Starting phenix.real_space_refine on Sun Oct 12 16:54:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szw_40922/10_2025/8szw_40922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szw_40922/10_2025/8szw_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 { model { file = "/net/cci-nas-00/data/ceres_data/8szw_40922/10_2025/8szw_40922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szw_40922/10_2025/8szw_40922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8szw_40922/10_2025/8szw_40922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szw_40922/10_2025/8szw_40922.map" } 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-2.0-5842/lib/python3.9/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: 6.21, per 1000 atoms: 0.24 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: 2.31 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.21 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: 6.57 Time building geometry restraints manager: 3.05 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=" CA LEU I 397 " pdb=" CB LEU I 397 " ideal model delta sigma weight residual 1.529 1.591 -0.062 1.55e-02 4.16e+03 1.58e+01 bond pdb=" N TYR I 395 " pdb=" CA TYR I 395 " ideal model delta sigma weight residual 1.457 1.507 -0.049 1.29e-02 6.01e+03 1.46e+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: 1.130 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: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.290 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 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= 0.189 Angle : 1.031 61.725 35910 Z= 0.421 Chirality : 0.048 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 aren 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 covalent geometry : bond 0.00340 (26420) covalent geometry : angle 0.72116 (35898) hydrogen bonds : bond 0.14996 ( 1044) hydrogen bonds : angle 6.08182 ( 2885) metal coordination : bond 0.11573 ( 8) metal coordination : angle 40.30062 ( 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 : 1.001 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: 0.6034 (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: 0.8302 (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: 0.8276 (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: 0.7806 (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: 0.6296 (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: 0.2239 time to fit residues: 205.2906 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 : 0.997 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 856 ASN ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.238368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.176204 restraints weight = 30205.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.170537 restraints weight = 37423.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.161987 restraints weight = 23550.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.161324 restraints weight = 24183.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162500 restraints weight = 23256.341| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 26428 Z= 0.396 Angle : 0.910 34.914 35910 Z= 0.446 Chirality : 0.050 0.232 4098 Planarity : 0.007 0.094 4527 Dihedral : 13.822 132.678 4140 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.06 % Favored : 91.75 % Rotamer: Outliers : 6.35 % Allowed : 19.79 % Favored : 73.86 % 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 aren not related in a simple way. whole: -1.12 (0.15), residues: 3165 helix: 0.82 (0.16), residues: 1071 sheet: -1.37 (0.24), residues: 413 loop : -1.66 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J1148 TYR 0.026 0.003 TYR I 5 PHE 0.028 0.002 PHE J 35 TRP 0.007 0.002 TRP I1276 HIS 0.008 0.002 HIS I 673 Details of bonding type rmsd covalent geometry : bond 0.00946 (26420) covalent geometry : angle 0.86112 (35898) hydrogen bonds : bond 0.05127 ( 1044) hydrogen bonds : angle 5.31723 ( 2885) metal coordination : bond 0.02444 ( 8) metal coordination : angle 16.16338 ( 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 629 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 457 time to evaluate : 1.169 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: symmetry clash REVERT: G 10 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7744 (mppt) REVERT: G 68 TYR cc_start: 0.9137 (m-80) cc_final: 0.8932 (m-80) REVERT: G 104 LYS cc_start: 0.8599 (tppt) cc_final: 0.8397 (tppp) REVERT: G 120 ASP cc_start: 0.8816 (p0) cc_final: 0.8433 (p0) REVERT: G 206 GLU cc_start: 0.7814 (tp30) cc_final: 0.7494 (tp30) REVERT: H 14 VAL cc_start: 0.6687 (OUTLIER) cc_final: 0.6351 (m) REVERT: I 161 LYS cc_start: 0.8917 (mmtp) cc_final: 0.8651 (mtpt) REVERT: I 367 TYR cc_start: 0.8978 (t80) cc_final: 0.8139 (t80) REVERT: I 394 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7775 (ttm110) REVERT: I 870 ILE cc_start: 0.8221 (mt) cc_final: 0.7714 (mt) REVERT: I 1092 THR cc_start: 0.9250 (m) cc_final: 0.9026 (p) REVERT: I 1131 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7452 (tpp) REVERT: I 1151 LEU cc_start: 0.7434 (tp) cc_final: 0.7093 (tp) REVERT: I 1161 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7852 (mp) REVERT: I 1303 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8317 (mttp) REVERT: I 1319 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7597 (ttp) REVERT: J 98 ARG cc_start: 0.7248 (tpp-160) cc_final: 0.6653 (tpp-160) REVERT: J 229 GLN cc_start: 0.8627 (mt0) cc_final: 0.8164 (mt0) REVERT: J 382 TYR cc_start: 0.7826 (m-10) cc_final: 0.6942 (m-10) REVERT: J 802 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7805 (t0) REVERT: J 811 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6689 (mt-10) REVERT: J 913 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6701 (mt-10) REVERT: J 979 ASN cc_start: 0.9076 (p0) cc_final: 0.8805 (p0) REVERT: J 981 GLU cc_start: 0.7757 (tt0) cc_final: 0.7551 (tm-30) REVERT: J 1019 ASN cc_start: 0.8520 (t0) cc_final: 0.7976 (m110) REVERT: J 1040 MET cc_start: 0.5376 (ttm) cc_final: 0.2437 (mtm) REVERT: J 1148 ARG cc_start: 0.6942 (ptp-110) cc_final: 0.6680 (ptp-110) REVERT: K 31 GLN cc_start: 0.7167 (tt0) cc_final: 0.6930 (tm-30) REVERT: K 48 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8100 (p) outliers start: 172 outliers final: 99 residues processed: 588 average time/residue: 0.2046 time to fit residues: 183.3403 Evaluate side-chains 517 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 409 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 50 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 140 ILE Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 177 TYR 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 48 LEU 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 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 93 SER Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 163 LYS Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 209 ILE 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 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 749 ASP Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 830 THR 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 953 LEU Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1161 LEU 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 1292 THR Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain I residue 1339 LEU 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 401 VAL 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 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 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 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 801 VAL 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 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 862 THR 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 1135 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 Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 119 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 237 optimal weight: 0.6980 chunk 249 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 213 optimal weight: 0.5980 chunk 159 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 GLN I1146 GLN I1157 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.247262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.198753 restraints weight = 30237.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.201966 restraints weight = 65010.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.204187 restraints weight = 35553.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.203238 restraints weight = 27151.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.206805 restraints weight = 20097.989| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26428 Z= 0.143 Angle : 0.702 29.645 35910 Z= 0.347 Chirality : 0.044 0.208 4098 Planarity : 0.004 0.052 4527 Dihedral : 13.578 133.986 4124 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.15 % Favored : 94.66 % Rotamer: Outliers : 4.13 % Allowed : 22.19 % Favored : 73.68 % 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 aren not related in a simple way. whole: -0.73 (0.15), residues: 3165 helix: 1.13 (0.16), residues: 1053 sheet: -1.13 (0.25), residues: 409 loop : -1.40 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 293 TYR 0.025 0.001 TYR H 185 PHE 0.022 0.001 PHE J 35 TRP 0.014 0.001 TRP I 807 HIS 0.004 0.001 HIS I1313 Details of bonding type rmsd covalent geometry : bond 0.00330 (26420) covalent geometry : angle 0.67369 (35898) hydrogen bonds : bond 0.03879 ( 1044) hydrogen bonds : angle 4.79195 ( 2885) metal coordination : bond 0.01386 ( 8) metal coordination : angle 10.91360 ( 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 572 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 460 time to evaluate : 1.178 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: symmetry clash REVERT: G 10 LYS cc_start: 0.7894 (mtmm) cc_final: 0.7666 (mppt) REVERT: G 97 GLU cc_start: 0.7027 (pp20) cc_final: 0.6732 (pp20) REVERT: G 104 LYS cc_start: 0.8313 (tppt) cc_final: 0.8104 (tppp) REVERT: G 130 ILE cc_start: 0.9058 (mt) cc_final: 0.8799 (mp) REVERT: H 14 VAL cc_start: 0.7103 (OUTLIER) cc_final: 0.6800 (m) REVERT: H 147 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7408 (mm-40) REVERT: I 80 PHE cc_start: 0.6546 (m-10) cc_final: 0.6304 (m-10) REVERT: I 130 MET cc_start: 0.7831 (ttm) cc_final: 0.7558 (ttm) REVERT: I 202 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7744 (mtp-110) REVERT: I 367 TYR cc_start: 0.7889 (t80) cc_final: 0.7528 (t80) REVERT: I 565 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6426 (pt0) REVERT: I 681 MET cc_start: 0.7003 (mmt) cc_final: 0.6772 (mmt) REVERT: I 1092 THR cc_start: 0.9335 (m) cc_final: 0.9060 (p) REVERT: I 1214 ASP cc_start: 0.8568 (t0) cc_final: 0.8321 (t0) REVERT: J 130 MET cc_start: 0.7148 (mmm) cc_final: 0.6830 (mtt) REVERT: J 229 GLN cc_start: 0.7973 (mt0) cc_final: 0.7672 (mt0) REVERT: J 382 TYR cc_start: 0.7755 (m-10) cc_final: 0.7094 (m-10) REVERT: J 718 SER cc_start: 0.8506 (t) cc_final: 0.8227 (p) REVERT: J 902 ASP cc_start: 0.7500 (t0) cc_final: 0.6488 (t0) REVERT: J 913 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6478 (mt-10) REVERT: J 1040 MET cc_start: 0.4546 (ttm) cc_final: 0.1973 (mtm) REVERT: K 48 VAL cc_start: 0.8456 (t) cc_final: 0.8164 (p) outliers start: 112 outliers final: 71 residues processed: 538 average time/residue: 0.2133 time to fit residues: 172.4451 Evaluate side-chains 490 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 416 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU 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 105 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 50 SER Chi-restraints excluded: chain H residue 85 LEU 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 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 469 VAL Chi-restraints excluded: chain I residue 481 LEU 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 565 GLU 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 800 MET Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1157 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 J residue 97 VAL Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 311 ARG Chi-restraints excluded: chain J residue 350 SER 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 545 HIS 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 807 LEU 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 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1310 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 147 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 114 optimal weight: 0.1980 chunk 222 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 184 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN G 227 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I 437 ASN 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 365 GLN J 665 GLN J1019 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.249397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.202015 restraints weight = 30039.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.203292 restraints weight = 64102.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.205975 restraints weight = 39182.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.205560 restraints weight = 26232.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.208399 restraints weight = 21214.823| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26428 Z= 0.132 Angle : 0.670 25.226 35910 Z= 0.332 Chirality : 0.043 0.193 4098 Planarity : 0.004 0.052 4527 Dihedral : 13.402 133.689 4110 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 3.88 % Allowed : 22.92 % Favored : 73.20 % 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 aren not related in a simple way. whole: -0.56 (0.15), residues: 3165 helix: 1.21 (0.16), residues: 1056 sheet: -0.91 (0.25), residues: 405 loop : -1.27 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 150 TYR 0.024 0.001 TYR H 185 PHE 0.021 0.001 PHE J 35 TRP 0.017 0.002 TRP J 33 HIS 0.007 0.001 HIS J1252 Details of bonding type rmsd covalent geometry : bond 0.00305 (26420) covalent geometry : angle 0.64999 (35898) hydrogen bonds : bond 0.03608 ( 1044) hydrogen bonds : angle 4.64150 ( 2885) metal coordination : bond 0.01039 ( 8) metal coordination : angle 8.88615 ( 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 547 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 442 time to evaluate : 1.040 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 33 ARG cc_start: 0.8084 (tpp80) cc_final: 0.7841 (tpp80) REVERT: G 97 GLU cc_start: 0.6965 (pp20) cc_final: 0.6700 (pp20) REVERT: G 104 LYS cc_start: 0.8324 (tppt) cc_final: 0.8068 (tppp) REVERT: G 170 ARG cc_start: 0.6577 (ttm170) cc_final: 0.6252 (ttm170) REVERT: H 14 VAL cc_start: 0.6992 (OUTLIER) cc_final: 0.6764 (m) REVERT: I 197 ARG cc_start: 0.7759 (ptm160) cc_final: 0.7439 (ptm160) REVERT: I 367 TYR cc_start: 0.7735 (t80) cc_final: 0.7423 (t80) REVERT: I 448 LEU cc_start: 0.8144 (mt) cc_final: 0.7793 (mt) REVERT: I 565 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6228 (pt0) REVERT: I 681 MET cc_start: 0.6970 (mmt) cc_final: 0.6721 (mmt) REVERT: I 781 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7411 (m-30) REVERT: I 866 ASP cc_start: 0.5974 (p0) cc_final: 0.5413 (p0) REVERT: I 1092 THR cc_start: 0.9345 (m) cc_final: 0.9051 (p) REVERT: I 1214 ASP cc_start: 0.8534 (t0) cc_final: 0.8319 (t0) REVERT: I 1216 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8158 (mtm-85) REVERT: J 130 MET cc_start: 0.7317 (mmm) cc_final: 0.7091 (mtt) REVERT: J 229 GLN cc_start: 0.7908 (mt0) cc_final: 0.7666 (mt0) REVERT: J 382 TYR cc_start: 0.7779 (m-10) cc_final: 0.6998 (m-10) REVERT: J 403 ARG cc_start: 0.7737 (tmm-80) cc_final: 0.6921 (ttp80) REVERT: J 405 GLU cc_start: 0.7760 (tt0) cc_final: 0.7308 (tt0) REVERT: J 713 GLU cc_start: 0.6482 (mp0) cc_final: 0.6177 (mp0) REVERT: J 718 SER cc_start: 0.8430 (t) cc_final: 0.8221 (p) REVERT: J 802 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7396 (t0) REVERT: J 902 ASP cc_start: 0.7531 (t0) cc_final: 0.6629 (t0) REVERT: J 913 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6505 (mt-10) REVERT: J 1040 MET cc_start: 0.4480 (ttm) cc_final: 0.1918 (mtm) REVERT: K 48 VAL cc_start: 0.8464 (t) cc_final: 0.8106 (p) outliers start: 105 outliers final: 71 residues processed: 516 average time/residue: 0.2140 time to fit residues: 166.1765 Evaluate side-chains 492 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 416 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU 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 105 SER Chi-restraints excluded: chain G residue 178 SER 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 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 85 LEU 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 377 THR Chi-restraints excluded: chain I residue 437 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 565 GLU 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 735 LYS 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 1056 VAL Chi-restraints excluded: chain I residue 1066 MET 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 1250 SER Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 311 ARG 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 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 545 HIS 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 802 ASP 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 913 GLU Chi-restraints excluded: chain J residue 996 LYS Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1283 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 259 optimal weight: 9.9990 chunk 275 optimal weight: 30.0000 chunk 221 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 152 optimal weight: 0.3980 chunk 306 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 125 optimal weight: 0.7980 chunk 218 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN H 41 ASN H 147 GLN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1136 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** J 365 GLN J 560 ASN J 665 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.247182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.199912 restraints weight = 30044.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.203752 restraints weight = 63064.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.204774 restraints weight = 30724.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.205128 restraints weight = 20492.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.208032 restraints weight = 17258.240| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26428 Z= 0.161 Angle : 0.684 21.738 35910 Z= 0.339 Chirality : 0.044 0.223 4098 Planarity : 0.005 0.075 4527 Dihedral : 13.374 133.228 4105 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.72 % Favored : 94.12 % Rotamer: Outliers : 4.13 % Allowed : 23.33 % Favored : 72.54 % 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 aren not related in a simple way. whole: -0.51 (0.15), residues: 3165 helix: 1.19 (0.16), residues: 1060 sheet: -0.80 (0.26), residues: 403 loop : -1.23 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I1033 TYR 0.024 0.001 TYR H 185 PHE 0.022 0.001 PHE J 35 TRP 0.015 0.001 TRP J1020 HIS 0.004 0.001 HIS I1313 Details of bonding type rmsd covalent geometry : bond 0.00382 (26420) covalent geometry : angle 0.66996 (35898) hydrogen bonds : bond 0.03639 ( 1044) hydrogen bonds : angle 4.57796 ( 2885) metal coordination : bond 0.00789 ( 8) metal coordination : angle 7.56484 ( 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 534 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 422 time to evaluate : 1.056 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 97 GLU cc_start: 0.6970 (pp20) cc_final: 0.6692 (pp20) REVERT: G 104 LYS cc_start: 0.8196 (tppt) cc_final: 0.7895 (tppp) REVERT: G 114 ASP cc_start: 0.6978 (m-30) cc_final: 0.6405 (m-30) REVERT: G 170 ARG cc_start: 0.6571 (ttm170) cc_final: 0.6246 (ttm170) REVERT: H 14 VAL cc_start: 0.6990 (OUTLIER) cc_final: 0.6599 (m) REVERT: I 123 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.5451 (t80) REVERT: I 187 GLU cc_start: 0.7660 (pt0) cc_final: 0.7404 (pt0) REVERT: I 197 ARG cc_start: 0.7812 (ptm160) cc_final: 0.7490 (ptm160) REVERT: I 200 ARG cc_start: 0.7346 (mtm-85) cc_final: 0.7124 (mtm180) REVERT: I 284 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.5939 (mm) REVERT: I 367 TYR cc_start: 0.7764 (t80) cc_final: 0.7487 (t80) REVERT: I 448 LEU cc_start: 0.8184 (mt) cc_final: 0.7981 (mt) REVERT: I 781 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: I 1092 THR cc_start: 0.9334 (m) cc_final: 0.9031 (p) REVERT: I 1131 MET cc_start: 0.8213 (ttm) cc_final: 0.7648 (tpp) REVERT: I 1203 ASP cc_start: 0.5713 (t0) cc_final: 0.5513 (t0) REVERT: I 1214 ASP cc_start: 0.8529 (t0) cc_final: 0.8323 (t0) REVERT: I 1216 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.8190 (mtm-85) REVERT: I 1315 MET cc_start: 0.7563 (ptp) cc_final: 0.6990 (ptp) REVERT: J 180 MET cc_start: 0.3771 (mtp) cc_final: 0.3502 (mmm) REVERT: J 229 GLN cc_start: 0.7855 (mt0) cc_final: 0.7625 (mt0) REVERT: J 382 TYR cc_start: 0.7820 (m-10) cc_final: 0.7008 (m-10) REVERT: J 403 ARG cc_start: 0.7789 (tmm-80) cc_final: 0.6622 (tmm-80) REVERT: J 405 GLU cc_start: 0.7754 (tt0) cc_final: 0.6861 (tt0) REVERT: J 491 LEU cc_start: 0.8764 (tp) cc_final: 0.8405 (mp) REVERT: J 713 GLU cc_start: 0.6486 (mp0) cc_final: 0.6150 (mp0) REVERT: J 718 SER cc_start: 0.8496 (t) cc_final: 0.8295 (p) REVERT: J 902 ASP cc_start: 0.7615 (t0) cc_final: 0.6351 (t0) REVERT: J 913 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6678 (mt-10) REVERT: J 1040 MET cc_start: 0.4480 (ttm) cc_final: 0.1907 (mtm) REVERT: J 1261 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8618 (pt) REVERT: K 48 VAL cc_start: 0.8393 (t) cc_final: 0.8043 (p) outliers start: 112 outliers final: 79 residues processed: 507 average time/residue: 0.2080 time to fit residues: 160.0018 Evaluate side-chains 484 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 399 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 LEU 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 105 SER Chi-restraints excluded: chain G residue 178 SER 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 101 ARG Chi-restraints excluded: chain I residue 118 LYS 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 442 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 735 LYS 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 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 1157 GLN Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1332 SER 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 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 507 VAL 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 746 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 807 LEU 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 991 THR Chi-restraints excluded: chain J residue 996 LYS Chi-restraints excluded: chain J residue 1024 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 200 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 318 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 258 optimal weight: 30.0000 chunk 53 optimal weight: 0.0270 chunk 193 optimal weight: 9.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN I 86 GLN I 437 ASN I 684 ASN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 GLN I1072 ASN ** 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 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.238230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.175083 restraints weight = 30049.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.169798 restraints weight = 36297.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.161262 restraints weight = 22542.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.160570 restraints weight = 21942.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.161698 restraints weight = 23168.461| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.096 26428 Z= 0.404 Angle : 0.851 18.722 35910 Z= 0.430 Chirality : 0.050 0.191 4098 Planarity : 0.006 0.072 4527 Dihedral : 13.591 131.838 4102 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.68 % Favored : 92.13 % Rotamer: Outliers : 5.46 % Allowed : 22.85 % Favored : 71.69 % 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 aren not related in a simple way. whole: -0.94 (0.15), residues: 3165 helix: 0.66 (0.16), residues: 1068 sheet: -0.96 (0.25), residues: 409 loop : -1.40 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J1148 TYR 0.024 0.002 TYR H 185 PHE 0.026 0.002 PHE J 437 TRP 0.033 0.003 TRP J 33 HIS 0.010 0.002 HIS I 673 Details of bonding type rmsd covalent geometry : bond 0.00963 (26420) covalent geometry : angle 0.84132 (35898) hydrogen bonds : bond 0.04685 ( 1044) hydrogen bonds : angle 5.03619 ( 2885) metal coordination : bond 0.01989 ( 8) metal coordination : angle 7.11777 ( 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 560 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 412 time to evaluate : 0.892 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: 0.7962 (mmm) cc_final: 0.7620 (mmm) REVERT: G 114 ASP cc_start: 0.7705 (m-30) cc_final: 0.7499 (m-30) REVERT: H 14 VAL cc_start: 0.6791 (OUTLIER) cc_final: 0.6464 (m) REVERT: H 66 HIS cc_start: 0.7785 (t-90) cc_final: 0.7448 (t-90) REVERT: H 78 ILE cc_start: 0.9584 (mm) cc_final: 0.9358 (mt) REVERT: I 123 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.5435 (t80) REVERT: I 130 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8075 (ttm) REVERT: I 284 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6750 (mm) REVERT: I 367 TYR cc_start: 0.8953 (t80) cc_final: 0.8108 (t80) REVERT: I 370 MET cc_start: 0.8468 (tpp) cc_final: 0.8196 (mmp) REVERT: I 476 LYS cc_start: 0.9026 (tppt) cc_final: 0.8309 (tptt) REVERT: I 672 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: I 1085 MET cc_start: 0.8852 (mmm) cc_final: 0.8388 (mmt) REVERT: I 1203 ASP cc_start: 0.6612 (t0) cc_final: 0.6348 (t0) REVERT: I 1274 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: I 1327 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7401 (mp) REVERT: J 382 TYR cc_start: 0.7909 (m-10) cc_final: 0.7006 (m-10) REVERT: J 403 ARG cc_start: 0.8091 (tmm-80) cc_final: 0.7114 (ttp80) REVERT: J 405 GLU cc_start: 0.8101 (tt0) cc_final: 0.7565 (tt0) REVERT: J 754 ILE cc_start: 0.8610 (mp) cc_final: 0.8304 (mt) REVERT: J 822 MET cc_start: 0.6652 (tpt) cc_final: 0.6219 (tpp) REVERT: J 878 ASP cc_start: 0.7238 (t0) cc_final: 0.7013 (t0) REVERT: J 913 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: J 1040 MET cc_start: 0.5432 (ttm) cc_final: 0.2505 (mtm) REVERT: J 1197 ASN cc_start: 0.7826 (t0) cc_final: 0.7168 (m-40) REVERT: K 48 VAL cc_start: 0.8508 (t) cc_final: 0.8177 (p) outliers start: 148 outliers final: 108 residues processed: 524 average time/residue: 0.1953 time to fit residues: 155.7517 Evaluate side-chains 513 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 397 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 105 SER Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 178 SER 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 41 ASN 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 142 MET Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 222 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 101 ARG 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 163 LYS Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 346 TYR 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 456 VAL Chi-restraints excluded: chain I residue 479 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 622 ASN 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 672 GLU Chi-restraints excluded: chain I residue 749 ASP 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 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 1066 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1243 MET Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1332 SER 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 434 ILE 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 507 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 582 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 728 SER Chi-restraints excluded: chain J residue 733 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 801 VAL 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 890 THR 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 1135 THR 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 1285 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 262 optimal weight: 9.9990 chunk 287 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 253 optimal weight: 0.7980 chunk 270 optimal weight: 7.9990 chunk 239 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 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 340 GLN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 665 GLN J 875 ASN ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.246899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.199568 restraints weight = 29985.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.202878 restraints weight = 64781.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.204318 restraints weight = 32001.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.204677 restraints weight = 20900.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.205598 restraints weight = 17930.816| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26428 Z= 0.141 Angle : 0.702 15.383 35910 Z= 0.347 Chirality : 0.044 0.261 4098 Planarity : 0.004 0.055 4527 Dihedral : 13.475 132.589 4102 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.34 % Favored : 94.47 % Rotamer: Outliers : 3.62 % Allowed : 24.81 % Favored : 71.58 % 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 aren not related in a simple way. whole: -0.61 (0.15), residues: 3165 helix: 0.97 (0.16), residues: 1051 sheet: -0.64 (0.26), residues: 391 loop : -1.23 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 371 TYR 0.025 0.001 TYR H 185 PHE 0.021 0.001 PHE I 337 TRP 0.025 0.002 TRP J 33 HIS 0.005 0.001 HIS J1252 Details of bonding type rmsd covalent geometry : bond 0.00329 (26420) covalent geometry : angle 0.68864 (35898) hydrogen bonds : bond 0.03601 ( 1044) hydrogen bonds : angle 4.62002 ( 2885) metal coordination : bond 0.01173 ( 8) metal coordination : angle 7.59760 ( 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 509 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 411 time to evaluate : 0.680 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 104 LYS cc_start: 0.8179 (tppp) cc_final: 0.7791 (tppp) REVERT: H 14 VAL cc_start: 0.6886 (OUTLIER) cc_final: 0.6628 (m) REVERT: I 123 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.4603 (t80) REVERT: I 187 GLU cc_start: 0.7479 (pt0) cc_final: 0.7253 (pt0) REVERT: I 284 LEU cc_start: 0.6115 (OUTLIER) cc_final: 0.5733 (mm) REVERT: I 528 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6631 (mtp-110) REVERT: J 33 TRP cc_start: 0.7183 (m-10) cc_final: 0.6552 (m-10) REVERT: J 382 TYR cc_start: 0.7838 (m-10) cc_final: 0.7046 (m-10) REVERT: J 403 ARG cc_start: 0.7783 (tmm-80) cc_final: 0.7547 (tmm-80) REVERT: J 811 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6858 (mt-10) REVERT: J 902 ASP cc_start: 0.7436 (t0) cc_final: 0.6519 (t0) REVERT: J 913 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6593 (mt-10) REVERT: J 1040 MET cc_start: 0.4261 (ttm) cc_final: 0.1757 (mtm) outliers start: 98 outliers final: 72 residues processed: 481 average time/residue: 0.2082 time to fit residues: 150.0882 Evaluate side-chains 466 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 388 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 105 SER Chi-restraints excluded: chain G residue 201 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 39 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 211 ILE 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 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 498 ILE Chi-restraints excluded: chain I residue 528 ARG Chi-restraints excluded: chain I residue 550 VAL 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 1096 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1332 SER 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 357 VAL 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 507 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 722 ILE 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 801 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 811 GLU 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 991 THR Chi-restraints excluded: chain J residue 996 LYS Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1221 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 1310 THR Chi-restraints excluded: chain J residue 1324 SER 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: 8.9990 chunk 188 optimal weight: 30.0000 chunk 320 optimal weight: 10.0000 chunk 311 optimal weight: 0.6980 chunk 296 optimal weight: 0.8980 chunk 278 optimal weight: 20.0000 chunk 187 optimal weight: 0.0570 chunk 196 optimal weight: 40.0000 chunk 192 optimal weight: 20.0000 chunk 297 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN I 437 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.246301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.200885 restraints weight = 29973.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.205799 restraints weight = 62982.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.203611 restraints weight = 24112.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.204305 restraints weight = 18159.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.204814 restraints weight = 14930.407| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26428 Z= 0.157 Angle : 0.699 13.471 35910 Z= 0.348 Chirality : 0.044 0.240 4098 Planarity : 0.004 0.056 4527 Dihedral : 13.446 132.201 4100 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.78 % Favored : 94.03 % Rotamer: Outliers : 3.77 % Allowed : 25.84 % Favored : 70.39 % 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 aren not related in a simple way. whole: -0.56 (0.15), residues: 3165 helix: 0.96 (0.16), residues: 1067 sheet: -0.68 (0.26), residues: 411 loop : -1.18 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 74 TYR 0.027 0.001 TYR H 185 PHE 0.010 0.001 PHE J 35 TRP 0.019 0.001 TRP J1020 HIS 0.005 0.001 HIS I 343 Details of bonding type rmsd covalent geometry : bond 0.00373 (26420) covalent geometry : angle 0.68955 (35898) hydrogen bonds : bond 0.03611 ( 1044) hydrogen bonds : angle 4.61189 ( 2885) metal coordination : bond 0.01004 ( 8) metal coordination : angle 6.44280 ( 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 490 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 388 time to evaluate : 0.995 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: 0.7545 (mmm) cc_final: 0.7068 (mmm) REVERT: G 100 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8223 (mt) REVERT: H 14 VAL cc_start: 0.7023 (OUTLIER) cc_final: 0.6757 (m) REVERT: I 123 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.4393 (t80) REVERT: I 187 GLU cc_start: 0.7600 (pt0) cc_final: 0.7318 (pt0) REVERT: I 197 ARG cc_start: 0.7610 (ptm160) cc_final: 0.7314 (mtm-85) REVERT: I 284 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5739 (mm) REVERT: I 476 LYS cc_start: 0.7974 (tptt) cc_final: 0.7529 (tptt) REVERT: I 528 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6642 (mtp-110) REVERT: J 340 GLN cc_start: 0.7563 (tt0) cc_final: 0.7258 (tt0) REVERT: J 382 TYR cc_start: 0.7851 (m-10) cc_final: 0.7087 (m-10) REVERT: J 403 ARG cc_start: 0.7752 (tmm-80) cc_final: 0.7009 (ttp80) REVERT: J 405 GLU cc_start: 0.7701 (tt0) cc_final: 0.7398 (tt0) REVERT: J 491 LEU cc_start: 0.8727 (tp) cc_final: 0.8381 (mp) REVERT: J 811 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: J 902 ASP cc_start: 0.7590 (t0) cc_final: 0.6356 (t0) REVERT: J 913 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6566 (mt-10) REVERT: J 992 LYS cc_start: 0.8192 (tppt) cc_final: 0.7714 (mmtm) REVERT: J 1040 MET cc_start: 0.4275 (ttm) cc_final: 0.1753 (mtm) REVERT: J 1148 ARG cc_start: 0.6784 (ptp-170) cc_final: 0.6332 (ptp90) REVERT: J 1197 ASN cc_start: 0.6969 (t0) cc_final: 0.6625 (m110) REVERT: J 1261 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8710 (pt) REVERT: K 48 VAL cc_start: 0.8395 (t) cc_final: 0.8057 (p) outliers start: 102 outliers final: 68 residues processed: 464 average time/residue: 0.2077 time to fit residues: 146.1164 Evaluate side-chains 452 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 376 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain G residue 105 SER 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 16 ILE 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 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 6 THR 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 434 ASP 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 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 630 VAL Chi-restraints excluded: chain I residue 655 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 1056 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1250 SER 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 453 VAL 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 525 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR 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 811 GLU Chi-restraints excluded: chain J residue 872 LEU 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 1024 THR Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 230 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 264 optimal weight: 0.7980 chunk 186 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 35 optimal weight: 30.0000 chunk 295 optimal weight: 8.9990 chunk 263 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN H 41 ASN 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** J 665 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.243276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.196383 restraints weight = 30153.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.201187 restraints weight = 63904.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.199153 restraints weight = 24615.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.199884 restraints weight = 18106.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.200391 restraints weight = 14761.998| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 26428 Z= 0.199 Angle : 0.726 13.266 35910 Z= 0.363 Chirality : 0.045 0.233 4098 Planarity : 0.005 0.055 4527 Dihedral : 13.500 131.949 4100 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.07 % Favored : 93.74 % Rotamer: Outliers : 3.43 % Allowed : 26.28 % Favored : 70.28 % 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 aren not related in a simple way. whole: -0.60 (0.15), residues: 3165 helix: 0.93 (0.16), residues: 1069 sheet: -0.70 (0.26), residues: 398 loop : -1.20 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 371 TYR 0.026 0.002 TYR H 185 PHE 0.017 0.001 PHE J 17 TRP 0.021 0.001 TRP J1020 HIS 0.006 0.001 HIS I 343 Details of bonding type rmsd covalent geometry : bond 0.00479 (26420) covalent geometry : angle 0.71737 (35898) hydrogen bonds : bond 0.03748 ( 1044) hydrogen bonds : angle 4.63658 ( 2885) metal coordination : bond 0.01169 ( 8) metal coordination : angle 6.23859 ( 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 482 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 389 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7704 (mmm) cc_final: 0.7392 (mmm) REVERT: G 93 GLN cc_start: 0.7657 (mp10) cc_final: 0.7256 (mm110) REVERT: H 14 VAL cc_start: 0.6837 (OUTLIER) cc_final: 0.6600 (m) REVERT: I 123 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.4709 (t80) REVERT: I 187 GLU cc_start: 0.7657 (pt0) cc_final: 0.7417 (pt0) REVERT: I 284 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5757 (mm) REVERT: I 476 LYS cc_start: 0.8127 (tptt) cc_final: 0.7645 (tptt) REVERT: I 528 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6808 (mtp-110) REVERT: I 1085 MET cc_start: 0.8771 (mmm) cc_final: 0.8323 (mmt) REVERT: J 382 TYR cc_start: 0.7872 (m-10) cc_final: 0.7090 (m-10) REVERT: J 403 ARG cc_start: 0.7849 (tmm-80) cc_final: 0.7098 (ttp80) REVERT: J 405 GLU cc_start: 0.7810 (tt0) cc_final: 0.7453 (tt0) REVERT: J 491 LEU cc_start: 0.8776 (tp) cc_final: 0.8407 (mp) REVERT: J 713 GLU cc_start: 0.6666 (mp0) cc_final: 0.6290 (mp0) REVERT: J 811 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6793 (mt-10) REVERT: J 822 MET cc_start: 0.6321 (tpt) cc_final: 0.5962 (tpp) REVERT: J 902 ASP cc_start: 0.7610 (t0) cc_final: 0.6674 (t0) REVERT: J 913 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6614 (mt-10) REVERT: J 992 LYS cc_start: 0.8215 (tppt) cc_final: 0.7721 (mmtm) REVERT: J 1040 MET cc_start: 0.4428 (ttm) cc_final: 0.1854 (mtm) REVERT: J 1148 ARG cc_start: 0.6808 (ptp-170) cc_final: 0.6370 (ptp90) REVERT: J 1261 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8798 (pt) outliers start: 93 outliers final: 71 residues processed: 460 average time/residue: 0.2009 time to fit residues: 140.6605 Evaluate side-chains 452 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 374 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 105 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 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 41 ASN 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 I residue 6 THR 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 437 ASN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 498 ILE 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 630 VAL Chi-restraints excluded: chain I residue 655 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 933 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 290 ILE 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 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 553 THR Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 665 GLN 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 811 GLU Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 890 THR 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 1024 THR Chi-restraints excluded: chain J residue 1221 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 1310 THR Chi-restraints excluded: chain J residue 1349 GLU 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: 0.6980 chunk 205 optimal weight: 6.9990 chunk 254 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 225 optimal weight: 0.0030 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN H 41 ASN I 437 ASN I 618 GLN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 GLN ** 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 J 665 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.243691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.181412 restraints weight = 30042.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.177808 restraints weight = 31352.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.169304 restraints weight = 19217.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.170324 restraints weight = 19872.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.170567 restraints weight = 17512.528| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26428 Z= 0.142 Angle : 0.723 13.488 35910 Z= 0.363 Chirality : 0.044 0.228 4098 Planarity : 0.005 0.057 4527 Dihedral : 13.503 132.209 4100 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.21 % Favored : 94.63 % Rotamer: Outliers : 2.84 % Allowed : 27.24 % Favored : 69.92 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: -0.52 (0.15), residues: 3165 helix: 0.96 (0.16), residues: 1062 sheet: -0.74 (0.26), residues: 408 loop : -1.09 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 293 TYR 0.028 0.001 TYR H 185 PHE 0.019 0.001 PHE J 17 TRP 0.023 0.001 TRP J1020 HIS 0.007 0.001 HIS I 343 Details of bonding type rmsd covalent geometry : bond 0.00332 (26420) covalent geometry : angle 0.71704 (35898) hydrogen bonds : bond 0.03591 ( 1044) hydrogen bonds : angle 4.59087 ( 2885) metal coordination : bond 0.00777 ( 8) metal coordination : angle 5.31678 ( 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 467 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 390 time to evaluate : 1.050 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: 0.7903 (mmm) cc_final: 0.7526 (mmm) REVERT: G 93 GLN cc_start: 0.7697 (mp10) cc_final: 0.7285 (mm110) REVERT: G 100 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8201 (mt) REVERT: H 14 VAL cc_start: 0.6635 (OUTLIER) cc_final: 0.5322 (t) REVERT: H 150 ARG cc_start: 0.6418 (tpt-90) cc_final: 0.6217 (tpt-90) REVERT: I 74 ARG cc_start: 0.7257 (ptt90) cc_final: 0.7024 (ptt-90) REVERT: I 123 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.4782 (t80) REVERT: I 187 GLU cc_start: 0.7942 (pt0) cc_final: 0.7639 (pt0) REVERT: I 197 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7382 (mtm-85) REVERT: I 284 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6496 (mm) REVERT: I 476 LYS cc_start: 0.8820 (tptt) cc_final: 0.8278 (tptt) REVERT: J 382 TYR cc_start: 0.7668 (m-10) cc_final: 0.6862 (m-10) REVERT: J 403 ARG cc_start: 0.7989 (tmm-80) cc_final: 0.7128 (tmm-80) REVERT: J 405 GLU cc_start: 0.7964 (tt0) cc_final: 0.7003 (tt0) REVERT: J 491 LEU cc_start: 0.8760 (tp) cc_final: 0.8518 (mp) REVERT: J 713 GLU cc_start: 0.6901 (mp0) cc_final: 0.6468 (mp0) REVERT: J 811 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6798 (mt-10) REVERT: J 822 MET cc_start: 0.6788 (tpt) cc_final: 0.6450 (tpp) REVERT: J 840 LEU cc_start: 0.8703 (tt) cc_final: 0.8495 (tp) REVERT: J 902 ASP cc_start: 0.7765 (t0) cc_final: 0.6853 (t0) REVERT: J 913 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: J 992 LYS cc_start: 0.8318 (tppt) cc_final: 0.7639 (mmtm) REVERT: J 1040 MET cc_start: 0.5256 (ttm) cc_final: 0.2310 (mtm) REVERT: J 1148 ARG cc_start: 0.6927 (ptp-170) cc_final: 0.6501 (ptp90) REVERT: J 1197 ASN cc_start: 0.8004 (t0) cc_final: 0.7007 (m110) outliers start: 77 outliers final: 61 residues processed: 450 average time/residue: 0.1991 time to fit residues: 137.1862 Evaluate side-chains 445 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 378 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 100 LEU Chi-restraints excluded: chain G residue 105 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 50 SER Chi-restraints excluded: chain H residue 51 MET 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 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 434 ASP Chi-restraints excluded: chain I residue 437 ASN 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 630 VAL Chi-restraints excluded: chain I residue 655 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 933 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 290 ILE 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 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 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 811 GLU 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 982 LEU Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1310 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: 9.9990 chunk 46 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 231 optimal weight: 0.5980 chunk 188 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 257 optimal weight: 8.9990 chunk 275 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 37 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN H 41 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 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.240015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.189777 restraints weight = 29944.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.184811 restraints weight = 46262.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.180932 restraints weight = 40175.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.181150 restraints weight = 38839.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.181528 restraints weight = 29304.863| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26428 Z= 0.208 Angle : 0.746 13.277 35910 Z= 0.375 Chirality : 0.045 0.215 4098 Planarity : 0.005 0.088 4527 Dihedral : 13.563 131.660 4100 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.74 % Rotamer: Outliers : 3.29 % Allowed : 26.69 % Favored : 70.03 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.56 (0.15), residues: 3165 helix: 0.90 (0.16), residues: 1071 sheet: -0.62 (0.27), residues: 398 loop : -1.16 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG I 371 TYR 0.026 0.002 TYR H 185 PHE 0.012 0.001 PHE I1164 TRP 0.057 0.003 TRP J 868 HIS 0.007 0.001 HIS I 343 Details of bonding type rmsd covalent geometry : bond 0.00500 (26420) covalent geometry : angle 0.73902 (35898) hydrogen bonds : bond 0.03752 ( 1044) hydrogen bonds : angle 4.65251 ( 2885) metal coordination : bond 0.01136 ( 8) metal coordination : angle 5.65269 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4789.62 seconds wall clock time: 83 minutes 36.50 seconds (5016.50 seconds total)