Starting phenix.real_space_refine on Sun Jul 5 17:27:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymy_73126/07_2026/9ymy_73126.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymy_73126/07_2026/9ymy_73126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ymy_73126/07_2026/9ymy_73126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymy_73126/07_2026/9ymy_73126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ymy_73126/07_2026/9ymy_73126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymy_73126/07_2026/9ymy_73126.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 56 5.49 5 Mg 1 5.21 5 S 118 5.16 5 C 17664 2.51 5 N 5036 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28457 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "P" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 441 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "Q" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "R" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna3p': 8} Chain: "I" Number of atoms: 10396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1318, 10396 Classifications: {'peptide': 1318} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1262} Chain breaks: 1 Chain: "G" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1729 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1710 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "J" Number of atoms: 10405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10405 Classifications: {'peptide': 1338} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1282} Chain breaks: 2 Chain: "L" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2433 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 7, 'TRANS': 290} Chain breaks: 3 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 16065 SG CYS J 70 54.747 15.747 117.632 1.00166.10 S ATOM 16079 SG CYS J 72 56.678 15.320 120.768 1.00170.32 S ATOM 16187 SG CYS J 85 53.068 15.089 120.847 1.00171.13 S ATOM 16211 SG CYS J 88 54.638 18.347 120.324 1.00161.37 S ATOM 21899 SG CYS J 814 27.594 72.487 88.939 1.00106.51 S ATOM 22464 SG CYS J 888 30.969 71.225 89.675 1.00 81.89 S ATOM 22515 SG CYS J 895 29.213 70.188 86.636 1.00 89.09 S ATOM 22536 SG CYS J 898 30.418 73.583 86.934 1.00107.33 S Time building chain proxies: 5.92, per 1000 atoms: 0.21 Number of scatterers: 28457 At special positions: 0 Unit cell: (160.82, 147.92, 196.08, 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 118 16.00 P 56 15.00 Mg 1 11.99 O 5580 8.00 N 5036 7.00 C 17664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " 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 ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6448 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 49 sheets defined 43.3% alpha, 16.9% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 33 removed outlier: 3.764A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.905A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.961A 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 removed outlier: 3.509A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) 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 327 removed outlier: 3.687A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.632A pdb=" N ARG I 352 " --> pdb=" O SER I 348 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL I 353 " --> pdb=" O GLU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.854A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.630A pdb=" N GLN I 463 " --> pdb=" O MET I 459 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.547A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.817A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.920A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.586A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 656 through 660 removed outlier: 4.367A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) Processing helix chain 'I' and resid 663 through 668 removed outlier: 3.750A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (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 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 859 through 863 Processing helix chain 'I' and resid 942 through 983 removed outlier: 3.614A pdb=" N GLN I 955 " --> pdb=" O MET I 951 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA I 956 " --> pdb=" O GLN I 952 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU I 962 " --> pdb=" O LYS I 958 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU I 963 " --> pdb=" O ASP I 959 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU I 967 " --> pdb=" O GLU I 963 " (cutoff:3.500A) Processing helix chain 'I' and resid 984 through 987 Processing helix chain 'I' and resid 994 through 1000 removed outlier: 3.920A pdb=" N LEU I1000 " --> pdb=" O TRP I 997 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.867A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.840A pdb=" N MET I1131 " --> pdb=" O LYS I1127 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.694A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 removed outlier: 3.511A pdb=" N ASP I1241 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1282 removed outlier: 3.556A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.815A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.939A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.661A 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 212 through 233 removed outlier: 3.575A pdb=" N GLU G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.575A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.643A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) 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 removed outlier: 3.586A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.532A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.511A pdb=" N MET J 192 " --> pdb=" O LEU J 188 " (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 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 263 through 286 removed outlier: 3.508A pdb=" N ARG J 275 " --> pdb=" O ARG J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.549A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 removed outlier: 3.631A pdb=" N GLU J 414 " --> pdb=" O ASP J 410 " (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 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.520A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 515 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 4.189A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER J 635 " --> pdb=" O TYR J 631 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 4.076A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 774 Processing helix chain 'J' and resid 775 through 788 removed outlier: 3.594A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 804 removed outlier: 3.522A pdb=" N ALA J 804 " --> pdb=" O LEU J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 removed outlier: 3.647A pdb=" N LEU J 840 " --> pdb=" O ARG J 836 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.505A pdb=" N SER J 887 " --> pdb=" O SER J 884 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1068 through 1073 Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1242 removed outlier: 3.913A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1260 removed outlier: 4.389A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1314 through 1316 No H-bonds generated for 'chain 'J' and resid 1314 through 1316' Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.554A pdb=" N GLN J1326 " --> pdb=" O ALA J1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.960A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1362 through 1375 Processing helix chain 'L' and resid 114 through 136 Processing helix chain 'L' and resid 137 through 153 Processing helix chain 'L' and resid 215 through 234 removed outlier: 4.254A pdb=" N GLU L 219 " --> pdb=" O GLU L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 259 Processing helix chain 'L' and resid 262 through 296 removed outlier: 3.562A pdb=" N GLU L 293 " --> pdb=" O LYS L 289 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN L 294 " --> pdb=" O LEU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 313 through 320 removed outlier: 3.746A pdb=" N ILE L 320 " --> pdb=" O PHE L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 330 Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 383 removed outlier: 3.707A pdb=" N MET L 379 " --> pdb=" O ALA L 375 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL L 380 " --> pdb=" O LYS L 376 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU L 381 " --> pdb=" O LYS L 377 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 393 removed outlier: 3.750A pdb=" N LYS L 393 " --> pdb=" O SER L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 417 Processing helix chain 'L' and resid 418 through 419 No H-bonds generated for 'chain 'L' and resid 418 through 419' Processing helix chain 'L' and resid 420 through 424 Processing helix chain 'L' and resid 429 through 447 removed outlier: 4.370A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 543 Processing sheet with id=AA1, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.574A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.458A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.763A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.666A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 285 through 287 removed outlier: 4.243A pdb=" N LEU I 237 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.604A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AA9, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.575A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB2, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.423A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.349A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AB5, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.399A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 830 through 841 removed outlier: 6.549A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AB9, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.934A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.973A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC3, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AC4, first strand: chain 'G' and resid 12 through 20 removed outlier: 4.943A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N HIS G 23 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 97 through 111 removed outlier: 10.187A pdb=" N VAL G 98 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N ARG G 143 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N LEU G 100 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N SER G 141 " --> pdb=" O LEU G 100 " (cutoff:3.500A) removed outlier: 11.250A pdb=" N LEU G 102 " --> pdb=" O SER G 139 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N SER G 139 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N LYS G 104 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N ASN G 137 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY G 106 " --> pdb=" O ASP G 135 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP G 135 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC7, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AC8, first strand: chain 'H' and resid 13 through 20 removed outlier: 3.543A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.629A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AD2, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AD3, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.418A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.565A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.658A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 253 through 254 removed outlier: 3.637A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AE1, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.916A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.842A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 951 through 952 removed outlier: 3.531A pdb=" N GLU J1015 " --> pdb=" O VAL J 952 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.002A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE8, first strand: chain 'J' and resid 1025 through 1027 removed outlier: 3.666A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.665A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1046 through 1051 removed outlier: 3.694A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU J1056 " --> pdb=" O ASP J1051 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1155 through 1156 removed outlier: 6.371A pdb=" N ILE J1155 " --> pdb=" O ILE J1210 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.723A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1231 hydrogen bonds defined for protein. 3441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 7.60 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8987 1.34 - 1.45: 3560 1.45 - 1.57: 16128 1.57 - 1.69: 109 1.69 - 1.81: 205 Bond restraints: 28989 Sorted by residual: bond pdb=" C3' DG P 63 " pdb=" C2' DG P 63 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" N9 DA P 64 " pdb=" C4 DA P 64 " ideal model delta sigma weight residual 1.374 1.394 -0.020 6.00e-03 2.78e+04 1.06e+01 bond pdb=" C3' DA P 70 " pdb=" C2' DA P 70 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.02e+00 bond pdb=" C3' DC Q 19 " pdb=" C2' DC Q 19 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.73e+00 bond pdb=" C3' DA P 64 " pdb=" C2' DA P 64 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.48e+00 ... (remaining 28984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 38763 1.64 - 3.28: 569 3.28 - 4.93: 33 4.93 - 6.57: 8 6.57 - 8.21: 1 Bond angle restraints: 39374 Sorted by residual: angle pdb=" N3 DT Q 15 " pdb=" C4 DT Q 15 " pdb=" O4 DT Q 15 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" O4' DC Q 33 " pdb=" C4' DC Q 33 " pdb=" C3' DC Q 33 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.03e+01 angle pdb=" O4' DT Q 32 " pdb=" C4' DT Q 32 " pdb=" C3' DT Q 32 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT Q 36 " pdb=" C4 DT Q 36 " pdb=" O4 DT Q 36 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT Q 24 " pdb=" C4 DT Q 24 " pdb=" O4 DT Q 24 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 39369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.01: 17360 31.01 - 62.03: 353 62.03 - 93.04: 15 93.04 - 124.05: 0 124.05 - 155.07: 1 Dihedral angle restraints: 17729 sinusoidal: 7722 harmonic: 10007 Sorted by residual: dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C4' DG P 63 " pdb=" C3' DG P 63 " pdb=" O3' DG P 63 " pdb=" P DA P 64 " ideal model delta sinusoidal sigma weight residual 220.00 64.93 155.07 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA PRO I1185 " pdb=" C PRO I1185 " pdb=" N VAL I1186 " pdb=" CA VAL I1186 " ideal model delta harmonic sigma weight residual 180.00 -164.29 -15.71 0 5.00e+00 4.00e-02 9.88e+00 ... (remaining 17726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2723 0.029 - 0.058: 1123 0.058 - 0.087: 353 0.087 - 0.116: 247 0.116 - 0.145: 53 Chirality restraints: 4499 Sorted by residual: chirality pdb=" CA ILE I 668 " pdb=" N ILE I 668 " pdb=" C ILE I 668 " pdb=" CB ILE I 668 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" P DA P 64 " pdb=" OP1 DA P 64 " pdb=" OP2 DA P 64 " pdb=" O5' DA P 64 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" C3' DG Q 23 " pdb=" C4' DG Q 23 " pdb=" O3' DG Q 23 " pdb=" C2' DG Q 23 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 4496 not shown) Planarity restraints: 4952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR L 429 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C THR L 429 " 0.049 2.00e-02 2.50e+03 pdb=" O THR L 429 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR L 430 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO I 590 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO I 190 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " -0.022 5.00e-02 4.00e+02 ... (remaining 4949 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 819 2.71 - 3.26: 27092 3.26 - 3.81: 43137 3.81 - 4.35: 54940 4.35 - 4.90: 94429 Nonbonded interactions: 220417 Sorted by model distance: nonbonded pdb=" O3' A R 9 " pdb="MG MG J1501 " model vdw 2.163 2.170 nonbonded pdb=" OG1 THR L 354 " pdb=" OE1 GLN L 357 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP I 189 " pdb=" N ASN I 193 " model vdw 2.225 3.120 nonbonded pdb=" OG SER I 759 " pdb=" OG1 THR I 763 " model vdw 2.228 3.040 nonbonded pdb=" OG SER J 977 " pdb=" OG1 THR J 980 " model vdw 2.251 3.040 ... (remaining 220412 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 4 through 158 or resid 167 through 233)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.670 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 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 0.129 28997 Z= 0.204 Angle : 0.496 8.212 39386 Z= 0.317 Chirality : 0.041 0.145 4499 Planarity : 0.003 0.042 4952 Dihedral : 12.043 155.067 11281 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.45 % Allowed : 5.05 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.14), residues: 3451 helix: 1.78 (0.15), residues: 1308 sheet: 0.57 (0.25), residues: 464 loop : -0.21 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 10 TYR 0.010 0.001 TYR J1365 PHE 0.014 0.001 PHE I 514 TRP 0.008 0.001 TRP J 409 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.20 (28989) covalent geometry : angle 0.49574 / 0.32 (39374) hydrogen bonds : bond 0.13834 / 13.60 ( 1286) hydrogen bonds : angle 5.50330 / 5.61 ( 3555) metal coordination : bond 0.09361 / 5.65 ( 8) metal coordination : angle 0.05651 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 394 time to evaluate : 1.130 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: K 35 LYS cc_start: 0.8989 (mptt) cc_final: 0.8428 (mmmt) REVERT: K 43 ASN cc_start: 0.8649 (t0) cc_final: 0.8290 (t0) REVERT: K 72 GLN cc_start: 0.8749 (tp40) cc_final: 0.8438 (tp-100) REVERT: I 291 TYR cc_start: 0.7993 (t80) cc_final: 0.7620 (t80) REVERT: I 600 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8848 (p) REVERT: I 639 LYS cc_start: 0.8857 (mttt) cc_final: 0.8632 (mttm) REVERT: I 997 TRP cc_start: 0.7616 (m-10) cc_final: 0.7281 (m-10) REVERT: I 1008 GLN cc_start: 0.7273 (tp40) cc_final: 0.6977 (mm-40) REVERT: G 197 ASP cc_start: 0.8582 (m-30) cc_final: 0.8176 (t70) REVERT: H 66 HIS cc_start: 0.8014 (t-90) cc_final: 0.7662 (t70) REVERT: H 147 GLN cc_start: 0.8758 (mt0) cc_final: 0.8281 (mt0) REVERT: J 1186 TYR cc_start: 0.7768 (t80) cc_final: 0.7223 (t80) REVERT: J 1193 TRP cc_start: 0.6765 (p-90) cc_final: 0.6447 (p-90) REVERT: L 277 MET cc_start: 0.6986 (tpt) cc_final: 0.6301 (tmm) REVERT: L 278 ASP cc_start: 0.7982 (m-30) cc_final: 0.7334 (m-30) REVERT: L 338 HIS cc_start: 0.8669 (t-90) cc_final: 0.8416 (m-70) outliers start: 43 outliers final: 12 residues processed: 434 average time/residue: 0.2396 time to fit residues: 154.6058 Evaluate side-chains 223 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1063 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 761 GLN I 952 GLN I 965 GLN I1220 GLN J 80 HIS ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.106475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.067151 restraints weight = 73565.063| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.87 r_work: 0.2929 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28997 Z= 0.122 Angle : 0.531 11.514 39386 Z= 0.286 Chirality : 0.042 0.240 4499 Planarity : 0.004 0.061 4952 Dihedral : 11.231 152.859 4462 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.21 % Allowed : 8.72 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.14), residues: 3451 helix: 1.97 (0.14), residues: 1325 sheet: 0.59 (0.25), residues: 438 loop : -0.13 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 233 TYR 0.015 0.001 TYR J1186 PHE 0.017 0.001 PHE I 230 TRP 0.022 0.002 TRP L 315 HIS 0.003 0.001 HIS J 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (28989) covalent geometry : angle 0.53061 / 0.29 (39374) hydrogen bonds : bond 0.04281 / 3.99 ( 1286) hydrogen bonds : angle 4.44179 / 4.51 ( 3555) metal coordination : bond 0.00626 / 0.33 ( 8) metal coordination : angle 1.08375 / 0.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 1.275 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: K 15 ASN cc_start: 0.7449 (t0) cc_final: 0.7214 (t0) REVERT: K 35 LYS cc_start: 0.8802 (mptt) cc_final: 0.8090 (mmmt) REVERT: K 43 ASN cc_start: 0.8709 (t0) cc_final: 0.8343 (t0) REVERT: K 72 GLN cc_start: 0.8594 (tp40) cc_final: 0.8299 (tp-100) REVERT: I 104 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8342 (tp) REVERT: I 233 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.5553 (ptp90) REVERT: I 236 LYS cc_start: 0.8238 (mmtp) cc_final: 0.8022 (pttm) REVERT: I 239 MET cc_start: 0.6834 (tmm) cc_final: 0.6430 (tmm) REVERT: I 315 MET cc_start: 0.8612 (mmm) cc_final: 0.8058 (mtp) REVERT: I 332 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7757 (mtp180) REVERT: I 600 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8714 (p) REVERT: I 997 TRP cc_start: 0.7746 (m-10) cc_final: 0.7425 (m-10) REVERT: I 1315 MET cc_start: 0.9366 (ptt) cc_final: 0.9065 (ptt) REVERT: G 197 ASP cc_start: 0.8678 (m-30) cc_final: 0.8139 (t70) REVERT: H 41 ASN cc_start: 0.8991 (t0) cc_final: 0.8741 (t0) REVERT: H 66 HIS cc_start: 0.8003 (t-90) cc_final: 0.7008 (t70) REVERT: J 130 MET cc_start: 0.8583 (ttm) cc_final: 0.8379 (ttm) REVERT: J 298 MET cc_start: 0.9044 (mtm) cc_final: 0.8775 (mtm) REVERT: J 1193 TRP cc_start: 0.6779 (p-90) cc_final: 0.6455 (p-90) REVERT: L 244 THR cc_start: 0.8171 (p) cc_final: 0.7421 (t) REVERT: L 297 MET cc_start: 0.7991 (ptt) cc_final: 0.7676 (ptm) outliers start: 36 outliers final: 20 residues processed: 257 average time/residue: 0.1959 time to fit residues: 79.3680 Evaluate side-chains 215 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1051 ASP Chi-restraints excluded: chain L residue 362 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 255 optimal weight: 6.9990 chunk 340 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 333 optimal weight: 0.7980 chunk 257 optimal weight: 4.9990 chunk 306 optimal weight: 0.0770 chunk 137 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 overall best weight: 2.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 952 GLN L 338 HIS ** L 362 ASN ** 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 = 0.3833 r_free = 0.3833 target = 0.104879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.065483 restraints weight = 73954.499| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.86 r_work: 0.2896 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28997 Z= 0.174 Angle : 0.518 8.537 39386 Z= 0.279 Chirality : 0.042 0.232 4499 Planarity : 0.004 0.046 4952 Dihedral : 11.340 154.210 4448 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.58 % Allowed : 9.57 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.14), residues: 3451 helix: 2.03 (0.14), residues: 1321 sheet: 0.59 (0.25), residues: 448 loop : -0.17 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG I 275 TYR 0.014 0.001 TYR I1018 PHE 0.016 0.001 PHE L 316 TRP 0.017 0.001 TRP L 315 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (28989) covalent geometry : angle 0.51758 / 0.28 (39374) hydrogen bonds : bond 0.04231 / 3.89 ( 1286) hydrogen bonds : angle 4.31733 / 4.42 ( 3555) metal coordination : bond 0.00864 / 0.53 ( 8) metal coordination : angle 1.31257 / 0.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.982 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: K 15 ASN cc_start: 0.7553 (t0) cc_final: 0.7236 (t0) REVERT: K 35 LYS cc_start: 0.8930 (mptt) cc_final: 0.8226 (mmmt) REVERT: K 43 ASN cc_start: 0.8706 (t0) cc_final: 0.8343 (t0) REVERT: K 44 ASP cc_start: 0.8691 (m-30) cc_final: 0.8378 (t0) REVERT: K 72 GLN cc_start: 0.8594 (tp40) cc_final: 0.8387 (tp40) REVERT: I 239 MET cc_start: 0.7166 (tmm) cc_final: 0.6751 (tmm) REVERT: I 332 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7785 (mtp180) REVERT: I 600 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8832 (p) REVERT: I 697 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.7952 (pmtt) REVERT: G 197 ASP cc_start: 0.8632 (m-30) cc_final: 0.8151 (t70) REVERT: H 75 GLN cc_start: 0.8787 (tt0) cc_final: 0.8581 (pt0) REVERT: J 180 MET cc_start: 0.5712 (tpp) cc_final: 0.5090 (mmm) REVERT: J 298 MET cc_start: 0.9054 (mtm) cc_final: 0.8726 (mtm) REVERT: J 1193 TRP cc_start: 0.6809 (p-90) cc_final: 0.6479 (p-90) outliers start: 47 outliers final: 27 residues processed: 237 average time/residue: 0.1811 time to fit residues: 68.5219 Evaluate side-chains 208 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1051 ASP Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1311 LYS Chi-restraints excluded: chain J residue 1340 LYS Chi-restraints excluded: chain L residue 286 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 134 optimal weight: 0.0010 chunk 340 optimal weight: 9.9990 chunk 320 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 245 optimal weight: 0.5980 chunk 173 optimal weight: 0.8980 chunk 312 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 212 optimal weight: 5.9990 chunk 323 optimal weight: 40.0000 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.106068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067056 restraints weight = 73636.029| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.86 r_work: 0.2934 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 28997 Z= 0.099 Angle : 0.474 8.413 39386 Z= 0.257 Chirality : 0.041 0.243 4499 Planarity : 0.003 0.046 4952 Dihedral : 11.364 152.406 4448 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.65 % Allowed : 9.77 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.14), residues: 3451 helix: 2.07 (0.14), residues: 1330 sheet: 0.71 (0.25), residues: 431 loop : -0.10 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 233 TYR 0.015 0.001 TYR H 185 PHE 0.012 0.001 PHE I 405 TRP 0.019 0.001 TRP J 868 HIS 0.003 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (28989) covalent geometry : angle 0.47402 / 0.26 (39374) hydrogen bonds : bond 0.03484 / 3.22 ( 1286) hydrogen bonds : angle 4.14482 / 4.24 ( 3555) metal coordination : bond 0.00306 / 0.15 ( 8) metal coordination : angle 1.08801 / 0.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 1.173 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: K 15 ASN cc_start: 0.7366 (t0) cc_final: 0.6474 (t0) REVERT: K 35 LYS cc_start: 0.8914 (mptt) cc_final: 0.8177 (mmmt) REVERT: K 43 ASN cc_start: 0.8794 (t0) cc_final: 0.8441 (t0) REVERT: K 44 ASP cc_start: 0.8751 (m-30) cc_final: 0.8476 (t0) REVERT: K 72 GLN cc_start: 0.8604 (tp40) cc_final: 0.8384 (tp-100) REVERT: I 478 ARG cc_start: 0.8850 (tpt-90) cc_final: 0.8431 (tpt170) REVERT: I 600 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8841 (p) REVERT: G 197 ASP cc_start: 0.8599 (m-30) cc_final: 0.8152 (t70) REVERT: H 41 ASN cc_start: 0.8921 (t0) cc_final: 0.8683 (t0) REVERT: J 140 TYR cc_start: 0.7624 (m-10) cc_final: 0.7227 (m-80) REVERT: J 298 MET cc_start: 0.9058 (mtm) cc_final: 0.8709 (mtm) REVERT: L 121 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7598 (ptpp) REVERT: L 276 MET cc_start: 0.8764 (mmm) cc_final: 0.8535 (ptt) outliers start: 49 outliers final: 28 residues processed: 242 average time/residue: 0.1912 time to fit residues: 73.7357 Evaluate side-chains 212 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 979 ASN Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1051 ASP Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1311 LYS Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 286 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 163 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 287 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 244 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN L 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.105950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066891 restraints weight = 73448.066| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.85 r_work: 0.2931 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 28997 Z= 0.101 Angle : 0.465 8.099 39386 Z= 0.251 Chirality : 0.041 0.238 4499 Planarity : 0.003 0.047 4952 Dihedral : 11.373 153.125 4448 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.52 % Allowed : 10.58 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.14), residues: 3451 helix: 2.14 (0.14), residues: 1333 sheet: 0.77 (0.25), residues: 429 loop : -0.08 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J1194 TYR 0.015 0.001 TYR H 185 PHE 0.017 0.001 PHE I 230 TRP 0.033 0.001 TRP J1193 HIS 0.006 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (28989) covalent geometry : angle 0.46417 / 0.25 (39374) hydrogen bonds : bond 0.03366 / 3.13 ( 1286) hydrogen bonds : angle 4.07237 / 4.19 ( 3555) metal coordination : bond 0.00373 / 0.20 ( 8) metal coordination : angle 1.12916 / 0.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 1.079 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: K 35 LYS cc_start: 0.8876 (mptt) cc_final: 0.8124 (mmmt) REVERT: K 43 ASN cc_start: 0.8792 (t0) cc_final: 0.8362 (t0) REVERT: K 44 ASP cc_start: 0.8631 (m-30) cc_final: 0.8349 (t0) REVERT: K 72 GLN cc_start: 0.8567 (tp40) cc_final: 0.8342 (tp-100) REVERT: I 239 MET cc_start: 0.6494 (tmm) cc_final: 0.5883 (tmm) REVERT: I 478 ARG cc_start: 0.8873 (tpt-90) cc_final: 0.8524 (tpt170) REVERT: I 600 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8828 (p) REVERT: I 697 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.7871 (pmtt) REVERT: I 1329 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8946 (tt0) REVERT: G 197 ASP cc_start: 0.8643 (m-30) cc_final: 0.8145 (t70) REVERT: H 41 ASN cc_start: 0.8947 (t0) cc_final: 0.8700 (t0) REVERT: J 227 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8689 (m-80) REVERT: J 298 MET cc_start: 0.9092 (mtm) cc_final: 0.8725 (mtm) REVERT: L 121 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7568 (ptpp) REVERT: L 281 ARG cc_start: 0.9343 (ptt180) cc_final: 0.9120 (mtt-85) outliers start: 45 outliers final: 30 residues processed: 233 average time/residue: 0.1889 time to fit residues: 70.1641 Evaluate side-chains 216 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 GLN Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 979 ASN Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1051 ASP Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1311 LYS Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 286 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 82 optimal weight: 8.9990 chunk 312 optimal weight: 4.9990 chunk 309 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 HIS L 338 HIS ** L 406 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 = 0.3843 r_free = 0.3843 target = 0.105443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066325 restraints weight = 73441.084| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.84 r_work: 0.2920 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28997 Z= 0.129 Angle : 0.477 8.061 39386 Z= 0.255 Chirality : 0.041 0.236 4499 Planarity : 0.003 0.049 4952 Dihedral : 11.412 153.867 4448 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.65 % Allowed : 10.74 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.14), residues: 3451 helix: 2.16 (0.14), residues: 1334 sheet: 0.78 (0.25), residues: 428 loop : -0.10 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 694 TYR 0.017 0.001 TYR I1018 PHE 0.011 0.001 PHE I 405 TRP 0.049 0.002 TRP I 997 HIS 0.007 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (28989) covalent geometry : angle 0.47693 / 0.26 (39374) hydrogen bonds : bond 0.03436 / 3.18 ( 1286) hydrogen bonds : angle 4.06296 / 4.19 ( 3555) metal coordination : bond 0.00536 / 0.31 ( 8) metal coordination : angle 1.13011 / 0.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 1.310 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: K 35 LYS cc_start: 0.8898 (mptt) cc_final: 0.8152 (mmmt) REVERT: K 43 ASN cc_start: 0.8773 (t0) cc_final: 0.8334 (t0) REVERT: K 44 ASP cc_start: 0.8678 (m-30) cc_final: 0.8416 (t0) REVERT: I 239 MET cc_start: 0.6568 (tmm) cc_final: 0.6214 (tmm) REVERT: I 600 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8835 (p) REVERT: I 697 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.7875 (pmtt) REVERT: G 197 ASP cc_start: 0.8626 (m-30) cc_final: 0.8158 (t70) REVERT: H 41 ASN cc_start: 0.8971 (t0) cc_final: 0.8723 (t0) REVERT: J 140 TYR cc_start: 0.7796 (m-10) cc_final: 0.7270 (m-80) REVERT: J 180 MET cc_start: 0.5990 (mmm) cc_final: 0.5638 (mmt) REVERT: J 227 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8743 (m-80) REVERT: J 298 MET cc_start: 0.9060 (mtm) cc_final: 0.8680 (mtm) REVERT: J 1146 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8376 (mm-30) REVERT: L 121 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7575 (ptpp) REVERT: L 281 ARG cc_start: 0.9346 (ptt180) cc_final: 0.9121 (mtt-85) REVERT: L 297 MET cc_start: 0.7323 (ptm) cc_final: 0.7022 (ppp) outliers start: 49 outliers final: 33 residues processed: 225 average time/residue: 0.2074 time to fit residues: 73.4726 Evaluate side-chains 217 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 GLN Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 979 ASN Chi-restraints excluded: chain J residue 1051 ASP Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1311 LYS Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 85 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 230 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 342 optimal weight: 20.0000 chunk 274 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 262 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN J 365 GLN L 338 HIS ** L 406 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 = 0.3850 r_free = 0.3850 target = 0.105848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066809 restraints weight = 73182.540| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.83 r_work: 0.2935 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28997 Z= 0.104 Angle : 0.463 7.993 39386 Z= 0.248 Chirality : 0.041 0.240 4499 Planarity : 0.003 0.050 4952 Dihedral : 11.422 153.652 4448 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.55 % Allowed : 11.08 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.14), residues: 3451 helix: 2.21 (0.14), residues: 1334 sheet: 0.79 (0.25), residues: 438 loop : -0.07 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 195 TYR 0.016 0.001 TYR H 185 PHE 0.012 0.001 PHE J 260 TRP 0.021 0.001 TRP I 997 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (28989) covalent geometry : angle 0.46256 / 0.25 (39374) hydrogen bonds : bond 0.03234 / 2.99 ( 1286) hydrogen bonds : angle 3.99845 / 4.12 ( 3555) metal coordination : bond 0.00394 / 0.22 ( 8) metal coordination : angle 1.10751 / 0.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 1.162 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: K 35 LYS cc_start: 0.8944 (mptt) cc_final: 0.8215 (mmmt) REVERT: K 43 ASN cc_start: 0.8711 (t0) cc_final: 0.8490 (t0) REVERT: K 44 ASP cc_start: 0.8602 (m-30) cc_final: 0.8327 (t0) REVERT: I 600 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8853 (p) REVERT: I 697 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.7898 (pmtt) REVERT: G 197 ASP cc_start: 0.8558 (m-30) cc_final: 0.8186 (t70) REVERT: H 41 ASN cc_start: 0.8922 (t0) cc_final: 0.8694 (t0) REVERT: J 180 MET cc_start: 0.6021 (mmm) cc_final: 0.5818 (mmt) REVERT: J 227 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8785 (m-80) REVERT: J 298 MET cc_start: 0.9028 (mtm) cc_final: 0.8653 (mtm) REVERT: J 821 MET cc_start: 0.8339 (tpp) cc_final: 0.8017 (tpp) REVERT: J 1146 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8357 (mm-30) REVERT: L 121 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7608 (ptpp) REVERT: L 281 ARG cc_start: 0.9342 (ptt180) cc_final: 0.9101 (mtt-85) REVERT: L 297 MET cc_start: 0.7330 (ptm) cc_final: 0.7026 (ppp) outliers start: 46 outliers final: 28 residues processed: 229 average time/residue: 0.2037 time to fit residues: 74.0395 Evaluate side-chains 214 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 979 ASN Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 345 optimal weight: 6.9990 chunk 323 optimal weight: 0.0980 chunk 106 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 249 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 651 HIS L 338 HIS ** L 406 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 = 0.3853 r_free = 0.3853 target = 0.105981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.066911 restraints weight = 73686.337| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.86 r_work: 0.2936 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 28997 Z= 0.103 Angle : 0.473 12.506 39386 Z= 0.252 Chirality : 0.040 0.239 4499 Planarity : 0.003 0.051 4952 Dihedral : 11.401 154.032 4448 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.41 % Allowed : 11.25 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.14), residues: 3451 helix: 2.21 (0.14), residues: 1334 sheet: 0.83 (0.25), residues: 446 loop : -0.04 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 542 TYR 0.015 0.001 TYR H 185 PHE 0.012 0.001 PHE I 230 TRP 0.017 0.001 TRP L 315 HIS 0.006 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (28989) covalent geometry : angle 0.47267 / 0.25 (39374) hydrogen bonds : bond 0.03181 / 2.94 ( 1286) hydrogen bonds : angle 3.97835 / 4.12 ( 3555) metal coordination : bond 0.00373 / 0.21 ( 8) metal coordination : angle 1.09987 / 0.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 1.105 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: K 35 LYS cc_start: 0.8955 (mptt) cc_final: 0.8223 (mmmt) REVERT: K 38 LEU cc_start: 0.8819 (mp) cc_final: 0.8573 (mp) REVERT: K 43 ASN cc_start: 0.8828 (t0) cc_final: 0.8399 (t0) REVERT: K 44 ASP cc_start: 0.8574 (m-30) cc_final: 0.8286 (t0) REVERT: I 439 LYS cc_start: 0.8649 (mmtm) cc_final: 0.8392 (mmtm) REVERT: I 478 ARG cc_start: 0.8837 (tpt-90) cc_final: 0.8630 (tpt170) REVERT: I 600 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8851 (p) REVERT: I 697 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.7901 (pmtt) REVERT: G 197 ASP cc_start: 0.8564 (m-30) cc_final: 0.8191 (t70) REVERT: H 41 ASN cc_start: 0.8930 (t0) cc_final: 0.8703 (t0) REVERT: H 183 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9154 (tp) REVERT: J 140 TYR cc_start: 0.7615 (m-10) cc_final: 0.6800 (m-80) REVERT: J 180 MET cc_start: 0.6045 (mmm) cc_final: 0.5801 (mmt) REVERT: J 227 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8793 (m-80) REVERT: J 298 MET cc_start: 0.9034 (mtm) cc_final: 0.8656 (mtm) REVERT: L 116 GLU cc_start: 0.5942 (mp0) cc_final: 0.5698 (pt0) REVERT: L 297 MET cc_start: 0.7326 (ptm) cc_final: 0.6987 (ppp) outliers start: 42 outliers final: 34 residues processed: 223 average time/residue: 0.2013 time to fit residues: 71.4768 Evaluate side-chains 221 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 979 ASN Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1051 ASP Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1311 LYS Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 235 optimal weight: 0.6980 chunk 264 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 313 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 307 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN L 338 HIS ** L 406 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 = 0.3856 r_free = 0.3856 target = 0.106204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.067054 restraints weight = 73494.092| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.86 r_work: 0.2936 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 28997 Z= 0.101 Angle : 0.472 11.369 39386 Z= 0.251 Chirality : 0.041 0.239 4499 Planarity : 0.003 0.050 4952 Dihedral : 11.373 154.227 4446 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.38 % Allowed : 11.49 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.15), residues: 3451 helix: 2.21 (0.14), residues: 1336 sheet: 0.84 (0.26), residues: 438 loop : -0.01 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 694 TYR 0.017 0.001 TYR H 185 PHE 0.012 0.001 PHE I 230 TRP 0.021 0.001 TRP L 315 HIS 0.004 0.000 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (28989) covalent geometry : angle 0.47153 / 0.25 (39374) hydrogen bonds : bond 0.03123 / 2.89 ( 1286) hydrogen bonds : angle 3.96066 / 4.11 ( 3555) metal coordination : bond 0.00363 / 0.20 ( 8) metal coordination : angle 1.07686 / 0.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 1.086 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: K 35 LYS cc_start: 0.8925 (mptt) cc_final: 0.8172 (mmmt) REVERT: K 38 LEU cc_start: 0.8810 (mp) cc_final: 0.8511 (mp) REVERT: K 43 ASN cc_start: 0.8826 (t0) cc_final: 0.8385 (t0) REVERT: K 44 ASP cc_start: 0.8560 (m-30) cc_final: 0.8262 (t0) REVERT: I 246 LEU cc_start: 0.8896 (mm) cc_final: 0.8542 (mm) REVERT: I 439 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8407 (mmtm) REVERT: I 600 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8821 (p) REVERT: I 697 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.7882 (pmtt) REVERT: G 197 ASP cc_start: 0.8591 (m-30) cc_final: 0.8186 (t70) REVERT: H 41 ASN cc_start: 0.8950 (t0) cc_final: 0.8693 (t0) REVERT: H 183 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9179 (tp) REVERT: J 130 MET cc_start: 0.8713 (ttm) cc_final: 0.8433 (ptm) REVERT: J 140 TYR cc_start: 0.7689 (m-10) cc_final: 0.6846 (m-80) REVERT: J 180 MET cc_start: 0.5938 (mmm) cc_final: 0.5705 (mmt) REVERT: J 227 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8765 (m-80) REVERT: J 298 MET cc_start: 0.9053 (mtm) cc_final: 0.8664 (mtm) REVERT: J 821 MET cc_start: 0.8306 (tpp) cc_final: 0.8014 (tpp) REVERT: L 121 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7651 (ptpp) REVERT: L 297 MET cc_start: 0.7277 (ptm) cc_final: 0.6971 (ppp) outliers start: 41 outliers final: 31 residues processed: 220 average time/residue: 0.2071 time to fit residues: 71.8702 Evaluate side-chains 221 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 979 ASN Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1051 ASP Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1311 LYS Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 133 optimal weight: 9.9990 chunk 242 optimal weight: 0.6980 chunk 294 optimal weight: 30.0000 chunk 103 optimal weight: 1.9990 chunk 339 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 340 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 792 ASN L 338 HIS ** L 406 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 = 0.3846 r_free = 0.3846 target = 0.105567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.066389 restraints weight = 73397.943| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.85 r_work: 0.2927 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28997 Z= 0.128 Angle : 0.488 11.364 39386 Z= 0.258 Chirality : 0.041 0.237 4499 Planarity : 0.003 0.050 4952 Dihedral : 11.383 154.890 4446 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.45 % Allowed : 11.49 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.14), residues: 3451 helix: 2.21 (0.14), residues: 1336 sheet: 0.81 (0.26), residues: 438 loop : -0.04 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 478 TYR 0.013 0.001 TYR I1018 PHE 0.011 0.001 PHE I 405 TRP 0.023 0.001 TRP L 315 HIS 0.003 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (28989) covalent geometry : angle 0.48795 / 0.26 (39374) hydrogen bonds : bond 0.03273 / 3.02 ( 1286) hydrogen bonds : angle 3.96360 / 4.13 ( 3555) metal coordination : bond 0.00530 / 0.32 ( 8) metal coordination : angle 1.11878 / 0.68 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 1.132 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: K 35 LYS cc_start: 0.8993 (mptt) cc_final: 0.8237 (mmmt) REVERT: K 38 LEU cc_start: 0.8844 (mp) cc_final: 0.8549 (mp) REVERT: K 43 ASN cc_start: 0.8787 (t0) cc_final: 0.8313 (t0) REVERT: K 44 ASP cc_start: 0.8644 (m-30) cc_final: 0.8401 (t0) REVERT: I 239 MET cc_start: 0.6884 (tmm) cc_final: 0.6186 (tmm) REVERT: I 291 TYR cc_start: 0.7787 (t80) cc_final: 0.7577 (t80) REVERT: I 600 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8849 (p) REVERT: I 697 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.7923 (pmtt) REVERT: G 197 ASP cc_start: 0.8573 (m-30) cc_final: 0.8211 (t70) REVERT: H 41 ASN cc_start: 0.8938 (t0) cc_final: 0.8707 (t0) REVERT: H 183 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9154 (tp) REVERT: J 130 MET cc_start: 0.8752 (ttm) cc_final: 0.8499 (ptm) REVERT: J 140 TYR cc_start: 0.7712 (m-10) cc_final: 0.6873 (m-80) REVERT: J 180 MET cc_start: 0.6045 (mmm) cc_final: 0.5812 (mmt) REVERT: J 227 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8751 (m-80) REVERT: J 298 MET cc_start: 0.9050 (mtm) cc_final: 0.8672 (mtm) REVERT: J 821 MET cc_start: 0.8386 (tpp) cc_final: 0.8086 (tpp) REVERT: L 121 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7578 (ptpp) REVERT: L 297 MET cc_start: 0.7305 (ptm) cc_final: 0.6978 (ppp) outliers start: 43 outliers final: 32 residues processed: 222 average time/residue: 0.1915 time to fit residues: 67.5662 Evaluate side-chains 221 residues out of total 2969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 233 ARG Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 979 ASN Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1051 ASP Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1311 LYS Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 91 optimal weight: 0.0770 chunk 218 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN L 338 HIS L 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.104909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065646 restraints weight = 73692.515| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.85 r_work: 0.2908 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28997 Z= 0.153 Angle : 0.508 11.383 39386 Z= 0.268 Chirality : 0.041 0.237 4499 Planarity : 0.003 0.050 4952 Dihedral : 11.405 155.246 4443 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.31 % Allowed : 11.86 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.14), residues: 3451 helix: 2.23 (0.14), residues: 1329 sheet: 0.88 (0.26), residues: 418 loop : -0.09 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 478 TYR 0.014 0.001 TYR I 123 PHE 0.013 0.001 PHE I 230 TRP 0.022 0.001 TRP L 315 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (28989) covalent geometry : angle 0.50719 / 0.27 (39374) hydrogen bonds : bond 0.03519 / 3.25 ( 1286) hydrogen bonds : angle 3.99011 / 4.17 ( 3555) metal coordination : bond 0.00680 / 0.42 ( 8) metal coordination : angle 1.28629 / 0.78 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8893.20 seconds wall clock time: 152 minutes 20.65 seconds (9140.65 seconds total)