0.2309 (mtm) REVERT: J 1148 ARG cc_start: 0.6932 (ptp-110) cc_final: 0.6724 (ptp-110) REVERT: K 48 VAL cc_start: 0.8506 (t) cc_final: 0.8253 (p) outliers start: 164 outliers final: 90 residues processed: 582 average time/residue: 0.1689 time to fit residues: 150.6968 Evaluate side-chains 505 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 409 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1188 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 728 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 811 GLU Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 996 LYS Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 119 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 237 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 143 optimal weight: 30.0000 chunk 169 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 213 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 GLN ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1157 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 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 = 0.4671 r_free = 0.4671 target = 0.246597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.199179 restraints weight = 30273.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.202202 restraints weight = 65758.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.203826 restraints weight = 33264.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.204590 restraints weight = 21427.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.205048 restraints weight = 18644.401| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26428 Z= 0.164 Angle : 0.748 32.517 35910 Z= 0.368 Chirality : 0.045 0.233 4098 Planarity : 0.005 0.057 4527 Dihedral : 13.683 131.595 4129 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 4.25 % Allowed : 22.37 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 3165 helix: 1.03 (0.16), residues: 1056 sheet: -1.27 (0.24), residues: 413 loop : -1.41 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 311 TYR 0.025 0.002 TYR H 185 PHE 0.021 0.002 PHE J 35 TRP 0.014 0.001 TRP I 807 HIS 0.006 0.001 HIS I1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (26420) covalent geometry : angle 0.70953 / 0.37 (35898) hydrogen bonds : bond 0.04276 / 2.91 ( 1044) hydrogen bonds : angle 4.92571 / 3.37 ( 2885) metal coordination : bond 0.01542 / 0.65 ( 8) metal coordination : angle 12.98057 / 7.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 445 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7657 (mppt) REVERT: G 206 GLU cc_start: 0.7763 (tp30) cc_final: 0.7528 (tp30) REVERT: H 14 VAL cc_start: 0.7133 (OUTLIER) cc_final: 0.6833 (m) REVERT: H 147 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7206 (mm-40) REVERT: I 367 TYR cc_start: 0.7708 (t80) cc_final: 0.7439 (t80) REVERT: I 1085 MET cc_start: 0.8740 (mmm) cc_final: 0.8180 (mmt) REVERT: I 1092 THR cc_start: 0.9320 (m) cc_final: 0.8985 (p) REVERT: I 1140 LYS cc_start: 0.7489 (mtmt) cc_final: 0.7161 (mtmm) REVERT: I 1203 ASP cc_start: 0.5907 (t0) cc_final: 0.5670 (t0) REVERT: I 1319 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.7061 (ttp) REVERT: J 29 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6748 (ptp) REVERT: J 35 PHE cc_start: 0.7099 (m-80) cc_final: 0.6894 (m-10) REVERT: J 130 MET cc_start: 0.6789 (mmm) cc_final: 0.6482 (mtt) REVERT: J 221 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8309 (mm) REVERT: J 229 GLN cc_start: 0.7858 (mt0) cc_final: 0.7563 (mt0) REVERT: J 382 TYR cc_start: 0.7842 (m-10) cc_final: 0.7098 (m-10) REVERT: J 707 ILE cc_start: 0.8140 (mp) cc_final: 0.7736 (mt) REVERT: J 718 SER cc_start: 0.8410 (t) cc_final: 0.8125 (p) REVERT: J 913 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6467 (mt-10) REVERT: J 1040 MET cc_start: 0.4135 (ttm) cc_final: 0.1714 (mtm) REVERT: K 31 GLN cc_start: 0.6260 (tt0) cc_final: 0.5913 (tm-30) REVERT: K 45 LYS cc_start: 0.7130 (mttt) cc_final: 0.6567 (mtpm) REVERT: K 48 VAL cc_start: 0.8494 (t) cc_final: 0.8220 (p) outliers start: 115 outliers final: 66 residues processed: 523 average time/residue: 0.1758 time to fit residues: 140.3618 Evaluate side-chains 476 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 405 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 996 LYS Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 147 optimal weight: 0.0670 chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 222 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN H 41 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1146 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 665 GLN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 929 GLN J1019 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.244512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.198534 restraints weight = 30000.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.202258 restraints weight = 66501.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.203129 restraints weight = 27990.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.203610 restraints weight = 20508.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.203985 restraints weight = 17729.152| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26428 Z= 0.214 Angle : 0.747 29.734 35910 Z= 0.369 Chirality : 0.045 0.258 4098 Planarity : 0.005 0.058 4527 Dihedral : 13.651 131.729 4117 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.32 % Favored : 93.49 % Rotamer: Outliers : 4.98 % Allowed : 22.70 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 3165 helix: 1.04 (0.16), residues: 1057 sheet: -1.08 (0.25), residues: 410 loop : -1.40 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 841 TYR 0.025 0.002 TYR H 185 PHE 0.016 0.001 PHE I 337 TRP 0.017 0.002 TRP J 33 HIS 0.005 0.001 HIS I1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (26420) covalent geometry : angle 0.72045 / 0.37 (35898) hydrogen bonds : bond 0.04210 / 2.87 ( 1044) hydrogen bonds : angle 4.87665 / 3.34 ( 2885) metal coordination : bond 0.01460 / 0.69 ( 8) metal coordination : angle 10.87639 / 6.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 410 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.7881 (mtmm) cc_final: 0.7678 (mppt) REVERT: G 206 GLU cc_start: 0.7769 (tp30) cc_final: 0.7504 (tp30) REVERT: H 14 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6750 (m) REVERT: I 367 TYR cc_start: 0.7604 (t80) cc_final: 0.7358 (t80) REVERT: I 370 MET cc_start: 0.7738 (tpp) cc_final: 0.7341 (tpp) REVERT: I 637 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8083 (ptm-80) REVERT: I 781 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6675 (m-30) REVERT: I 866 ASP cc_start: 0.6511 (p0) cc_final: 0.6130 (p0) REVERT: I 944 ARG cc_start: 0.7316 (tpp80) cc_final: 0.6770 (tpp80) REVERT: I 1092 THR cc_start: 0.9300 (m) cc_final: 0.9031 (p) REVERT: I 1140 LYS cc_start: 0.7506 (mtmt) cc_final: 0.7246 (mtmm) REVERT: I 1214 ASP cc_start: 0.8534 (t0) cc_final: 0.8288 (t0) REVERT: J 130 MET cc_start: 0.6866 (mmm) cc_final: 0.6571 (mtt) REVERT: J 221 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8323 (mm) REVERT: J 229 GLN cc_start: 0.7762 (mt0) cc_final: 0.7537 (mt0) REVERT: J 382 TYR cc_start: 0.7863 (m-10) cc_final: 0.7171 (m-10) REVERT: J 707 ILE cc_start: 0.8123 (mp) cc_final: 0.7673 (mt) REVERT: J 713 GLU cc_start: 0.6546 (mp0) cc_final: 0.6256 (mp0) REVERT: J 718 SER cc_start: 0.8511 (t) cc_final: 0.8241 (p) REVERT: J 802 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7452 (t70) REVERT: J 913 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6464 (mt-10) REVERT: J 1040 MET cc_start: 0.4319 (ttm) cc_final: 0.1885 (mtm) REVERT: K 48 VAL cc_start: 0.8552 (t) cc_final: 0.8207 (p) outliers start: 135 outliers final: 91 residues processed: 502 average time/residue: 0.1698 time to fit residues: 130.6745 Evaluate side-chains 484 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 387 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1243 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 996 LYS Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 259 optimal weight: 2.9990 chunk 275 optimal weight: 30.0000 chunk 221 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 306 optimal weight: 0.0270 chunk 92 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 218 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN G 227 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 GLN ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 665 GLN J 875 ASN ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** 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 = 0.4679 r_free = 0.4679 target = 0.247818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.200904 restraints weight = 29945.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.204069 restraints weight = 64319.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.205853 restraints weight = 31532.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.205976 restraints weight = 20848.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.207370 restraints weight = 17347.729| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26428 Z= 0.142 Angle : 0.699 27.121 35910 Z= 0.346 Chirality : 0.044 0.271 4098 Planarity : 0.005 0.063 4527 Dihedral : 13.589 132.081 4114 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 3.80 % Allowed : 24.36 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3165 helix: 1.13 (0.16), residues: 1052 sheet: -0.94 (0.25), residues: 408 loop : -1.31 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 31 TYR 0.026 0.001 TYR H 185 PHE 0.017 0.001 PHE G 8 TRP 0.025 0.002 TRP J 33 HIS 0.004 0.001 HIS J1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (26420) covalent geometry : angle 0.67685 / 0.34 (35898) hydrogen bonds : bond 0.03868 / 2.65 ( 1044) hydrogen bonds : angle 4.71500 / 3.21 ( 2885) metal coordination : bond 0.01082 / 0.52 ( 8) metal coordination : angle 9.46865 / 5.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 422 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7649 (mppt) REVERT: G 97 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6820 (pp20) REVERT: G 170 ARG cc_start: 0.6558 (ttm170) cc_final: 0.6225 (ttm170) REVERT: G 206 GLU cc_start: 0.7774 (tp30) cc_final: 0.7504 (tp30) REVERT: H 14 VAL cc_start: 0.7098 (OUTLIER) cc_final: 0.6776 (m) REVERT: H 38 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8253 (m) REVERT: I 284 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5744 (mm) REVERT: I 367 TYR cc_start: 0.7618 (t80) cc_final: 0.7379 (t80) REVERT: I 781 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6466 (m-30) REVERT: I 1092 THR cc_start: 0.9291 (m) cc_final: 0.8997 (p) REVERT: I 1203 ASP cc_start: 0.5885 (t0) cc_final: 0.5670 (t0) REVERT: I 1303 LYS cc_start: 0.8308 (mttp) cc_final: 0.7897 (ttmm) REVERT: J 33 TRP cc_start: 0.7247 (m-10) cc_final: 0.7024 (m-10) REVERT: J 102 MET cc_start: 0.5923 (ttp) cc_final: 0.5711 (ttp) REVERT: J 130 MET cc_start: 0.7098 (mmm) cc_final: 0.6838 (mtt) REVERT: J 221 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8379 (mm) REVERT: J 229 GLN cc_start: 0.7776 (mt0) cc_final: 0.7533 (mt0) REVERT: J 382 TYR cc_start: 0.7810 (m-10) cc_final: 0.7116 (m-10) REVERT: J 707 ILE cc_start: 0.8075 (mp) cc_final: 0.7611 (mt) REVERT: J 713 GLU cc_start: 0.6479 (mp0) cc_final: 0.6263 (mp0) REVERT: J 718 SER cc_start: 0.8469 (t) cc_final: 0.8239 (p) REVERT: J 902 ASP cc_start: 0.7402 (t0) cc_final: 0.6471 (t0) REVERT: J 913 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6505 (mt-10) REVERT: J 1040 MET cc_start: 0.4321 (ttm) cc_final: 0.1884 (mtm) REVERT: K 45 LYS cc_start: 0.6848 (mttt) cc_final: 0.6320 (mtpm) REVERT: K 48 VAL cc_start: 0.8459 (t) cc_final: 0.8109 (p) outliers start: 103 outliers final: 77 residues processed: 490 average time/residue: 0.1685 time to fit residues: 126.7794 Evaluate side-chains 479 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 395 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 996 LYS Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 200 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 318 optimal weight: 50.0000 chunk 109 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 41 ASN H 66 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN J 560 ASN J 665 GLN J1019 ASN ** J1259 GLN ** 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 = 0.4642 r_free = 0.4642 target = 0.243107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.179391 restraints weight = 29974.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.179977 restraints weight = 31234.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.174603 restraints weight = 20411.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.172430 restraints weight = 17962.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.173449 restraints weight = 21257.442| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 26428 Z= 0.245 Angle : 0.744 24.926 35910 Z= 0.372 Chirality : 0.046 0.253 4098 Planarity : 0.005 0.064 4527 Dihedral : 13.635 131.810 4110 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.45 % Favored : 93.36 % Rotamer: Outliers : 5.24 % Allowed : 23.66 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3165 helix: 1.01 (0.16), residues: 1054 sheet: -0.98 (0.25), residues: 411 loop : -1.36 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 10 TYR 0.058 0.002 TYR I1229 PHE 0.013 0.002 PHE J 35 TRP 0.017 0.001 TRP J 33 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (26420) covalent geometry : angle 0.72679 / 0.37 (35898) hydrogen bonds : bond 0.04142 / 2.83 ( 1044) hydrogen bonds : angle 4.81339 / 3.29 ( 2885) metal coordination : bond 0.01384 / 0.75 ( 8) metal coordination : angle 8.84566 / 4.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 399 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7758 (mppt) REVERT: G 51 MET cc_start: 0.7812 (mmm) cc_final: 0.7433 (mmm) REVERT: G 103 ASN cc_start: 0.8432 (t0) cc_final: 0.8170 (t0) REVERT: G 206 GLU cc_start: 0.7857 (tp30) cc_final: 0.7589 (tp30) REVERT: G 218 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7647 (mtp-110) REVERT: H 14 VAL cc_start: 0.6775 (OUTLIER) cc_final: 0.6440 (m) REVERT: H 18 GLN cc_start: 0.7979 (pm20) cc_final: 0.7710 (pm20) REVERT: H 84 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8385 (t0) REVERT: H 150 ARG cc_start: 0.6024 (mtt-85) cc_final: 0.5706 (mtt-85) REVERT: H 174 ASP cc_start: 0.6530 (m-30) cc_final: 0.6216 (m-30) REVERT: I 123 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.5178 (t80) REVERT: I 284 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6330 (mm) REVERT: I 367 TYR cc_start: 0.8556 (t80) cc_final: 0.7893 (t80) REVERT: I 528 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7065 (mtp-110) REVERT: I 637 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8354 (ptm-80) REVERT: I 684 ASN cc_start: 0.7933 (t0) cc_final: 0.7661 (t0) REVERT: I 781 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: I 944 ARG cc_start: 0.7203 (tpp80) cc_final: 0.6929 (tpp80) REVERT: I 1092 THR cc_start: 0.9292 (m) cc_final: 0.9054 (p) REVERT: I 1203 ASP cc_start: 0.6348 (t0) cc_final: 0.6049 (t0) REVERT: I 1214 ASP cc_start: 0.8629 (t0) cc_final: 0.8408 (t0) REVERT: I 1216 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8217 (mtm-85) REVERT: I 1303 LYS cc_start: 0.8618 (mttp) cc_final: 0.8172 (ttmm) REVERT: J 33 TRP cc_start: 0.7418 (m-10) cc_final: 0.6999 (m-10) REVERT: J 102 MET cc_start: 0.6790 (ttp) cc_final: 0.6442 (ttp) REVERT: J 221 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8894 (mm) REVERT: J 229 GLN cc_start: 0.8369 (mt0) cc_final: 0.7989 (mt0) REVERT: J 352 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7697 (ptm160) REVERT: J 382 TYR cc_start: 0.7772 (m-10) cc_final: 0.6973 (m-10) REVERT: J 449 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7454 (tt) REVERT: J 466 MET cc_start: 0.7677 (mtp) cc_final: 0.7405 (mtm) REVERT: J 644 MET cc_start: 0.7058 (mpp) cc_final: 0.6759 (mpp) REVERT: J 707 ILE cc_start: 0.8175 (mp) cc_final: 0.7794 (mt) REVERT: J 713 GLU cc_start: 0.6858 (mp0) cc_final: 0.6548 (mp0) REVERT: J 718 SER cc_start: 0.8648 (t) cc_final: 0.8397 (p) REVERT: J 913 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6611 (mt-10) REVERT: J 921 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: J 992 LYS cc_start: 0.8281 (tppt) cc_final: 0.7548 (mmtm) REVERT: J 1040 MET cc_start: 0.5255 (ttm) cc_final: 0.2452 (mtm) REVERT: K 31 GLN cc_start: 0.6402 (tm-30) cc_final: 0.6161 (tm-30) REVERT: K 48 VAL cc_start: 0.8533 (t) cc_final: 0.8142 (p) outliers start: 142 outliers final: 104 residues processed: 500 average time/residue: 0.1717 time to fit residues: 131.4955 Evaluate side-chains 506 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 390 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1243 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 481 ARG Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 921 GLN Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 996 LYS Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 262 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 253 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 239 optimal weight: 0.0030 chunk 96 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 41 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 ASN I 618 GLN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1146 GLN ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.247818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.199411 restraints weight = 30041.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.202768 restraints weight = 61158.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.203945 restraints weight = 33798.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.204619 restraints weight = 21114.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.205772 restraints weight = 18214.598| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26428 Z= 0.138 Angle : 0.701 22.627 35910 Z= 0.347 Chirality : 0.044 0.220 4098 Planarity : 0.005 0.085 4527 Dihedral : 13.615 132.249 4110 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.62 % Favored : 94.25 % Rotamer: Outliers : 4.02 % Allowed : 24.66 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3165 helix: 1.14 (0.16), residues: 1050 sheet: -0.86 (0.26), residues: 403 loop : -1.24 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 26 TYR 0.046 0.001 TYR I1229 PHE 0.021 0.001 PHE G 231 TRP 0.018 0.001 TRP J1020 HIS 0.006 0.001 HIS J1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (26420) covalent geometry : angle 0.67805 / 0.35 (35898) hydrogen bonds : bond 0.03784 / 2.60 ( 1044) hydrogen bonds : angle 4.66004 / 3.18 ( 2885) metal coordination : bond 0.00902 / 0.46 ( 8) metal coordination : angle 9.81662 / 5.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 420 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7656 (mppt) REVERT: G 97 GLU cc_start: 0.7041 (pp20) cc_final: 0.6732 (pp20) REVERT: G 103 ASN cc_start: 0.7919 (t0) cc_final: 0.7668 (t0) REVERT: G 141 SER cc_start: 0.8152 (t) cc_final: 0.7768 (t) REVERT: G 206 GLU cc_start: 0.7767 (tp30) cc_final: 0.7500 (tp30) REVERT: H 14 VAL cc_start: 0.7038 (OUTLIER) cc_final: 0.6707 (m) REVERT: I 123 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.4643 (t80) REVERT: I 197 ARG cc_start: 0.7480 (ptm160) cc_final: 0.7217 (mtm-85) REVERT: I 284 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5802 (mm) REVERT: I 448 LEU cc_start: 0.8124 (mt) cc_final: 0.7910 (mt) REVERT: I 781 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6574 (m-30) REVERT: I 932 GLN cc_start: 0.7514 (mp10) cc_final: 0.7271 (mp10) REVERT: I 1092 THR cc_start: 0.9198 (m) cc_final: 0.8960 (p) REVERT: I 1140 LYS cc_start: 0.7358 (mtmt) cc_final: 0.7063 (mtmm) REVERT: I 1203 ASP cc_start: 0.5893 (t0) cc_final: 0.5536 (t0) REVERT: I 1214 ASP cc_start: 0.8484 (t0) cc_final: 0.8224 (t0) REVERT: I 1216 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.8019 (mtm-85) REVERT: I 1303 LYS cc_start: 0.8279 (mttp) cc_final: 0.7851 (ttmm) REVERT: J 382 TYR cc_start: 0.7824 (m-10) cc_final: 0.7096 (m-10) REVERT: J 403 ARG cc_start: 0.7670 (tmm-80) cc_final: 0.7050 (tmm-80) REVERT: J 491 LEU cc_start: 0.8694 (tp) cc_final: 0.8327 (mp) REVERT: J 718 SER cc_start: 0.8378 (t) cc_final: 0.8178 (p) REVERT: J 902 ASP cc_start: 0.7411 (t0) cc_final: 0.6464 (t0) REVERT: J 913 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6576 (mt-10) REVERT: J 921 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: J 992 LYS cc_start: 0.8067 (tppt) cc_final: 0.7627 (mmtm) REVERT: J 1040 MET cc_start: 0.4485 (ttm) cc_final: 0.1984 (mtm) REVERT: K 48 VAL cc_start: 0.8420 (t) cc_final: 0.8085 (p) outliers start: 109 outliers final: 84 residues processed: 495 average time/residue: 0.1709 time to fit residues: 128.7003 Evaluate side-chains 484 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 394 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 437 ASN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1146 GLN Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 481 ARG Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 921 GLN Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 996 LYS Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 284 optimal weight: 5.9990 chunk 188 optimal weight: 30.0000 chunk 320 optimal weight: 30.0000 chunk 311 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 278 optimal weight: 20.0000 chunk 187 optimal weight: 0.7980 chunk 196 optimal weight: 20.0000 chunk 192 optimal weight: 8.9990 chunk 297 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 ASN I 684 ASN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1146 GLN ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 665 GLN ** J1259 GLN ** 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 = 0.4647 r_free = 0.4647 target = 0.243711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.192144 restraints weight = 30049.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176848 restraints weight = 44964.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.173258 restraints weight = 40547.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.173865 restraints weight = 36475.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.175035 restraints weight = 29017.569| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 26428 Z= 0.252 Angle : 0.761 21.740 35910 Z= 0.381 Chirality : 0.046 0.227 4098 Planarity : 0.005 0.086 4527 Dihedral : 13.702 131.926 4107 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.64 % Favored : 93.18 % Rotamer: Outliers : 4.43 % Allowed : 24.84 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 3165 helix: 0.90 (0.16), residues: 1064 sheet: -0.93 (0.26), residues: 406 loop : -1.33 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 74 TYR 0.055 0.002 TYR I1229 PHE 0.017 0.002 PHE G 231 TRP 0.019 0.001 TRP J1020 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.25 (26420) covalent geometry : angle 0.74223 / 0.38 (35898) hydrogen bonds : bond 0.04094 / 2.79 ( 1044) hydrogen bonds : angle 4.79725 / 3.28 ( 2885) metal coordination : bond 0.01448 / 0.71 ( 8) metal coordination : angle 9.12435 / 5.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 399 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7785 (mppt) REVERT: G 51 MET cc_start: 0.7609 (mmm) cc_final: 0.7300 (mmm) REVERT: G 130 ILE cc_start: 0.9079 (mp) cc_final: 0.8777 (mt) REVERT: G 218 ARG cc_start: 0.7533 (mtp-110) cc_final: 0.6932 (mtp-110) REVERT: H 14 VAL cc_start: 0.6905 (OUTLIER) cc_final: 0.6511 (m) REVERT: I 123 TYR cc_start: 0.6446 (OUTLIER) cc_final: 0.4891 (t80) REVERT: I 197 ARG cc_start: 0.7952 (ptm160) cc_final: 0.7435 (mtm-85) REVERT: I 284 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6423 (mm) REVERT: I 342 ASP cc_start: 0.8739 (t0) cc_final: 0.8384 (t70) REVERT: I 781 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.6808 (m-30) REVERT: I 1022 LYS cc_start: 0.9057 (ptpp) cc_final: 0.8759 (ptpp) REVERT: I 1203 ASP cc_start: 0.6241 (t0) cc_final: 0.5838 (t0) REVERT: I 1214 ASP cc_start: 0.8529 (t0) cc_final: 0.8308 (t0) REVERT: I 1303 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7975 (ttmm) REVERT: J 352 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7753 (ptm160) REVERT: J 382 TYR cc_start: 0.7801 (m-10) cc_final: 0.6974 (m-10) REVERT: J 449 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7433 (tt) REVERT: J 491 LEU cc_start: 0.8798 (tp) cc_final: 0.8401 (mp) REVERT: J 707 ILE cc_start: 0.8123 (mp) cc_final: 0.7667 (mt) REVERT: J 718 SER cc_start: 0.8475 (t) cc_final: 0.8270 (p) REVERT: J 754 ILE cc_start: 0.8563 (mp) cc_final: 0.8246 (mt) REVERT: J 902 ASP cc_start: 0.7598 (t0) cc_final: 0.6298 (t0) REVERT: J 913 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: J 921 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: J 992 LYS cc_start: 0.8262 (tppt) cc_final: 0.7651 (mmtm) REVERT: J 1040 MET cc_start: 0.5292 (ttm) cc_final: 0.2463 (mtm) REVERT: K 48 VAL cc_start: 0.8547 (t) cc_final: 0.8179 (p) outliers start: 120 outliers final: 94 residues processed: 484 average time/residue: 0.1756 time to fit residues: 129.3841 Evaluate side-chains 481 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 378 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 437 ASN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1243 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 921 GLN Chi-restraints excluded: chain J residue 953 LYS Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 996 LYS Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 230 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 254 optimal weight: 0.9990 chunk 264 optimal weight: 0.4980 chunk 186 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 295 optimal weight: 5.9990 chunk 263 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 93 GLN G 147 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 ASN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.247026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.201314 restraints weight = 29956.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.206418 restraints weight = 62410.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.204912 restraints weight = 27442.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.204840 restraints weight = 24146.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.205375 restraints weight = 18819.705| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26428 Z= 0.154 Angle : 0.729 19.907 35910 Z= 0.364 Chirality : 0.044 0.216 4098 Planarity : 0.005 0.077 4527 Dihedral : 13.672 131.952 4107 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 3.65 % Allowed : 25.88 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3165 helix: 0.98 (0.16), residues: 1051 sheet: -0.79 (0.26), residues: 403 loop : -1.26 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 297 TYR 0.060 0.002 TYR I1229 PHE 0.027 0.001 PHE J 35 TRP 0.053 0.002 TRP J 33 HIS 0.005 0.001 HIS I 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (26420) covalent geometry : angle 0.71280 / 0.36 (35898) hydrogen bonds : bond 0.03818 / 2.60 ( 1044) hydrogen bonds : angle 4.69735 / 3.22 ( 2885) metal coordination : bond 0.01020 / 0.45 ( 8) metal coordination : angle 8.30389 / 4.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 393 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 51 MET cc_start: 0.7483 (mmm) cc_final: 0.7145 (mmm) REVERT: G 97 GLU cc_start: 0.7022 (pp20) cc_final: 0.6706 (pp20) REVERT: G 150 ARG cc_start: 0.7357 (ttp80) cc_final: 0.7129 (ttm170) REVERT: G 218 ARG cc_start: 0.7375 (mtp-110) cc_final: 0.6861 (mtp-110) REVERT: H 14 VAL cc_start: 0.7026 (OUTLIER) cc_final: 0.6635 (m) REVERT: H 84 ASN cc_start: 0.8323 (t0) cc_final: 0.8010 (t0) REVERT: I 123 TYR cc_start: 0.6281 (OUTLIER) cc_final: 0.4387 (t80) REVERT: I 197 ARG cc_start: 0.7666 (ptm160) cc_final: 0.7305 (mtm-85) REVERT: I 284 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5646 (mm) REVERT: I 528 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6606 (mtp-110) REVERT: I 672 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7271 (pt0) REVERT: I 684 ASN cc_start: 0.7777 (t0) cc_final: 0.7512 (t0) REVERT: I 781 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: I 1085 MET cc_start: 0.8765 (mmm) cc_final: 0.8238 (mmt) REVERT: I 1214 ASP cc_start: 0.8557 (t0) cc_final: 0.8288 (t0) REVERT: I 1303 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7925 (ttmm) REVERT: J 180 MET cc_start: 0.5836 (mtm) cc_final: 0.5556 (mpp) REVERT: J 382 TYR cc_start: 0.7848 (m-10) cc_final: 0.7091 (m-10) REVERT: J 491 LEU cc_start: 0.8729 (tp) cc_final: 0.8372 (mp) REVERT: J 707 ILE cc_start: 0.8095 (mp) cc_final: 0.7585 (mt) REVERT: J 718 SER cc_start: 0.8415 (t) cc_final: 0.8203 (p) REVERT: J 754 ILE cc_start: 0.8471 (mp) cc_final: 0.8161 (mt) REVERT: J 902 ASP cc_start: 0.7435 (t0) cc_final: 0.6047 (t0) REVERT: J 913 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6645 (mt-10) REVERT: J 921 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: J 992 LYS cc_start: 0.8106 (tppt) cc_final: 0.7666 (mmtm) REVERT: J 1040 MET cc_start: 0.4442 (ttm) cc_final: 0.1948 (mtm) REVERT: K 48 VAL cc_start: 0.8397 (t) cc_final: 0.8054 (p) outliers start: 99 outliers final: 75 residues processed: 471 average time/residue: 0.1724 time to fit residues: 123.8246 Evaluate side-chains 461 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 377 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 437 ASN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 728 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 921 GLN Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 212 optimal weight: 0.4980 chunk 205 optimal weight: 30.0000 chunk 254 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 197 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 136 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 ASN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.248519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.202938 restraints weight = 30005.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.206162 restraints weight = 63521.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.206279 restraints weight = 31793.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.206694 restraints weight = 21681.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.207368 restraints weight = 18541.402| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26428 Z= 0.143 Angle : 0.732 17.796 35910 Z= 0.368 Chirality : 0.045 0.210 4098 Planarity : 0.005 0.074 4527 Dihedral : 13.638 131.871 4105 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.62 % Favored : 94.25 % Rotamer: Outliers : 3.17 % Allowed : 26.47 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 3165 helix: 0.97 (0.16), residues: 1055 sheet: -0.75 (0.27), residues: 378 loop : -1.22 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 297 TYR 0.031 0.001 TYR I1229 PHE 0.023 0.001 PHE J 17 TRP 0.032 0.002 TRP J 33 HIS 0.006 0.001 HIS I 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (26420) covalent geometry : angle 0.71934 / 0.37 (35898) hydrogen bonds : bond 0.03731 / 2.54 ( 1044) hydrogen bonds : angle 4.67272 / 3.21 ( 2885) metal coordination : bond 0.00864 / 0.38 ( 8) metal coordination : angle 7.32054 / 4.13 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 398 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 51 MET cc_start: 0.7457 (mmm) cc_final: 0.7102 (mmm) REVERT: G 97 GLU cc_start: 0.6952 (pp20) cc_final: 0.6637 (pp20) REVERT: G 150 ARG cc_start: 0.7345 (ttp80) cc_final: 0.7068 (ttp80) REVERT: G 218 ARG cc_start: 0.7418 (mtp-110) cc_final: 0.6923 (mtp-110) REVERT: H 14 VAL cc_start: 0.7065 (OUTLIER) cc_final: 0.6732 (m) REVERT: H 84 ASN cc_start: 0.8252 (t0) cc_final: 0.7826 (t0) REVERT: I 123 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.4494 (t80) REVERT: I 197 ARG cc_start: 0.7640 (ptm160) cc_final: 0.7314 (mtm-85) REVERT: I 284 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5664 (mm) REVERT: I 672 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7085 (pt0) REVERT: I 684 ASN cc_start: 0.7761 (t0) cc_final: 0.7513 (t0) REVERT: I 717 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7547 (t) REVERT: I 781 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6627 (m-30) REVERT: I 1027 LYS cc_start: 0.7929 (pttm) cc_final: 0.7281 (mtmm) REVERT: I 1214 ASP cc_start: 0.8515 (t0) cc_final: 0.8239 (t0) REVERT: I 1303 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7841 (ttmm) REVERT: J 382 TYR cc_start: 0.7826 (m-10) cc_final: 0.7027 (m-10) REVERT: J 491 LEU cc_start: 0.8660 (tp) cc_final: 0.8327 (mp) REVERT: J 707 ILE cc_start: 0.8077 (mp) cc_final: 0.7541 (mt) REVERT: J 902 ASP cc_start: 0.7439 (t0) cc_final: 0.6009 (t0) REVERT: J 913 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6650 (mt-10) REVERT: J 921 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: J 992 LYS cc_start: 0.8111 (tppt) cc_final: 0.7643 (mmtm) REVERT: J 1040 MET cc_start: 0.4391 (ttm) cc_final: 0.1903 (mtm) outliers start: 86 outliers final: 68 residues processed: 461 average time/residue: 0.1812 time to fit residues: 127.6390 Evaluate side-chains 452 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 375 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1024 GLU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1126 ASP Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 728 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 921 GLN Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 231 optimal weight: 0.0370 chunk 188 optimal weight: 30.0000 chunk 206 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 257 optimal weight: 7.9990 chunk 275 optimal weight: 20.0000 chunk 100 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 93 GLN G 147 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.242657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.197007 restraints weight = 29985.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.200774 restraints weight = 65261.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.197067 restraints weight = 24580.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.197958 restraints weight = 17661.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.198492 restraints weight = 13980.676| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 26428 Z= 0.264 Angle : 0.792 16.204 35910 Z= 0.400 Chirality : 0.047 0.202 4098 Planarity : 0.005 0.072 4527 Dihedral : 13.685 131.385 4102 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.54 % Favored : 93.27 % Rotamer: Outliers : 3.40 % Allowed : 26.36 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 3165 helix: 0.79 (0.16), residues: 1052 sheet: -0.90 (0.27), residues: 370 loop : -1.28 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 26 TYR 0.029 0.002 TYR I1018 PHE 0.014 0.002 PHE G 231 TRP 0.033 0.002 TRP J 33 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.26 (26420) covalent geometry : angle 0.78044 / 0.40 (35898) hydrogen bonds : bond 0.04123 / 2.81 ( 1044) hydrogen bonds : angle 4.82827 / 3.31 ( 2885) metal coordination : bond 0.01469 / 0.77 ( 8) metal coordination : angle 7.30498 / 4.12 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3932.50 seconds wall clock time: 68 minutes 41.99 seconds (4121.99 seconds total)