Starting phenix.real_space_refine on Sun Jun 22 12:33:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szw_40922/06_2025/8szw_40922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szw_40922/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8szw_40922/06_2025/8szw_40922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szw_40922/06_2025/8szw_40922.map" model { file = "/net/cci-nas-00/data/ceres_data/8szw_40922/06_2025/8szw_40922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szw_40922/06_2025/8szw_40922.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.80, per 1000 atoms: 0.57 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: 6.79 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 9.64 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: 12.16 Time building geometry restraints manager: 8.03 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: 0.770 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: 0.030 Extract box with map and model: 0.910 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 72.020 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.440 ------------------------------------------------------------------------------- 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 : 9.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (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 TRP 0.018 0.001 TRP I 807 HIS 0.007 0.001 HIS J1366 PHE 0.016 0.001 PHE J1325 TYR 0.030 0.001 TYR I 395 ARG 0.012 0.001 ARG K 25 Details of bonding type rmsd hydrogen bonds : bond 0.14996 ( 1044) hydrogen bonds : angle 6.08182 ( 2885) metal coordination : bond 0.11573 ( 8) metal coordination : angle 40.30062 ( 12) covalent geometry : bond 0.00340 (26420) covalent geometry : angle 0.72116 (35898) *********************** 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 : 2.649 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: 0.5243 time to fit residues: 487.1984 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 : 2.513 ------------------------------------------------------------------------------- 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 271 optimal weight: 30.0000 chunk 243 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 251 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 291 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 150 HIS I 387 ASN I 725 GLN I 832 HIS I 856 ASN I1072 ASN ** I1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1146 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 495 ASN J 921 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.246472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.202181 restraints weight = 30055.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.206347 restraints weight = 64010.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.203935 restraints weight = 24552.954| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26428 Z= 0.198 Angle : 0.757 33.992 35910 Z= 0.366 Chirality : 0.045 0.231 4098 Planarity : 0.005 0.088 4527 Dihedral : 13.544 133.325 4140 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.07 % Favored : 93.74 % Rotamer: Outliers : 4.58 % Allowed : 19.68 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3165 helix: 1.30 (0.16), residues: 1065 sheet: -1.34 (0.24), residues: 434 loop : -1.40 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1020 HIS 0.005 0.001 HIS I1313 PHE 0.028 0.002 PHE J 35 TYR 0.022 0.002 TYR H 185 ARG 0.008 0.001 ARG J1148 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 1044) hydrogen bonds : angle 4.92880 ( 2885) metal coordination : bond 0.02003 ( 8) metal coordination : angle 15.24340 ( 12) covalent geometry : bond 0.00470 (26420) covalent geometry : angle 0.70447 (35898) *********************** 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 590 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 466 time to evaluate : 2.671 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: G 10 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7661 (mppt) REVERT: G 104 LYS cc_start: 0.8317 (tppt) cc_final: 0.7855 (tppp) REVERT: G 114 ASP cc_start: 0.6851 (m-30) cc_final: 0.6208 (m-30) REVERT: G 120 ASP cc_start: 0.8309 (p0) cc_final: 0.7902 (p0) REVERT: H 14 VAL cc_start: 0.7216 (OUTLIER) cc_final: 0.6900 (m) REVERT: I 80 PHE cc_start: 0.6708 (m-10) cc_final: 0.6354 (m-10) REVERT: I 367 TYR cc_start: 0.7600 (t80) cc_final: 0.7391 (t80) REVERT: I 766 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8301 (p0) REVERT: I 824 GLN cc_start: 0.8218 (mt0) cc_final: 0.7986 (tt0) REVERT: I 870 ILE cc_start: 0.8067 (mt) cc_final: 0.7806 (mt) REVERT: I 1092 THR cc_start: 0.9258 (m) cc_final: 0.8992 (p) REVERT: I 1151 LEU cc_start: 0.7276 (tp) cc_final: 0.6958 (tp) REVERT: I 1214 ASP cc_start: 0.8591 (t0) cc_final: 0.8320 (t0) REVERT: I 1229 TYR cc_start: 0.8246 (m-80) cc_final: 0.7999 (m-80) REVERT: J 188 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7767 (mm) REVERT: J 229 GLN cc_start: 0.7812 (mt0) cc_final: 0.7568 (mt0) REVERT: J 382 TYR cc_start: 0.7804 (m-10) cc_final: 0.7138 (m-10) REVERT: J 403 ARG cc_start: 0.7822 (tmm-80) cc_final: 0.7099 (ttp80) REVERT: J 405 GLU cc_start: 0.7874 (tt0) cc_final: 0.7479 (tt0) REVERT: J 718 SER cc_start: 0.8504 (t) cc_final: 0.8240 (p) REVERT: J 902 ASP cc_start: 0.7300 (t0) cc_final: 0.6203 (t0) REVERT: J 913 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6508 (mt-10) REVERT: J 1040 MET cc_start: 0.4124 (ttm) cc_final: 0.1652 (mtm) outliers start: 124 outliers final: 66 residues processed: 555 average time/residue: 0.5273 time to fit residues: 446.8648 Evaluate side-chains 476 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 406 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 140 ILE 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 85 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 204 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 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 766 ASN 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 924 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 188 LEU 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 526 VAL 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 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 1146 GLU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 65 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 98 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 287 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1146 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** 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 = 0.4684 r_free = 0.4684 target = 0.248459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.202219 restraints weight = 30168.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.206523 restraints weight = 60934.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.207053 restraints weight = 27700.385| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26428 Z= 0.151 Angle : 0.696 29.339 35910 Z= 0.344 Chirality : 0.044 0.209 4098 Planarity : 0.005 0.053 4527 Dihedral : 13.497 133.539 4122 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 4.36 % Allowed : 20.34 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3165 helix: 1.20 (0.16), residues: 1062 sheet: -1.13 (0.24), residues: 424 loop : -1.25 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP J 868 HIS 0.005 0.001 HIS I1313 PHE 0.021 0.001 PHE J 35 TYR 0.024 0.001 TYR H 185 ARG 0.009 0.001 ARG J 202 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 1044) hydrogen bonds : angle 4.71828 ( 2885) metal coordination : bond 0.01359 ( 8) metal coordination : angle 10.62964 ( 12) covalent geometry : bond 0.00353 (26420) covalent geometry : angle 0.66825 (35898) *********************** 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 556 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 438 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 130 ILE cc_start: 0.8965 (mt) cc_final: 0.8752 (mp) REVERT: G 228 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8756 (mp) REVERT: H 14 VAL cc_start: 0.7061 (OUTLIER) cc_final: 0.6804 (m) REVERT: I 130 MET cc_start: 0.7676 (ttm) cc_final: 0.7419 (ttm) REVERT: I 781 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6536 (m-30) REVERT: I 1092 THR cc_start: 0.9284 (m) cc_final: 0.9019 (p) REVERT: I 1140 LYS cc_start: 0.7401 (mtmt) cc_final: 0.7180 (mtmm) REVERT: I 1203 ASP cc_start: 0.6063 (t0) cc_final: 0.5685 (t0) REVERT: I 1214 ASP cc_start: 0.8592 (t0) cc_final: 0.8319 (t0) REVERT: I 1229 TYR cc_start: 0.8214 (m-80) cc_final: 0.7978 (m-80) REVERT: I 1319 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.7046 (ttp) REVERT: J 130 MET cc_start: 0.6781 (mmm) cc_final: 0.6309 (mtt) REVERT: J 229 GLN cc_start: 0.7766 (mt0) cc_final: 0.7550 (mt0) REVERT: J 382 TYR cc_start: 0.7809 (m-10) cc_final: 0.7094 (m-10) REVERT: J 718 SER cc_start: 0.8383 (t) cc_final: 0.8168 (p) REVERT: J 902 ASP cc_start: 0.7315 (t0) cc_final: 0.6352 (t0) REVERT: J 913 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6473 (mt-10) REVERT: J 1040 MET cc_start: 0.3930 (ttm) cc_final: 0.1578 (mtm) outliers start: 118 outliers final: 74 residues processed: 519 average time/residue: 0.4416 time to fit residues: 344.8387 Evaluate side-chains 473 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 394 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 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 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 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 924 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1146 GLN Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 242 LEU 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 728 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 982 LEU 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 1280 VAL Chi-restraints excluded: chain J residue 1314 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1351 VAL 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 70 optimal weight: 30.0000 chunk 111 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 169 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 6 optimal weight: 0.0040 chunk 86 optimal weight: 9.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN H 147 GLN I 513 GLN I 628 HIS ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 GLN I1146 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1019 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS ** 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 = 0.4632 r_free = 0.4632 target = 0.242582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.177916 restraints weight = 30134.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.176598 restraints weight = 35593.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.178816 restraints weight = 30302.347| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26428 Z= 0.186 Angle : 0.691 25.553 35910 Z= 0.344 Chirality : 0.044 0.234 4098 Planarity : 0.005 0.050 4527 Dihedral : 13.457 132.916 4111 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 4.98 % Allowed : 21.52 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3165 helix: 1.20 (0.16), residues: 1055 sheet: -1.04 (0.25), residues: 418 loop : -1.22 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 33 HIS 0.005 0.001 HIS I 447 PHE 0.021 0.001 PHE J 35 TYR 0.024 0.001 TYR H 185 ARG 0.012 0.001 ARG H 143 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 1044) hydrogen bonds : angle 4.69326 ( 2885) metal coordination : bond 0.01232 ( 8) metal coordination : angle 9.07531 ( 12) covalent geometry : bond 0.00444 (26420) covalent geometry : angle 0.67129 (35898) *********************** 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 551 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 416 time to evaluate : 2.737 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: H 14 VAL cc_start: 0.6902 (OUTLIER) cc_final: 0.6585 (m) REVERT: I 123 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.6294 (t80) REVERT: I 866 ASP cc_start: 0.6207 (p0) cc_final: 0.5704 (p0) REVERT: I 1203 ASP cc_start: 0.6094 (t0) cc_final: 0.5798 (t0) REVERT: I 1214 ASP cc_start: 0.8637 (t0) cc_final: 0.8325 (t0) REVERT: J 33 TRP cc_start: 0.7367 (m-10) cc_final: 0.7048 (m-10) REVERT: J 102 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.6164 (ttp) REVERT: J 229 GLN cc_start: 0.7916 (mt0) cc_final: 0.7676 (mt0) REVERT: J 382 TYR cc_start: 0.7797 (m-10) cc_final: 0.6995 (m-10) REVERT: J 491 LEU cc_start: 0.8675 (tp) cc_final: 0.8425 (mp) REVERT: J 718 SER cc_start: 0.8536 (t) cc_final: 0.8277 (p) REVERT: J 902 ASP cc_start: 0.7531 (t0) cc_final: 0.6563 (t0) REVERT: J 913 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6442 (mt-10) REVERT: J 921 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: J 1040 MET cc_start: 0.4500 (ttm) cc_final: 0.1934 (mtm) outliers start: 135 outliers final: 94 residues processed: 509 average time/residue: 0.4189 time to fit residues: 324.1127 Evaluate side-chains 491 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 392 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 187 VAL 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 41 ASN Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 98 VAL 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 171 LEU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 525 THR 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 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 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 924 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 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 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 921 GLN 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 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1314 LEU 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 Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 226 optimal weight: 0.6980 chunk 231 optimal weight: 0.3980 chunk 282 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 176 optimal weight: 0.0470 chunk 145 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 316 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** 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 = 0.4695 r_free = 0.4695 target = 0.249628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.205201 restraints weight = 30211.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.210056 restraints weight = 61008.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.205159 restraints weight = 26458.896| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26428 Z= 0.130 Angle : 0.655 21.860 35910 Z= 0.326 Chirality : 0.043 0.213 4098 Planarity : 0.004 0.055 4527 Dihedral : 13.401 132.902 4111 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.31 % Favored : 94.57 % Rotamer: Outliers : 3.88 % Allowed : 22.78 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3165 helix: 1.22 (0.16), residues: 1056 sheet: -0.95 (0.25), residues: 405 loop : -1.15 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J1020 HIS 0.005 0.001 HIS J1252 PHE 0.020 0.001 PHE J 35 TYR 0.026 0.001 TYR H 185 ARG 0.010 0.001 ARG J1148 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 1044) hydrogen bonds : angle 4.55574 ( 2885) metal coordination : bond 0.00911 ( 8) metal coordination : angle 7.71478 ( 12) covalent geometry : bond 0.00300 (26420) covalent geometry : angle 0.64003 (35898) *********************** 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 527 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 422 time to evaluate : 2.986 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 33 ARG cc_start: 0.7712 (tpp80) cc_final: 0.7189 (tpt90) REVERT: H 14 VAL cc_start: 0.7033 (OUTLIER) cc_final: 0.6793 (m) REVERT: H 84 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7548 (t0) REVERT: I 123 TYR cc_start: 0.6733 (OUTLIER) cc_final: 0.6053 (t80) REVERT: I 130 MET cc_start: 0.7754 (ttm) cc_final: 0.7456 (ttm) REVERT: I 197 ARG cc_start: 0.7692 (ptm160) cc_final: 0.7149 (mmm-85) REVERT: I 284 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.5876 (mm) REVERT: I 448 LEU cc_start: 0.8135 (mt) cc_final: 0.7744 (mt) REVERT: I 565 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6521 (pt0) REVERT: I 681 MET cc_start: 0.7157 (mmt) cc_final: 0.6928 (mmt) REVERT: I 717 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7700 (t) REVERT: I 781 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6567 (m-30) REVERT: I 1214 ASP cc_start: 0.8544 (t0) cc_final: 0.8136 (t0) REVERT: J 33 TRP cc_start: 0.7410 (m-10) cc_final: 0.7140 (m-10) REVERT: J 221 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8342 (mm) REVERT: J 229 GLN cc_start: 0.7856 (mt0) cc_final: 0.7627 (mt0) REVERT: J 382 TYR cc_start: 0.7831 (m-10) cc_final: 0.6974 (m-10) REVERT: J 491 LEU cc_start: 0.8635 (tp) cc_final: 0.8335 (mp) REVERT: J 510 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7895 (mt) REVERT: J 713 GLU cc_start: 0.6523 (mp0) cc_final: 0.6201 (mp0) REVERT: J 902 ASP cc_start: 0.7444 (t0) cc_final: 0.6401 (t0) REVERT: J 913 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6490 (mt-10) REVERT: J 921 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: J 1040 MET cc_start: 0.4416 (ttm) cc_final: 0.1871 (mtm) outliers start: 105 outliers final: 73 residues processed: 496 average time/residue: 0.4684 time to fit residues: 354.9014 Evaluate side-chains 486 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 402 time to evaluate : 2.870 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain G residue 171 LEU 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 84 ASN Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 212 ASP 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 284 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 772 SER 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 924 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 510 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 728 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 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 921 GLN Chi-restraints excluded: chain J residue 996 LYS Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1314 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 117 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 262 optimal weight: 8.9990 chunk 130 optimal weight: 0.0970 chunk 244 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 228 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 140 optimal weight: 50.0000 chunk 161 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 ASN ** I 519 ASN ** 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** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.249122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.202578 restraints weight = 30079.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.206195 restraints weight = 62406.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.207324 restraints weight = 30397.000| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26428 Z= 0.129 Angle : 0.652 18.733 35910 Z= 0.323 Chirality : 0.043 0.202 4098 Planarity : 0.004 0.080 4527 Dihedral : 13.369 132.671 4111 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.15 % Favored : 94.76 % Rotamer: Outliers : 4.50 % Allowed : 22.52 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3165 helix: 1.27 (0.16), residues: 1056 sheet: -0.79 (0.26), residues: 389 loop : -1.09 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J1020 HIS 0.004 0.001 HIS J1252 PHE 0.022 0.001 PHE J 35 TYR 0.025 0.001 TYR H 185 ARG 0.009 0.001 ARG J 293 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 1044) hydrogen bonds : angle 4.49149 ( 2885) metal coordination : bond 0.01132 ( 8) metal coordination : angle 8.18716 ( 12) covalent geometry : bond 0.00301 (26420) covalent geometry : angle 0.63456 (35898) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 419 time to evaluate : 2.739 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 33 ARG cc_start: 0.7596 (tpp80) cc_final: 0.7142 (tpt90) REVERT: G 141 SER cc_start: 0.8116 (t) cc_final: 0.7285 (t) REVERT: H 12 ARG cc_start: 0.6971 (ptt90) cc_final: 0.6567 (ptt90) REVERT: H 14 VAL cc_start: 0.6993 (OUTLIER) cc_final: 0.6730 (m) REVERT: I 123 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.5705 (t80) REVERT: I 143 ARG cc_start: 0.8568 (ttm110) cc_final: 0.8164 (ttm110) REVERT: I 187 GLU cc_start: 0.7531 (pt0) cc_final: 0.7292 (pt0) REVERT: I 284 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5600 (mm) REVERT: I 448 LEU cc_start: 0.8098 (mt) cc_final: 0.7677 (mt) REVERT: I 565 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6273 (pt0) REVERT: I 781 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6586 (m-30) REVERT: I 1214 ASP cc_start: 0.8532 (t0) cc_final: 0.8212 (t0) REVERT: I 1253 LEU cc_start: 0.8937 (tt) cc_final: 0.8513 (mp) REVERT: J 382 TYR cc_start: 0.7802 (m-10) cc_final: 0.6954 (m-10) REVERT: J 491 LEU cc_start: 0.8638 (tp) cc_final: 0.8349 (mp) REVERT: J 510 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7766 (mt) REVERT: J 902 ASP cc_start: 0.7409 (t0) cc_final: 0.6420 (t0) REVERT: J 913 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6610 (mt-10) REVERT: J 921 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: J 1040 MET cc_start: 0.4123 (ttm) cc_final: 0.1684 (mtm) REVERT: K 31 GLN cc_start: 0.6204 (OUTLIER) cc_final: 0.5585 (tm-30) outliers start: 122 outliers final: 81 residues processed: 509 average time/residue: 0.4786 time to fit residues: 373.9950 Evaluate side-chains 481 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 391 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 98 VAL 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 284 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 437 ASN 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 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 242 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 510 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 728 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 921 GLN Chi-restraints excluded: chain J residue 982 LEU 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 1196 LEU 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 1309 ILE Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1314 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 31 GLN 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 288 optimal weight: 8.9990 chunk 2 optimal weight: 0.2980 chunk 315 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 304 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 273 optimal weight: 20.0000 chunk 235 optimal weight: 0.7980 chunk 310 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 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 875 ASN ** K 31 GLN ** 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 = 0.4690 r_free = 0.4690 target = 0.248869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.202362 restraints weight = 30261.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.206035 restraints weight = 63389.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.207067 restraints weight = 29951.675| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26428 Z= 0.135 Angle : 0.675 16.762 35910 Z= 0.335 Chirality : 0.043 0.221 4098 Planarity : 0.004 0.067 4527 Dihedral : 13.330 132.345 4106 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.72 % Rotamer: Outliers : 3.91 % Allowed : 23.33 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3165 helix: 1.21 (0.16), residues: 1058 sheet: -0.75 (0.26), residues: 390 loop : -1.06 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J1020 HIS 0.004 0.001 HIS I 343 PHE 0.026 0.001 PHE J 35 TYR 0.027 0.001 TYR H 185 ARG 0.017 0.001 ARG J 123 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 1044) hydrogen bonds : angle 4.47475 ( 2885) metal coordination : bond 0.00967 ( 8) metal coordination : angle 7.17943 ( 12) covalent geometry : bond 0.00316 (26420) covalent geometry : angle 0.66175 (35898) *********************** 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 508 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 402 time to evaluate : 2.619 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 33 ARG cc_start: 0.7498 (tpp80) cc_final: 0.7092 (tpt90) REVERT: G 141 SER cc_start: 0.8024 (t) cc_final: 0.7703 (m) REVERT: G 218 ARG cc_start: 0.7416 (mtp-110) cc_final: 0.6993 (mtp-110) REVERT: H 12 ARG cc_start: 0.7036 (ptt90) cc_final: 0.6639 (ptt90) REVERT: H 14 VAL cc_start: 0.7167 (OUTLIER) cc_final: 0.6909 (m) REVERT: H 84 ASN cc_start: 0.8104 (t0) cc_final: 0.7399 (t0) REVERT: I 123 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.5907 (t80) REVERT: I 143 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8118 (ttm110) REVERT: I 187 GLU cc_start: 0.7455 (pt0) cc_final: 0.7215 (pt0) REVERT: I 284 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5608 (mm) REVERT: I 448 LEU cc_start: 0.8033 (mt) cc_final: 0.7618 (mt) REVERT: I 781 ASP cc_start: 0.6667 (OUTLIER) cc_final: 0.6463 (m-30) REVERT: I 1161 LEU cc_start: 0.7849 (mt) cc_final: 0.7531 (mt) REVERT: I 1214 ASP cc_start: 0.8548 (t0) cc_final: 0.8216 (t0) REVERT: I 1253 LEU cc_start: 0.8922 (tt) cc_final: 0.8509 (mp) REVERT: J 382 TYR cc_start: 0.7812 (m-10) cc_final: 0.6969 (m-10) REVERT: J 491 LEU cc_start: 0.8661 (tp) cc_final: 0.8370 (mp) REVERT: J 902 ASP cc_start: 0.7430 (t0) cc_final: 0.6417 (t0) REVERT: J 913 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6600 (mt-10) REVERT: J 992 LYS cc_start: 0.8029 (tppt) cc_final: 0.7592 (mmtm) REVERT: J 1040 MET cc_start: 0.4087 (ttm) cc_final: 0.1651 (mtm) REVERT: J 1189 MET cc_start: 0.7340 (tpp) cc_final: 0.6994 (tmm) REVERT: J 1197 ASN cc_start: 0.6961 (t0) cc_final: 0.6740 (m110) outliers start: 106 outliers final: 80 residues processed: 475 average time/residue: 0.4370 time to fit residues: 319.0040 Evaluate side-chains 469 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 384 time to evaluate : 3.020 ------------------------------------------------------------------------------- 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 171 LEU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE 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 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 210 LEU Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 437 ASN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 147 ILE 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 507 VAL Chi-restraints excluded: chain J residue 525 MET 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 728 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 913 GLU 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 1196 LEU Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1314 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 70 optimal weight: 30.0000 chunk 235 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 252 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 168 optimal weight: 0.0040 chunk 170 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1136 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 560 ASN ** J 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 962 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.249019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.201320 restraints weight = 30305.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.203479 restraints weight = 62616.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.205294 restraints weight = 34442.694| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26428 Z= 0.130 Angle : 0.678 16.204 35910 Z= 0.334 Chirality : 0.043 0.224 4098 Planarity : 0.004 0.059 4527 Dihedral : 13.325 132.119 4103 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.91 % Rotamer: Outliers : 3.65 % Allowed : 24.03 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3165 helix: 1.24 (0.16), residues: 1054 sheet: -0.64 (0.27), residues: 383 loop : -1.02 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J1020 HIS 0.003 0.000 HIS J1252 PHE 0.010 0.001 PHE J 62 TYR 0.028 0.001 TYR H 185 ARG 0.012 0.001 ARG J 123 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 1044) hydrogen bonds : angle 4.42755 ( 2885) metal coordination : bond 0.00837 ( 8) metal coordination : angle 6.28431 ( 12) covalent geometry : bond 0.00305 (26420) covalent geometry : angle 0.66816 (35898) *********************** 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 501 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 402 time to evaluate : 2.873 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 130 ILE cc_start: 0.8897 (mp) cc_final: 0.8578 (mt) REVERT: G 218 ARG cc_start: 0.7426 (mtp-110) cc_final: 0.7034 (mtp-110) REVERT: H 12 ARG cc_start: 0.7118 (ptt90) cc_final: 0.6768 (ptt90) REVERT: H 14 VAL cc_start: 0.7074 (OUTLIER) cc_final: 0.6837 (m) REVERT: H 84 ASN cc_start: 0.8006 (t0) cc_final: 0.7347 (t0) REVERT: I 197 ARG cc_start: 0.7512 (ptm160) cc_final: 0.7106 (mmm-85) REVERT: I 284 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.5592 (mm) REVERT: I 448 LEU cc_start: 0.7973 (mt) cc_final: 0.7529 (mt) REVERT: I 781 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.6420 (m-30) REVERT: I 1161 LEU cc_start: 0.7704 (mt) cc_final: 0.7491 (mt) REVERT: I 1214 ASP cc_start: 0.8578 (t0) cc_final: 0.8227 (t0) REVERT: I 1253 LEU cc_start: 0.8852 (tt) cc_final: 0.8485 (mp) REVERT: J 33 TRP cc_start: 0.7264 (m-10) cc_final: 0.6707 (m-10) REVERT: J 382 TYR cc_start: 0.7799 (m-10) cc_final: 0.6912 (m-10) REVERT: J 491 LEU cc_start: 0.8623 (tp) cc_final: 0.8378 (mp) REVERT: J 702 GLN cc_start: 0.7580 (pp30) cc_final: 0.7271 (pp30) REVERT: J 902 ASP cc_start: 0.7450 (t0) cc_final: 0.6452 (t0) REVERT: J 913 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6632 (mt-10) REVERT: J 992 LYS cc_start: 0.8067 (tppt) cc_final: 0.7603 (mmtm) REVERT: J 1040 MET cc_start: 0.4088 (ttm) cc_final: 0.1594 (mtm) REVERT: J 1197 ASN cc_start: 0.7005 (t0) cc_final: 0.6763 (m110) REVERT: J 1292 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8037 (mp) outliers start: 99 outliers final: 80 residues processed: 471 average time/residue: 0.4295 time to fit residues: 307.9763 Evaluate side-chains 479 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 394 time to evaluate : 2.618 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 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 I residue 47 TYR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 210 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 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 681 MET 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 924 VAL Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 147 ILE 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 407 VAL Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 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 776 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 865 HIS 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 991 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1314 LEU 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 117 optimal weight: 8.9990 chunk 228 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 238 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 116 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 573 ASN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.247223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.199227 restraints weight = 30162.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.201424 restraints weight = 63445.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.203977 restraints weight = 35696.013| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26428 Z= 0.167 Angle : 0.704 15.658 35910 Z= 0.351 Chirality : 0.044 0.214 4098 Planarity : 0.004 0.058 4527 Dihedral : 13.404 131.453 4103 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.31 % Rotamer: Outliers : 3.40 % Allowed : 24.84 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3165 helix: 1.21 (0.16), residues: 1053 sheet: -0.47 (0.27), residues: 380 loop : -0.97 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J1020 HIS 0.009 0.001 HIS I 343 PHE 0.013 0.001 PHE J 62 TYR 0.026 0.001 TYR H 185 ARG 0.015 0.001 ARG I 371 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 1044) hydrogen bonds : angle 4.47165 ( 2885) metal coordination : bond 0.00909 ( 8) metal coordination : angle 5.95904 ( 12) covalent geometry : bond 0.00400 (26420) covalent geometry : angle 0.69595 (35898) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6330 Ramachandran restraints generated. 3165 Oldfield, 0 Emsley, 3165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 400 time to evaluate : 2.880 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 33 ARG cc_start: 0.7579 (tpp80) cc_final: 0.7147 (tpt90) REVERT: G 51 MET cc_start: 0.7471 (mmm) cc_final: 0.7161 (mmm) REVERT: G 120 ASP cc_start: 0.7934 (p0) cc_final: 0.7558 (p0) REVERT: G 130 ILE cc_start: 0.8927 (mp) cc_final: 0.8597 (mt) REVERT: H 12 ARG cc_start: 0.7106 (ptt90) cc_final: 0.6722 (ptt90) REVERT: H 14 VAL cc_start: 0.7158 (OUTLIER) cc_final: 0.6916 (m) REVERT: H 84 ASN cc_start: 0.8126 (t0) cc_final: 0.7648 (t0) REVERT: I 123 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.5443 (t80) REVERT: I 197 ARG cc_start: 0.7653 (ptm160) cc_final: 0.7262 (mmm-85) REVERT: I 284 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5562 (mm) REVERT: I 448 LEU cc_start: 0.7989 (mt) cc_final: 0.7604 (mt) REVERT: I 476 LYS cc_start: 0.7896 (tptt) cc_final: 0.7475 (tptt) REVERT: I 1214 ASP cc_start: 0.8618 (t0) cc_final: 0.8332 (t0) REVERT: I 1253 LEU cc_start: 0.8864 (tt) cc_final: 0.8455 (mp) REVERT: J 33 TRP cc_start: 0.7236 (m-10) cc_final: 0.6692 (m-10) REVERT: J 382 TYR cc_start: 0.7805 (m-10) cc_final: 0.6929 (m-10) REVERT: J 491 LEU cc_start: 0.8727 (tp) cc_final: 0.8431 (mp) REVERT: J 702 GLN cc_start: 0.7498 (pp30) cc_final: 0.7189 (pp30) REVERT: J 902 ASP cc_start: 0.7446 (t0) cc_final: 0.6154 (t0) REVERT: J 913 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6672 (mt-10) REVERT: J 992 LYS cc_start: 0.8119 (tppt) cc_final: 0.7649 (mmtm) REVERT: J 1040 MET cc_start: 0.4197 (ttm) cc_final: 0.1710 (mtm) REVERT: J 1292 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8061 (mp) outliers start: 92 outliers final: 72 residues processed: 465 average time/residue: 0.5173 time to fit residues: 375.2072 Evaluate side-chains 458 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 381 time to evaluate : 6.602 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain G residue 171 LEU 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 50 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 153 VAL 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 210 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 525 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 147 ILE 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 407 VAL Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL 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 760 THR Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 865 HIS 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 991 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 1292 LEU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1314 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 222 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 163 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 192 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 406 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 932 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** ** K 31 GLN ** 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 = 0.4691 r_free = 0.4691 target = 0.248704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.200739 restraints weight = 30041.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.202783 restraints weight = 62211.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.205304 restraints weight = 37727.879| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3751 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 : 0.703 15.602 35910 Z= 0.351 Chirality : 0.043 0.216 4098 Planarity : 0.005 0.094 4527 Dihedral : 13.410 131.191 4100 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.72 % Rotamer: Outliers : 2.88 % Allowed : 25.47 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3165 helix: 1.22 (0.16), residues: 1055 sheet: -0.52 (0.27), residues: 391 loop : -0.96 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J1020 HIS 0.005 0.001 HIS J1252 PHE 0.019 0.001 PHE J 17 TYR 0.026 0.001 TYR H 185 ARG 0.021 0.001 ARG I 371 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 1044) hydrogen bonds : angle 4.43876 ( 2885) metal coordination : bond 0.00828 ( 8) metal coordination : angle 5.35969 ( 12) covalent geometry : bond 0.00337 (26420) covalent geometry : angle 0.69642 (35898) ********************** 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 478 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 400 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.7449 (tpp80) cc_final: 0.6960 (tpt90) REVERT: G 51 MET cc_start: 0.7508 (mmm) cc_final: 0.7266 (mmm) REVERT: G 130 ILE cc_start: 0.8892 (mp) cc_final: 0.8583 (mt) REVERT: H 12 ARG cc_start: 0.7127 (ptt90) cc_final: 0.6759 (ptt90) REVERT: H 14 VAL cc_start: 0.6921 (OUTLIER) cc_final: 0.5846 (t) REVERT: H 84 ASN cc_start: 0.8076 (t0) cc_final: 0.7409 (t0) REVERT: I 123 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.5451 (t80) REVERT: I 197 ARG cc_start: 0.7651 (ptm160) cc_final: 0.7400 (mtm-85) REVERT: I 284 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5573 (mm) REVERT: I 448 LEU cc_start: 0.7897 (mt) cc_final: 0.7459 (mt) REVERT: I 476 LYS cc_start: 0.7814 (tptt) cc_final: 0.7300 (tptt) REVERT: I 1214 ASP cc_start: 0.8615 (t0) cc_final: 0.8306 (t0) REVERT: I 1253 LEU cc_start: 0.8833 (tt) cc_final: 0.8420 (mp) REVERT: J 180 MET cc_start: 0.3051 (mmp) cc_final: 0.2490 (mmp) REVERT: J 382 TYR cc_start: 0.7788 (m-10) cc_final: 0.6918 (m-10) REVERT: J 403 ARG cc_start: 0.7613 (tmm-80) cc_final: 0.6885 (tmm-80) REVERT: J 491 LEU cc_start: 0.8680 (tp) cc_final: 0.8398 (mp) REVERT: J 902 ASP cc_start: 0.7508 (t0) cc_final: 0.6493 (t0) REVERT: J 913 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6506 (mt-10) REVERT: J 992 LYS cc_start: 0.8099 (tppt) cc_final: 0.7638 (mmtm) REVERT: J 1040 MET cc_start: 0.4167 (ttm) cc_final: 0.1663 (mtm) REVERT: J 1175 LEU cc_start: 0.7328 (mp) cc_final: 0.6699 (mp) REVERT: J 1197 ASN cc_start: 0.6782 (t0) cc_final: 0.6158 (m110) REVERT: J 1292 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8013 (mp) REVERT: J 1345 ARG cc_start: 0.6562 (tmt170) cc_final: 0.6283 (tmt170) REVERT: K 31 GLN cc_start: 0.6012 (tm-30) cc_final: 0.5719 (tm-30) outliers start: 78 outliers final: 69 residues processed: 455 average time/residue: 0.4252 time to fit residues: 297.7194 Evaluate side-chains 465 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 391 time to evaluate : 2.698 ------------------------------------------------------------------------------- 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 83 LEU 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 50 SER Chi-restraints excluded: chain H residue 153 VAL 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 210 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 550 VAL Chi-restraints excluded: chain I residue 554 HIS Chi-restraints excluded: chain I residue 607 SER Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1315 MET Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 147 ILE 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 407 VAL Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL 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 776 THR Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 865 HIS 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 991 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 1292 LEU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1314 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1356 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 277 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 chunk 144 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 180 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.248597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.201722 restraints weight = 30116.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.204012 restraints weight = 63543.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.205307 restraints weight = 35600.808| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.3854 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= 0.143 Angle : 0.702 15.152 35910 Z= 0.350 Chirality : 0.043 0.212 4098 Planarity : 0.004 0.059 4527 Dihedral : 13.454 130.643 4100 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 2.69 % Allowed : 25.99 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3165 helix: 1.20 (0.16), residues: 1057 sheet: -0.48 (0.27), residues: 389 loop : -0.90 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J1020 HIS 0.007 0.001 HIS J 104 PHE 0.017 0.001 PHE J 62 TYR 0.027 0.001 TYR H 185 ARG 0.010 0.001 ARG J 293 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 1044) hydrogen bonds : angle 4.45250 ( 2885) metal coordination : bond 0.00820 ( 8) metal coordination : angle 5.01185 ( 12) covalent geometry : bond 0.00339 (26420) covalent geometry : angle 0.69617 (35898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9552.27 seconds wall clock time: 169 minutes 20.62 seconds (10160.62 seconds total)