Starting phenix.real_space_refine on Sun Oct 13 08:08:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/10_2024/8dgf_27422.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/10_2024/8dgf_27422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/10_2024/8dgf_27422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/10_2024/8dgf_27422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/10_2024/8dgf_27422.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgf_27422/10_2024/8dgf_27422.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 234 5.16 5 C 41812 2.51 5 N 10676 2.21 5 O 12220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 158 residue(s): 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 64958 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 12805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1541, 12805 Classifications: {'peptide': 1541} Link IDs: {'PTRANS': 44, 'TRANS': 1496} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 12756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 12756 Classifications: {'peptide': 1534} Link IDs: {'PTRANS': 44, 'TRANS': 1489} Chain breaks: 4 Chain: "C" Number of atoms: 12805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1541, 12805 Classifications: {'peptide': 1541} Link IDs: {'PTRANS': 44, 'TRANS': 1496} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 12756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 12756 Classifications: {'peptide': 1534} Link IDs: {'PTRANS': 44, 'TRANS': 1489} Chain breaks: 4 Chain: "E" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3427 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 19, 'TRANS': 418} Chain breaks: 1 Chain: "F" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3427 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 19, 'TRANS': 418} Chain breaks: 1 Chain: "G" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3427 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 19, 'TRANS': 418} Chain breaks: 1 Chain: "H" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3427 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 19, 'TRANS': 418} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 35.62, per 1000 atoms: 0.55 Number of scatterers: 64958 At special positions: 0 Unit cell: (255.487, 261.694, 196.529, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 234 16.00 P 12 15.00 Mg 4 11.99 O 12220 8.00 N 10676 7.00 C 41812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1439 " - pdb=" SG CYS A1490 " distance=2.05 Simple disulfide: pdb=" SG CYS B1439 " - pdb=" SG CYS B1490 " distance=2.05 Simple disulfide: pdb=" SG CYS C1439 " - pdb=" SG CYS C1490 " distance=2.05 Simple disulfide: pdb=" SG CYS D1439 " - pdb=" SG CYS D1490 " distance=2.05 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: 14.61 Conformation dependent library (CDL) restraints added in 7.6 seconds 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15148 Finding SS restraints... Secondary structure from input PDB file: 473 helices and 56 sheets defined 67.9% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.18 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 16 through 33 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 44 through 48 removed outlier: 4.118A pdb=" N ILE A 48 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 74 through 89 removed outlier: 3.529A pdb=" N TYR A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 165 through 174 removed outlier: 4.085A pdb=" N HIS A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.542A pdb=" N VAL A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.685A pdb=" N ILE A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 removed outlier: 3.825A pdb=" N LYS A 265 " --> pdb=" O SER A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 268 through 274 removed outlier: 4.191A pdb=" N GLY A 274 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 307 through 320 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 332 through 343 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 401 through 414 Processing helix chain 'A' and resid 418 through 436 removed outlier: 3.746A pdb=" N GLU A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 469 through 487 removed outlier: 3.789A pdb=" N GLU A 473 " --> pdb=" O HIS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 501 through 518 Processing helix chain 'A' and resid 522 through 533 removed outlier: 3.771A pdb=" N PHE A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 551 removed outlier: 3.976A pdb=" N LYS A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 561 removed outlier: 4.287A pdb=" N PHE A 557 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 568 removed outlier: 4.101A pdb=" N SER A 568 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 615 through 627 Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 635 through 638 removed outlier: 4.362A pdb=" N PHE A 638 " --> pdb=" O ASN A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 635 through 638' Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 653 through 673 Processing helix chain 'A' and resid 685 through 693 removed outlier: 3.644A pdb=" N THR A 689 " --> pdb=" O ASN A 685 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 693 " --> pdb=" O THR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 712 Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 740 through 753 removed outlier: 3.657A pdb=" N GLN A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 782 removed outlier: 3.909A pdb=" N HIS A 779 " --> pdb=" O ARG A 776 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 782 " --> pdb=" O HIS A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 798 removed outlier: 3.895A pdb=" N GLN A 796 " --> pdb=" O TYR A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 819 removed outlier: 3.501A pdb=" N HIS A 819 " --> pdb=" O ILE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 859 through 877 Processing helix chain 'A' and resid 881 through 896 removed outlier: 3.569A pdb=" N ASN A 895 " --> pdb=" O PHE A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 912 removed outlier: 4.041A pdb=" N SER A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 924 removed outlier: 4.040A pdb=" N VAL A 922 " --> pdb=" O ASN A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 927 No H-bonds generated for 'chain 'A' and resid 925 through 927' Processing helix chain 'A' and resid 928 through 948 removed outlier: 3.750A pdb=" N THR A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A 944 " --> pdb=" O ASP A 940 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER A 945 " --> pdb=" O ARG A 941 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 946 " --> pdb=" O THR A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 973 removed outlier: 3.783A pdb=" N ASP A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 979 removed outlier: 3.626A pdb=" N THR A 979 " --> pdb=" O HIS A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 988 Processing helix chain 'A' and resid 997 through 1017 Processing helix chain 'A' and resid 1021 through 1025 Processing helix chain 'A' and resid 1026 through 1038 Processing helix chain 'A' and resid 1039 through 1042 removed outlier: 6.008A pdb=" N ARG A1042 " --> pdb=" O MET A1039 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1039 through 1042' Processing helix chain 'A' and resid 1064 through 1082 Processing helix chain 'A' and resid 1084 through 1096 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1110 through 1127 Processing helix chain 'A' and resid 1130 through 1138 removed outlier: 3.839A pdb=" N LEU A1136 " --> pdb=" O ASP A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1152 Processing helix chain 'A' and resid 1157 through 1173 removed outlier: 3.783A pdb=" N LYS A1173 " --> pdb=" O LEU A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1177 Processing helix chain 'A' and resid 1187 through 1193 Processing helix chain 'A' and resid 1194 through 1202 removed outlier: 3.667A pdb=" N ILE A1198 " --> pdb=" O ALA A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1218 removed outlier: 3.764A pdb=" N PHE A1218 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1240 removed outlier: 3.765A pdb=" N VAL A1237 " --> pdb=" O PHE A1233 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A1240 " --> pdb=" O MET A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1277 Proline residue: A1261 - end of helix removed outlier: 3.648A pdb=" N VAL A1264 " --> pdb=" O LYS A1260 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A1265 " --> pdb=" O PRO A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1295 Processing helix chain 'A' and resid 1295 through 1305 Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 4.571A pdb=" N LYS A1317 " --> pdb=" O SER A1314 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A1318 " --> pdb=" O MET A1315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1314 through 1318' Processing helix chain 'A' and resid 1319 through 1328 Processing helix chain 'A' and resid 1336 through 1355 removed outlier: 3.543A pdb=" N LEU A1345 " --> pdb=" O LYS A1341 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A1348 " --> pdb=" O SER A1344 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A1353 " --> pdb=" O ARG A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1362 Processing helix chain 'A' and resid 1364 through 1381 removed outlier: 3.766A pdb=" N ARG A1374 " --> pdb=" O SER A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1391 Processing helix chain 'A' and resid 1391 through 1397 removed outlier: 3.504A pdb=" N GLY A1397 " --> pdb=" O PRO A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1419 removed outlier: 3.504A pdb=" N GLU A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1440 removed outlier: 3.610A pdb=" N PHE A1431 " --> pdb=" O VAL A1427 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A1432 " --> pdb=" O TRP A1428 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP A1433 " --> pdb=" O ASP A1429 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LYS A1434 " --> pdb=" O LEU A1430 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A1440 " --> pdb=" O VAL A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1456 Processing helix chain 'A' and resid 1473 through 1475 No H-bonds generated for 'chain 'A' and resid 1473 through 1475' Processing helix chain 'A' and resid 1476 through 1487 removed outlier: 4.169A pdb=" N PHE A1480 " --> pdb=" O ASN A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1503 removed outlier: 3.856A pdb=" N LEU A1494 " --> pdb=" O CYS A1490 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A1502 " --> pdb=" O ALA A1498 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A1503 " --> pdb=" O LYS A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1507 No H-bonds generated for 'chain 'A' and resid 1505 through 1507' Processing helix chain 'A' and resid 1508 through 1523 removed outlier: 4.183A pdb=" N THR A1514 " --> pdb=" O ASN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1528 Processing helix chain 'A' and resid 1534 through 1557 removed outlier: 3.649A pdb=" N ASN A1548 " --> pdb=" O ARG A1544 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A1549 " --> pdb=" O ARG A1545 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU A1552 " --> pdb=" O ASN A1548 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG A1553 " --> pdb=" O ASN A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1574 removed outlier: 3.987A pdb=" N ILE A1567 " --> pdb=" O GLU A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1587 Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 16 through 33 removed outlier: 3.609A pdb=" N ASN B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 74 through 89 removed outlier: 3.799A pdb=" N LEU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.840A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.876A pdb=" N HIS B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.635A pdb=" N LEU B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.623A pdb=" N GLU B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 removed outlier: 3.604A pdb=" N ILE B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 removed outlier: 3.726A pdb=" N LYS B 265 " --> pdb=" O SER B 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 297 through 304 removed outlier: 3.588A pdb=" N LEU B 302 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 332 through 345 removed outlier: 3.678A pdb=" N PHE B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 375 through 382 Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.676A pdb=" N PHE B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 414 Processing helix chain 'B' and resid 418 through 436 removed outlier: 3.776A pdb=" N GLU B 422 " --> pdb=" O LYS B 418 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 469 through 488 removed outlier: 3.514A pdb=" N GLU B 473 " --> pdb=" O HIS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 501 through 516 Processing helix chain 'B' and resid 522 through 532 removed outlier: 3.800A pdb=" N PHE B 526 " --> pdb=" O SER B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 550 removed outlier: 3.914A pdb=" N LYS B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 561 removed outlier: 4.206A pdb=" N PHE B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 568 removed outlier: 3.563A pdb=" N SER B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.594A pdb=" N THR B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 595 Processing helix chain 'B' and resid 615 through 627 Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 635 through 638 removed outlier: 4.416A pdb=" N PHE B 638 " --> pdb=" O ASN B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 635 through 638' Processing helix chain 'B' and resid 639 through 648 Processing helix chain 'B' and resid 653 through 673 Processing helix chain 'B' and resid 685 through 693 removed outlier: 3.512A pdb=" N THR B 689 " --> pdb=" O ASN B 685 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 693 " --> pdb=" O THR B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 696 No H-bonds generated for 'chain 'B' and resid 694 through 696' Processing helix chain 'B' and resid 697 through 712 Processing helix chain 'B' and resid 720 through 730 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 740 through 753 removed outlier: 3.731A pdb=" N GLN B 746 " --> pdb=" O GLU B 742 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 773 Processing helix chain 'B' and resid 775 through 782 removed outlier: 4.345A pdb=" N HIS B 779 " --> pdb=" O ARG B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 798 removed outlier: 3.897A pdb=" N GLN B 796 " --> pdb=" O TYR B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 819 Processing helix chain 'B' and resid 845 through 850 Processing helix chain 'B' and resid 859 through 877 Processing helix chain 'B' and resid 881 through 896 removed outlier: 3.556A pdb=" N ASN B 895 " --> pdb=" O PHE B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 912 removed outlier: 4.023A pdb=" N SER B 902 " --> pdb=" O SER B 898 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 904 " --> pdb=" O SER B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 924 removed outlier: 4.010A pdb=" N VAL B 922 " --> pdb=" O ASN B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 927 No H-bonds generated for 'chain 'B' and resid 925 through 927' Processing helix chain 'B' and resid 928 through 948 removed outlier: 3.913A pdb=" N THR B 942 " --> pdb=" O VAL B 938 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER B 945 " --> pdb=" O ARG B 941 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 946 " --> pdb=" O THR B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 972 removed outlier: 3.749A pdb=" N ASP B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 979 removed outlier: 6.038A pdb=" N HIS B 976 " --> pdb=" O ASP B 973 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 979 " --> pdb=" O HIS B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 988 Processing helix chain 'B' and resid 997 through 1017 Processing helix chain 'B' and resid 1021 through 1025 Processing helix chain 'B' and resid 1026 through 1038 Processing helix chain 'B' and resid 1039 through 1042 removed outlier: 6.061A pdb=" N ARG B1042 " --> pdb=" O MET B1039 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1039 through 1042' Processing helix chain 'B' and resid 1064 through 1082 removed outlier: 3.697A pdb=" N TYR B1070 " --> pdb=" O LYS B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1096 Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1110 through 1127 removed outlier: 3.508A pdb=" N ALA B1114 " --> pdb=" O ASN B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1138 removed outlier: 3.934A pdb=" N LEU B1136 " --> pdb=" O ASP B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1152 removed outlier: 3.582A pdb=" N ASP B1143 " --> pdb=" O ASN B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1172 Processing helix chain 'B' and resid 1173 through 1177 Processing helix chain 'B' and resid 1187 through 1193 Processing helix chain 'B' and resid 1194 through 1202 removed outlier: 3.707A pdb=" N ILE B1198 " --> pdb=" O ALA B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1218 removed outlier: 3.701A pdb=" N PHE B1218 " --> pdb=" O LEU B1214 " (cutoff:3.500A) Processing helix chain 'B' and resid 1231 through 1240 removed outlier: 3.736A pdb=" N VAL B1237 " --> pdb=" O PHE B1233 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B1240 " --> pdb=" O MET B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1245 through 1277 Proline residue: B1261 - end of helix removed outlier: 3.636A pdb=" N VAL B1264 " --> pdb=" O LYS B1260 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B1265 " --> pdb=" O PRO B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1286 through 1295 Processing helix chain 'B' and resid 1295 through 1305 Processing helix chain 'B' and resid 1308 through 1312 Processing helix chain 'B' and resid 1314 through 1318 removed outlier: 4.622A pdb=" N LYS B1317 " --> pdb=" O SER B1314 " (cutoff:3.500A) Processing helix chain 'B' and resid 1319 through 1328 Processing helix chain 'B' and resid 1336 through 1355 removed outlier: 3.583A pdb=" N LEU B1345 " --> pdb=" O LYS B1341 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B1348 " --> pdb=" O SER B1344 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B1353 " --> pdb=" O ARG B1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 1358 through 1362 Processing helix chain 'B' and resid 1364 through 1381 removed outlier: 3.770A pdb=" N ARG B1374 " --> pdb=" O SER B1370 " (cutoff:3.500A) Processing helix chain 'B' and resid 1386 through 1391 Processing helix chain 'B' and resid 1391 through 1397 Processing helix chain 'B' and resid 1402 through 1419 removed outlier: 3.558A pdb=" N GLU B1406 " --> pdb=" O GLU B1402 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B1408 " --> pdb=" O ILE B1404 " (cutoff:3.500A) Processing helix chain 'B' and resid 1420 through 1431 removed outlier: 3.593A pdb=" N PHE B1431 " --> pdb=" O VAL B1427 " (cutoff:3.500A) Processing helix chain 'B' and resid 1431 through 1440 removed outlier: 3.776A pdb=" N LYS B1440 " --> pdb=" O VAL B1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1456 Processing helix chain 'B' and resid 1473 through 1475 No H-bonds generated for 'chain 'B' and resid 1473 through 1475' Processing helix chain 'B' and resid 1476 through 1487 removed outlier: 4.209A pdb=" N PHE B1480 " --> pdb=" O ASN B1476 " (cutoff:3.500A) Processing helix chain 'B' and resid 1490 through 1503 removed outlier: 3.881A pdb=" N LEU B1494 " --> pdb=" O CYS B1490 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN B1502 " --> pdb=" O ALA B1498 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B1503 " --> pdb=" O LYS B1499 " (cutoff:3.500A) Processing helix chain 'B' and resid 1505 through 1507 No H-bonds generated for 'chain 'B' and resid 1505 through 1507' Processing helix chain 'B' and resid 1508 through 1523 removed outlier: 4.215A pdb=" N THR B1514 " --> pdb=" O ASN B1510 " (cutoff:3.500A) Processing helix chain 'B' and resid 1524 through 1528 Processing helix chain 'B' and resid 1534 through 1557 removed outlier: 3.640A pdb=" N ASN B1549 " --> pdb=" O ARG B1545 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU B1552 " --> pdb=" O ASN B1548 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B1553 " --> pdb=" O ASN B1549 " (cutoff:3.500A) Processing helix chain 'B' and resid 1557 through 1574 removed outlier: 3.916A pdb=" N ILE B1567 " --> pdb=" O GLU B1563 " (cutoff:3.500A) Processing helix chain 'B' and resid 1576 through 1587 Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 16 through 33 Processing helix chain 'C' and resid 38 through 43 Processing helix chain 'C' and resid 44 through 48 removed outlier: 4.112A pdb=" N ILE C 48 " --> pdb=" O GLN C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 74 through 89 removed outlier: 3.548A pdb=" N TYR C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 165 through 174 removed outlier: 4.073A pdb=" N HIS C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE C 172 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.634A pdb=" N VAL C 224 " --> pdb=" O HIS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.690A pdb=" N ILE C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 265 removed outlier: 3.796A pdb=" N LYS C 265 " --> pdb=" O SER C 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 307 through 320 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 384 through 392 Processing helix chain 'C' and resid 401 through 414 Processing helix chain 'C' and resid 418 through 436 removed outlier: 3.752A pdb=" N GLU C 422 " --> pdb=" O LYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 455 Processing helix chain 'C' and resid 469 through 487 removed outlier: 3.781A pdb=" N GLU C 473 " --> pdb=" O HIS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'C' and resid 501 through 518 Processing helix chain 'C' and resid 522 through 533 removed outlier: 3.748A pdb=" N PHE C 526 " --> pdb=" O SER C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 551 removed outlier: 3.960A pdb=" N LYS C 541 " --> pdb=" O SER C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 561 removed outlier: 4.302A pdb=" N PHE C 557 " --> pdb=" O ASN C 553 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 568 removed outlier: 4.086A pdb=" N SER C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 584 Processing helix chain 'C' and resid 588 through 595 Processing helix chain 'C' and resid 615 through 627 Processing helix chain 'C' and resid 627 through 632 Processing helix chain 'C' and resid 635 through 638 removed outlier: 4.383A pdb=" N PHE C 638 " --> pdb=" O ASN C 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 635 through 638' Processing helix chain 'C' and resid 639 through 648 Processing helix chain 'C' and resid 653 through 673 Processing helix chain 'C' and resid 685 through 693 removed outlier: 3.655A pdb=" N THR C 689 " --> pdb=" O ASN C 685 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY C 693 " --> pdb=" O THR C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 712 Processing helix chain 'C' and resid 720 through 730 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 740 through 753 removed outlier: 3.708A pdb=" N GLN C 746 " --> pdb=" O GLU C 742 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 773 Processing helix chain 'C' and resid 775 through 782 removed outlier: 4.192A pdb=" N HIS C 779 " --> pdb=" O ARG C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 798 removed outlier: 3.905A pdb=" N GLN C 796 " --> pdb=" O TYR C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 819 Processing helix chain 'C' and resid 845 through 850 Processing helix chain 'C' and resid 851 through 853 No H-bonds generated for 'chain 'C' and resid 851 through 853' Processing helix chain 'C' and resid 859 through 877 Processing helix chain 'C' and resid 881 through 896 removed outlier: 3.570A pdb=" N ASN C 895 " --> pdb=" O PHE C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 912 removed outlier: 4.059A pdb=" N SER C 902 " --> pdb=" O SER C 898 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 904 " --> pdb=" O SER C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 924 removed outlier: 4.058A pdb=" N VAL C 922 " --> pdb=" O ASN C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 928 through 948 removed outlier: 3.748A pdb=" N THR C 942 " --> pdb=" O VAL C 938 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS C 944 " --> pdb=" O ASP C 940 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER C 945 " --> pdb=" O ARG C 941 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 946 " --> pdb=" O THR C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 973 removed outlier: 3.802A pdb=" N ASP C 967 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 979 removed outlier: 3.620A pdb=" N THR C 979 " --> pdb=" O HIS C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 988 Processing helix chain 'C' and resid 997 through 1017 Processing helix chain 'C' and resid 1021 through 1025 Processing helix chain 'C' and resid 1026 through 1038 Processing helix chain 'C' and resid 1039 through 1042 removed outlier: 5.995A pdb=" N ARG C1042 " --> pdb=" O MET C1039 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1039 through 1042' Processing helix chain 'C' and resid 1064 through 1082 Processing helix chain 'C' and resid 1084 through 1096 Processing helix chain 'C' and resid 1098 through 1104 Processing helix chain 'C' and resid 1110 through 1127 Processing helix chain 'C' and resid 1130 through 1138 removed outlier: 3.819A pdb=" N LEU C1136 " --> pdb=" O ASP C1132 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1152 Processing helix chain 'C' and resid 1157 through 1173 removed outlier: 3.791A pdb=" N LYS C1173 " --> pdb=" O LEU C1169 " (cutoff:3.500A) Processing helix chain 'C' and resid 1174 through 1177 Processing helix chain 'C' and resid 1187 through 1193 Processing helix chain 'C' and resid 1194 through 1202 removed outlier: 3.652A pdb=" N ILE C1198 " --> pdb=" O ALA C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1205 through 1218 removed outlier: 3.756A pdb=" N PHE C1218 " --> pdb=" O LEU C1214 " (cutoff:3.500A) Processing helix chain 'C' and resid 1231 through 1240 removed outlier: 3.737A pdb=" N VAL C1237 " --> pdb=" O PHE C1233 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C1240 " --> pdb=" O MET C1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 1245 through 1277 Proline residue: C1261 - end of helix removed outlier: 3.647A pdb=" N VAL C1264 " --> pdb=" O LYS C1260 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE C1265 " --> pdb=" O PRO C1261 " (cutoff:3.500A) Processing helix chain 'C' and resid 1286 through 1295 Processing helix chain 'C' and resid 1295 through 1305 Processing helix chain 'C' and resid 1308 through 1312 removed outlier: 3.707A pdb=" N LEU C1312 " --> pdb=" O ILE C1309 " (cutoff:3.500A) Processing helix chain 'C' and resid 1319 through 1328 Processing helix chain 'C' and resid 1336 through 1355 removed outlier: 3.549A pdb=" N LEU C1345 " --> pdb=" O LYS C1341 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS C1348 " --> pdb=" O SER C1344 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER C1353 " --> pdb=" O ARG C1349 " (cutoff:3.500A) Processing helix chain 'C' and resid 1358 through 1362 Processing helix chain 'C' and resid 1364 through 1381 removed outlier: 3.781A pdb=" N ARG C1374 " --> pdb=" O SER C1370 " (cutoff:3.500A) Processing helix chain 'C' and resid 1386 through 1391 Processing helix chain 'C' and resid 1391 through 1397 removed outlier: 3.516A pdb=" N GLY C1397 " --> pdb=" O PRO C1393 " (cutoff:3.500A) Processing helix chain 'C' and resid 1402 through 1419 Processing helix chain 'C' and resid 1420 through 1440 removed outlier: 3.615A pdb=" N PHE C1431 " --> pdb=" O VAL C1427 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C1432 " --> pdb=" O TRP C1428 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASP C1433 " --> pdb=" O ASP C1429 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS C1434 " --> pdb=" O LEU C1430 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS C1440 " --> pdb=" O VAL C1436 " (cutoff:3.500A) Processing helix chain 'C' and resid 1447 through 1456 Processing helix chain 'C' and resid 1473 through 1475 No H-bonds generated for 'chain 'C' and resid 1473 through 1475' Processing helix chain 'C' and resid 1476 through 1487 removed outlier: 4.166A pdb=" N PHE C1480 " --> pdb=" O ASN C1476 " (cutoff:3.500A) Processing helix chain 'C' and resid 1490 through 1503 removed outlier: 3.862A pdb=" N LEU C1494 " --> pdb=" O CYS C1490 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN C1502 " --> pdb=" O ALA C1498 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN C1503 " --> pdb=" O LYS C1499 " (cutoff:3.500A) Processing helix chain 'C' and resid 1505 through 1507 No H-bonds generated for 'chain 'C' and resid 1505 through 1507' Processing helix chain 'C' and resid 1508 through 1523 removed outlier: 4.164A pdb=" N THR C1514 " --> pdb=" O ASN C1510 " (cutoff:3.500A) Processing helix chain 'C' and resid 1524 through 1528 Processing helix chain 'C' and resid 1534 through 1557 removed outlier: 3.668A pdb=" N ASN C1548 " --> pdb=" O ARG C1544 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C1549 " --> pdb=" O ARG C1545 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU C1552 " --> pdb=" O ASN C1548 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG C1553 " --> pdb=" O ASN C1549 " (cutoff:3.500A) Processing helix chain 'C' and resid 1557 through 1574 removed outlier: 4.005A pdb=" N ILE C1567 " --> pdb=" O GLU C1563 " (cutoff:3.500A) Processing helix chain 'C' and resid 1576 through 1587 Processing helix chain 'D' and resid 5 through 13 Processing helix chain 'D' and resid 16 through 33 removed outlier: 3.612A pdb=" N ASN D 20 " --> pdb=" O ASN D 16 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 74 through 89 removed outlier: 3.814A pdb=" N LEU D 78 " --> pdb=" O ASN D 74 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 145 removed outlier: 3.834A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 156 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.880A pdb=" N HIS D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 195 removed outlier: 3.615A pdb=" N LEU D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 226 removed outlier: 3.626A pdb=" N GLU D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 251 removed outlier: 3.619A pdb=" N ILE D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 265 removed outlier: 3.721A pdb=" N LYS D 265 " --> pdb=" O SER D 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 262 through 265' Processing helix chain 'D' and resid 268 through 273 Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 297 through 304 removed outlier: 3.566A pdb=" N LEU D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 Processing helix chain 'D' and resid 332 through 345 removed outlier: 3.628A pdb=" N PHE D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 369 Processing helix chain 'D' and resid 375 through 382 Processing helix chain 'D' and resid 384 through 394 removed outlier: 3.682A pdb=" N PHE D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 414 Processing helix chain 'D' and resid 418 through 436 removed outlier: 3.797A pdb=" N GLU D 422 " --> pdb=" O LYS D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 455 Processing helix chain 'D' and resid 469 through 487 removed outlier: 3.505A pdb=" N GLU D 473 " --> pdb=" O HIS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 499 removed outlier: 3.949A pdb=" N GLY D 499 " --> pdb=" O PHE D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 516 Processing helix chain 'D' and resid 522 through 532 removed outlier: 3.780A pdb=" N PHE D 526 " --> pdb=" O SER D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 550 removed outlier: 3.881A pdb=" N LYS D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 561 removed outlier: 4.188A pdb=" N PHE D 557 " --> pdb=" O ASN D 553 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE D 558 " --> pdb=" O SER D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 568 removed outlier: 3.580A pdb=" N SER D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 584 removed outlier: 3.600A pdb=" N THR D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 595 Processing helix chain 'D' and resid 615 through 627 Processing helix chain 'D' and resid 627 through 632 Processing helix chain 'D' and resid 635 through 638 removed outlier: 4.397A pdb=" N PHE D 638 " --> pdb=" O ASN D 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 635 through 638' Processing helix chain 'D' and resid 639 through 648 Processing helix chain 'D' and resid 653 through 673 Processing helix chain 'D' and resid 685 through 693 removed outlier: 3.532A pdb=" N THR D 689 " --> pdb=" O ASN D 685 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY D 693 " --> pdb=" O THR D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 696 No H-bonds generated for 'chain 'D' and resid 694 through 696' Processing helix chain 'D' and resid 697 through 712 Processing helix chain 'D' and resid 720 through 730 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 740 through 753 removed outlier: 3.725A pdb=" N GLN D 746 " --> pdb=" O GLU D 742 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 773 Processing helix chain 'D' and resid 775 through 782 removed outlier: 4.315A pdb=" N HIS D 779 " --> pdb=" O ARG D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 798 removed outlier: 3.887A pdb=" N GLN D 796 " --> pdb=" O TYR D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 819 Processing helix chain 'D' and resid 845 through 850 Processing helix chain 'D' and resid 859 through 877 Processing helix chain 'D' and resid 881 through 896 removed outlier: 3.545A pdb=" N ASN D 895 " --> pdb=" O PHE D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 912 removed outlier: 4.036A pdb=" N SER D 902 " --> pdb=" O SER D 898 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 904 " --> pdb=" O SER D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 924 removed outlier: 3.994A pdb=" N VAL D 922 " --> pdb=" O ASN D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 927 through 948 removed outlier: 4.230A pdb=" N ARG D 931 " --> pdb=" O LYS D 927 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 942 " --> pdb=" O VAL D 938 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS D 944 " --> pdb=" O ASP D 940 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER D 945 " --> pdb=" O ARG D 941 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 946 " --> pdb=" O THR D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 973 removed outlier: 3.743A pdb=" N ASP D 967 " --> pdb=" O LEU D 963 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP D 973 " --> pdb=" O ILE D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 974 through 979 removed outlier: 3.532A pdb=" N THR D 979 " --> pdb=" O HIS D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 988 Processing helix chain 'D' and resid 997 through 1017 Processing helix chain 'D' and resid 1021 through 1025 Processing helix chain 'D' and resid 1026 through 1038 Processing helix chain 'D' and resid 1039 through 1042 removed outlier: 6.045A pdb=" N ARG D1042 " --> pdb=" O MET D1039 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1039 through 1042' Processing helix chain 'D' and resid 1064 through 1082 removed outlier: 3.645A pdb=" N TYR D1070 " --> pdb=" O LYS D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1096 Processing helix chain 'D' and resid 1098 through 1104 Processing helix chain 'D' and resid 1110 through 1127 removed outlier: 3.523A pdb=" N ALA D1114 " --> pdb=" O ASN D1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 1130 through 1138 removed outlier: 3.927A pdb=" N LEU D1136 " --> pdb=" O ASP D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1139 through 1152 removed outlier: 3.558A pdb=" N ASP D1143 " --> pdb=" O ASN D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1157 through 1172 Processing helix chain 'D' and resid 1173 through 1177 Processing helix chain 'D' and resid 1187 through 1193 Processing helix chain 'D' and resid 1194 through 1202 removed outlier: 3.697A pdb=" N ILE D1198 " --> pdb=" O ALA D1194 " (cutoff:3.500A) Processing helix chain 'D' and resid 1205 through 1218 removed outlier: 3.696A pdb=" N PHE D1218 " --> pdb=" O LEU D1214 " (cutoff:3.500A) Processing helix chain 'D' and resid 1231 through 1240 removed outlier: 3.747A pdb=" N VAL D1237 " --> pdb=" O PHE D1233 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS D1240 " --> pdb=" O MET D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1245 through 1277 Proline residue: D1261 - end of helix removed outlier: 3.596A pdb=" N VAL D1264 " --> pdb=" O LYS D1260 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D1265 " --> pdb=" O PRO D1261 " (cutoff:3.500A) Processing helix chain 'D' and resid 1286 through 1295 Processing helix chain 'D' and resid 1295 through 1305 Processing helix chain 'D' and resid 1308 through 1312 Processing helix chain 'D' and resid 1314 through 1318 removed outlier: 4.623A pdb=" N LYS D1317 " --> pdb=" O SER D1314 " (cutoff:3.500A) Processing helix chain 'D' and resid 1319 through 1328 Processing helix chain 'D' and resid 1336 through 1355 removed outlier: 3.576A pdb=" N LEU D1345 " --> pdb=" O LYS D1341 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D1348 " --> pdb=" O SER D1344 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D1353 " --> pdb=" O ARG D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1358 through 1362 Processing helix chain 'D' and resid 1364 through 1381 removed outlier: 3.778A pdb=" N ARG D1374 " --> pdb=" O SER D1370 " (cutoff:3.500A) Processing helix chain 'D' and resid 1383 through 1385 No H-bonds generated for 'chain 'D' and resid 1383 through 1385' Processing helix chain 'D' and resid 1386 through 1391 Processing helix chain 'D' and resid 1391 through 1397 Processing helix chain 'D' and resid 1402 through 1419 removed outlier: 3.574A pdb=" N GLU D1406 " --> pdb=" O GLU D1402 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE D1408 " --> pdb=" O ILE D1404 " (cutoff:3.500A) Processing helix chain 'D' and resid 1420 through 1431 removed outlier: 3.572A pdb=" N PHE D1431 " --> pdb=" O VAL D1427 " (cutoff:3.500A) Processing helix chain 'D' and resid 1431 through 1440 removed outlier: 3.765A pdb=" N LYS D1440 " --> pdb=" O VAL D1436 " (cutoff:3.500A) Processing helix chain 'D' and resid 1447 through 1456 Processing helix chain 'D' and resid 1473 through 1475 No H-bonds generated for 'chain 'D' and resid 1473 through 1475' Processing helix chain 'D' and resid 1476 through 1487 removed outlier: 4.194A pdb=" N PHE D1480 " --> pdb=" O ASN D1476 " (cutoff:3.500A) Processing helix chain 'D' and resid 1490 through 1503 removed outlier: 3.890A pdb=" N LEU D1494 " --> pdb=" O CYS D1490 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D1502 " --> pdb=" O ALA D1498 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN D1503 " --> pdb=" O LYS D1499 " (cutoff:3.500A) Processing helix chain 'D' and resid 1505 through 1507 No H-bonds generated for 'chain 'D' and resid 1505 through 1507' Processing helix chain 'D' and resid 1508 through 1523 removed outlier: 4.220A pdb=" N THR D1514 " --> pdb=" O ASN D1510 " (cutoff:3.500A) Processing helix chain 'D' and resid 1524 through 1528 Processing helix chain 'D' and resid 1534 through 1557 removed outlier: 3.583A pdb=" N ASN D1548 " --> pdb=" O ARG D1544 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN D1549 " --> pdb=" O ARG D1545 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU D1552 " --> pdb=" O ASN D1548 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG D1553 " --> pdb=" O ASN D1549 " (cutoff:3.500A) Processing helix chain 'D' and resid 1557 through 1574 removed outlier: 3.901A pdb=" N ILE D1567 " --> pdb=" O GLU D1563 " (cutoff:3.500A) Processing helix chain 'D' and resid 1576 through 1587 Processing helix chain 'E' and resid 8 through 12 Processing helix chain 'E' and resid 14 through 23 Processing helix chain 'E' and resid 26 through 39 removed outlier: 3.788A pdb=" N TYR E 39 " --> pdb=" O ASN E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 45 Processing helix chain 'E' and resid 62 through 79 removed outlier: 3.573A pdb=" N LEU E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 99 removed outlier: 3.680A pdb=" N GLN E 97 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 126 Processing helix chain 'E' and resid 127 through 143 removed outlier: 4.184A pdb=" N THR E 131 " --> pdb=" O SER E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 268 through 271 removed outlier: 3.615A pdb=" N GLU E 271 " --> pdb=" O TYR E 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 268 through 271' Processing helix chain 'E' and resid 272 through 292 removed outlier: 3.630A pdb=" N ASN E 281 " --> pdb=" O ARG E 277 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 285 " --> pdb=" O ASN E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 313 removed outlier: 3.829A pdb=" N THR E 312 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 325 No H-bonds generated for 'chain 'E' and resid 323 through 325' Processing helix chain 'E' and resid 337 through 356 Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.984A pdb=" N GLU E 380 " --> pdb=" O TYR E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 396 removed outlier: 4.159A pdb=" N GLY E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL E 388 " --> pdb=" O THR E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 433 through 441 Processing helix chain 'E' and resid 442 through 453 Processing helix chain 'F' and resid 8 through 13 removed outlier: 3.680A pdb=" N ALA F 11 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN F 13 " --> pdb=" O PHE F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 23 Processing helix chain 'F' and resid 26 through 39 removed outlier: 3.752A pdb=" N TYR F 39 " --> pdb=" O ASN F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 45 Processing helix chain 'F' and resid 62 through 79 Processing helix chain 'F' and resid 91 through 99 removed outlier: 3.646A pdb=" N GLN F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 126 removed outlier: 3.520A pdb=" N LEU F 105 " --> pdb=" O GLN F 101 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 143 removed outlier: 4.280A pdb=" N THR F 131 " --> pdb=" O SER F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 165 No H-bonds generated for 'chain 'F' and resid 163 through 165' Processing helix chain 'F' and resid 189 through 191 No H-bonds generated for 'chain 'F' and resid 189 through 191' Processing helix chain 'F' and resid 192 through 198 Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 268 through 271 removed outlier: 3.627A pdb=" N GLU F 271 " --> pdb=" O TYR F 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 268 through 271' Processing helix chain 'F' and resid 272 through 292 removed outlier: 3.617A pdb=" N ASN F 281 " --> pdb=" O ARG F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 313 removed outlier: 3.645A pdb=" N THR F 312 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 356 Processing helix chain 'F' and resid 377 through 382 Processing helix chain 'F' and resid 382 through 396 removed outlier: 3.702A pdb=" N GLY F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL F 388 " --> pdb=" O THR F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 411 Processing helix chain 'F' and resid 433 through 441 removed outlier: 3.673A pdb=" N ASP F 438 " --> pdb=" O GLY F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 452 Processing helix chain 'G' and resid 8 through 12 removed outlier: 3.522A pdb=" N ALA G 11 " --> pdb=" O GLU G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 26 through 39 removed outlier: 3.776A pdb=" N TYR G 39 " --> pdb=" O ASN G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 45 Processing helix chain 'G' and resid 62 through 79 removed outlier: 3.614A pdb=" N LEU G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 99 removed outlier: 3.712A pdb=" N GLN G 97 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 126 Processing helix chain 'G' and resid 127 through 143 removed outlier: 4.114A pdb=" N THR G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 165 No H-bonds generated for 'chain 'G' and resid 163 through 165' Processing helix chain 'G' and resid 189 through 191 No H-bonds generated for 'chain 'G' and resid 189 through 191' Processing helix chain 'G' and resid 192 through 197 Processing helix chain 'G' and resid 247 through 249 No H-bonds generated for 'chain 'G' and resid 247 through 249' Processing helix chain 'G' and resid 268 through 271 removed outlier: 3.604A pdb=" N GLU G 271 " --> pdb=" O TYR G 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 268 through 271' Processing helix chain 'G' and resid 272 through 292 removed outlier: 3.614A pdb=" N ASN G 281 " --> pdb=" O ARG G 277 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA G 285 " --> pdb=" O ASN G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 313 removed outlier: 3.845A pdb=" N THR G 312 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 325 No H-bonds generated for 'chain 'G' and resid 323 through 325' Processing helix chain 'G' and resid 337 through 356 Processing helix chain 'G' and resid 376 through 381 removed outlier: 3.938A pdb=" N GLU G 380 " --> pdb=" O TYR G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 396 removed outlier: 4.022A pdb=" N GLY G 387 " --> pdb=" O ASP G 383 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL G 388 " --> pdb=" O THR G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 411 Processing helix chain 'G' and resid 433 through 441 Processing helix chain 'G' and resid 442 through 453 Processing helix chain 'H' and resid 8 through 12 removed outlier: 3.617A pdb=" N ALA H 11 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 23 Processing helix chain 'H' and resid 26 through 39 removed outlier: 3.768A pdb=" N TYR H 39 " --> pdb=" O ASN H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 45 Processing helix chain 'H' and resid 62 through 79 Processing helix chain 'H' and resid 91 through 99 removed outlier: 3.655A pdb=" N GLN H 97 " --> pdb=" O PHE H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 126 removed outlier: 3.547A pdb=" N LEU H 105 " --> pdb=" O GLN H 101 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 143 removed outlier: 4.269A pdb=" N THR H 131 " --> pdb=" O SER H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'H' and resid 192 through 197 Processing helix chain 'H' and resid 247 through 249 No H-bonds generated for 'chain 'H' and resid 247 through 249' Processing helix chain 'H' and resid 268 through 271 removed outlier: 3.625A pdb=" N GLU H 271 " --> pdb=" O TYR H 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 268 through 271' Processing helix chain 'H' and resid 272 through 292 removed outlier: 3.609A pdb=" N ASN H 281 " --> pdb=" O ARG H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 313 removed outlier: 3.738A pdb=" N THR H 312 " --> pdb=" O VAL H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 356 Processing helix chain 'H' and resid 377 through 382 Processing helix chain 'H' and resid 382 through 396 removed outlier: 4.033A pdb=" N VAL H 388 " --> pdb=" O THR H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 411 Processing helix chain 'H' and resid 433 through 440 removed outlier: 3.720A pdb=" N ASP H 438 " --> pdb=" O GLY H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 453 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 55 removed outlier: 6.647A pdb=" N ILE A 95 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ARG A 151 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE A 97 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA3, first strand: chain 'A' and resid 256 through 260 removed outlier: 6.683A pdb=" N TYR A 257 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ASP A 296 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 259 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 228 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N LEU A 351 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 230 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 Processing sheet with id=AA5, first strand: chain 'A' and resid 458 through 461 Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AA7, first strand: chain 'A' and resid 828 through 835 removed outlier: 6.827A pdb=" N LYS A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 991 through 992 Processing sheet with id=AA9, first strand: chain 'A' and resid 1044 through 1051 removed outlier: 3.573A pdb=" N VAL E 296 " --> pdb=" O PHE A1059 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1222 through 1223 removed outlier: 3.684A pdb=" N GLY A1228 " --> pdb=" O ILE A1223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 53 through 55 removed outlier: 6.800A pdb=" N ILE B 95 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ARG B 151 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE B 97 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB4, first strand: chain 'B' and resid 256 through 260 removed outlier: 3.506A pdb=" N GLY B 233 " --> pdb=" O THR B 328 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 395 through 396 Processing sheet with id=AB6, first strand: chain 'B' and resid 458 through 461 Processing sheet with id=AB7, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AB8, first strand: chain 'B' and resid 828 through 835 removed outlier: 6.772A pdb=" N LYS B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 991 through 992 Processing sheet with id=AC1, first strand: chain 'B' and resid 1044 through 1051 Processing sheet with id=AC2, first strand: chain 'B' and resid 1222 through 1223 removed outlier: 3.681A pdb=" N GLY B1228 " --> pdb=" O ILE B1223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 53 through 55 removed outlier: 6.639A pdb=" N ILE C 95 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ARG C 151 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE C 97 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AC5, first strand: chain 'C' and resid 256 through 260 removed outlier: 6.686A pdb=" N TYR C 257 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASP C 296 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE C 259 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 395 through 396 Processing sheet with id=AC7, first strand: chain 'C' and resid 458 through 461 Processing sheet with id=AC8, first strand: chain 'C' and resid 585 through 587 Processing sheet with id=AC9, first strand: chain 'C' and resid 828 through 835 removed outlier: 6.827A pdb=" N LYS C 838 " --> pdb=" O ILE C 834 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 991 through 992 Processing sheet with id=AD2, first strand: chain 'C' and resid 1044 through 1051 removed outlier: 3.582A pdb=" N VAL G 296 " --> pdb=" O PHE C1059 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1222 through 1223 removed outlier: 3.710A pdb=" N GLY C1228 " --> pdb=" O ILE C1223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 53 through 55 removed outlier: 6.794A pdb=" N ILE D 95 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG D 151 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE D 97 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 201 through 203 Processing sheet with id=AD6, first strand: chain 'D' and resid 256 through 260 removed outlier: 3.510A pdb=" N GLY D 233 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE D 228 " --> pdb=" O GLY D 349 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N LEU D 351 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE D 230 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 395 through 396 Processing sheet with id=AD8, first strand: chain 'D' and resid 458 through 461 Processing sheet with id=AD9, first strand: chain 'D' and resid 585 through 587 Processing sheet with id=AE1, first strand: chain 'D' and resid 828 through 835 removed outlier: 6.773A pdb=" N LYS D 838 " --> pdb=" O ILE D 834 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 991 through 992 Processing sheet with id=AE3, first strand: chain 'D' and resid 1044 through 1051 Processing sheet with id=AE4, first strand: chain 'D' and resid 1222 through 1223 removed outlier: 3.680A pdb=" N GLY D1228 " --> pdb=" O ILE D1223 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 86 through 90 Processing sheet with id=AE6, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AE7, first strand: chain 'E' and resid 167 through 171 removed outlier: 6.802A pdb=" N VAL E 168 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE E 180 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN E 170 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU E 178 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR E 186 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 167 through 171 removed outlier: 6.802A pdb=" N VAL E 168 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE E 180 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN E 170 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU E 178 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR E 186 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 89 through 90 Processing sheet with id=AF1, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AF2, first strand: chain 'F' and resid 167 through 171 removed outlier: 6.767A pdb=" N VAL F 168 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE F 180 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN F 170 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU F 178 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR F 186 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 167 through 171 removed outlier: 6.767A pdb=" N VAL F 168 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE F 180 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN F 170 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU F 178 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR F 186 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 86 through 90 Processing sheet with id=AF5, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AF6, first strand: chain 'G' and resid 167 through 171 removed outlier: 6.791A pdb=" N VAL G 168 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE G 180 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN G 170 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU G 178 " --> pdb=" O LEU G 219 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 167 through 171 removed outlier: 6.791A pdb=" N VAL G 168 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE G 180 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN G 170 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU G 178 " --> pdb=" O LEU G 219 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 89 through 90 Processing sheet with id=AF9, first strand: chain 'H' and resid 160 through 162 Processing sheet with id=AG1, first strand: chain 'H' and resid 167 through 171 removed outlier: 6.773A pdb=" N VAL H 168 " --> pdb=" O ILE H 180 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE H 180 " --> pdb=" O VAL H 168 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN H 170 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU H 178 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR H 186 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 167 through 171 removed outlier: 6.773A pdb=" N VAL H 168 " --> pdb=" O ILE H 180 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE H 180 " --> pdb=" O VAL H 168 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN H 170 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU H 178 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR H 186 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 3663 hydrogen bonds defined for protein. 10437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 38.59 Time building geometry restraints manager: 17.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.44 - 0.77: 1 0.77 - 1.09: 1 1.09 - 1.41: 27692 1.41 - 1.73: 38334 1.73 - 2.06: 366 Warning: very small bond lengths. Bond restraints: 66394 Sorted by residual: bond pdb=" CG PRO E 324 " pdb=" CD PRO E 324 " ideal model delta sigma weight residual 1.503 0.445 1.058 3.40e-02 8.65e+02 9.68e+02 bond pdb=" CG PRO G 454 " pdb=" CD PRO G 454 " ideal model delta sigma weight residual 1.503 0.852 0.651 3.40e-02 8.65e+02 3.67e+02 bond pdb=" C PHE E 80 " pdb=" O PHE E 80 " ideal model delta sigma weight residual 1.235 1.288 -0.053 4.70e-03 4.53e+04 1.29e+02 bond pdb=" CB PRO E 324 " pdb=" CG PRO E 324 " ideal model delta sigma weight residual 1.492 2.056 -0.564 5.00e-02 4.00e+02 1.27e+02 bond pdb=" CG PRO F 324 " pdb=" CD PRO F 324 " ideal model delta sigma weight residual 1.503 1.124 0.379 3.40e-02 8.65e+02 1.24e+02 ... (remaining 66389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 89784 21.21 - 42.41: 3 42.41 - 63.62: 0 63.62 - 84.82: 0 84.82 - 106.03: 1 Bond angle restraints: 89788 Sorted by residual: angle pdb=" CB PRO E 324 " pdb=" CG PRO E 324 " pdb=" CD PRO E 324 " ideal model delta sigma weight residual 106.10 0.07 106.03 3.20e+00 9.77e-02 1.10e+03 angle pdb=" N PRO G 454 " pdb=" CD PRO G 454 " pdb=" CG PRO G 454 " ideal model delta sigma weight residual 103.20 72.77 30.43 1.50e+00 4.44e-01 4.12e+02 angle pdb=" CA PRO E 324 " pdb=" N PRO E 324 " pdb=" CD PRO E 324 " ideal model delta sigma weight residual 112.00 90.20 21.80 1.40e+00 5.10e-01 2.42e+02 angle pdb=" CA PRO G 454 " pdb=" CB PRO G 454 " pdb=" CG PRO G 454 " ideal model delta sigma weight residual 104.50 82.49 22.01 1.90e+00 2.77e-01 1.34e+02 angle pdb=" N PRO F 324 " pdb=" CD PRO F 324 " pdb=" CG PRO F 324 " ideal model delta sigma weight residual 103.20 85.88 17.32 1.50e+00 4.44e-01 1.33e+02 ... (remaining 89783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 36577 17.99 - 35.99: 2635 35.99 - 53.98: 594 53.98 - 71.97: 150 71.97 - 89.97: 88 Dihedral angle restraints: 40044 sinusoidal: 16630 harmonic: 23414 Sorted by residual: dihedral pdb=" CA ASP A 445 " pdb=" C ASP A 445 " pdb=" N THR A 446 " pdb=" CA THR A 446 " ideal model delta harmonic sigma weight residual 180.00 -150.15 -29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ASP C 445 " pdb=" C ASP C 445 " pdb=" N THR C 446 " pdb=" CA THR C 446 " ideal model delta harmonic sigma weight residual -180.00 -150.19 -29.81 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA LEU H 330 " pdb=" C LEU H 330 " pdb=" N GLN H 331 " pdb=" CA GLN H 331 " ideal model delta harmonic sigma weight residual -180.00 -153.07 -26.93 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 40041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 8118 0.076 - 0.152: 1554 0.152 - 0.228: 145 0.228 - 0.304: 20 0.304 - 0.379: 5 Chirality restraints: 9842 Sorted by residual: chirality pdb=" CG LEU H 398 " pdb=" CB LEU H 398 " pdb=" CD1 LEU H 398 " pdb=" CD2 LEU H 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CG LEU G 398 " pdb=" CB LEU G 398 " pdb=" CD1 LEU G 398 " pdb=" CD2 LEU G 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.92 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CG LEU E 398 " pdb=" CB LEU E 398 " pdb=" CD1 LEU E 398 " pdb=" CD2 LEU E 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 9839 not shown) Planarity restraints: 11402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 323 " -0.094 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO F 324 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A1143 " -0.026 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" CG ASP A1143 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASP A1143 " -0.033 2.00e-02 2.50e+03 pdb=" OD2 ASP A1143 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C1143 " -0.026 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" CG ASP C1143 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASP C1143 " -0.032 2.00e-02 2.50e+03 pdb=" OD2 ASP C1143 " -0.031 2.00e-02 2.50e+03 ... (remaining 11399 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 332 2.65 - 3.21: 57729 3.21 - 3.78: 91883 3.78 - 4.34: 131517 4.34 - 4.90: 216210 Nonbonded interactions: 497671 Sorted by model distance: nonbonded pdb=" O2B ATP B1601 " pdb="MG MG B1602 " model vdw 2.088 2.170 nonbonded pdb=" O2B ATP D1601 " pdb="MG MG D1602 " model vdw 2.091 2.170 nonbonded pdb=" OG1 THR C1026 " pdb=" OE1 GLU C1027 " model vdw 2.127 3.040 nonbonded pdb=" O1G ATP A1601 " pdb="MG MG A1602 " model vdw 2.128 2.170 nonbonded pdb=" O1G ATP C1601 " pdb="MG MG C1602 " model vdw 2.130 2.170 ... (remaining 497666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 103 or resid 130 through 1587 or resid 1601 thro \ ugh 1602)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 103 or resid 130 through 1587 or resid 1601 thro \ ugh 1602)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' 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: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 2.510 Check model and map are aligned: 0.430 Set scattering table: 0.590 Process input model: 143.720 Find NCS groups from input model: 3.680 Set up NCS constraints: 0.440 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: 0.030 Load rotamer database and sin/cos tables:15.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 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 : 0.009 1.058 66394 Z= 0.627 Angle : 1.207 106.028 89788 Z= 0.651 Chirality : 0.060 0.379 9842 Planarity : 0.009 0.132 11402 Dihedral : 14.361 89.966 24884 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.53 % Allowed : 8.87 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.09), residues: 7844 helix: 0.01 (0.07), residues: 4658 sheet: 0.00 (0.20), residues: 624 loop : 0.21 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.005 TRP C1242 HIS 0.024 0.004 HIS H 205 PHE 0.078 0.005 PHE H 80 TYR 0.067 0.004 TYR B 338 ARG 0.019 0.002 ARG C1359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 953 time to evaluate : 6.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7218 (tttt) cc_final: 0.6541 (tttp) REVERT: A 177 GLU cc_start: 0.7115 (pt0) cc_final: 0.6688 (pp20) REVERT: A 492 ASN cc_start: 0.6488 (m-40) cc_final: 0.5985 (m110) REVERT: A 537 SER cc_start: 0.7277 (m) cc_final: 0.6998 (t) REVERT: A 665 LYS cc_start: 0.6061 (mttm) cc_final: 0.5804 (tttt) REVERT: A 934 MET cc_start: 0.2566 (ttm) cc_final: 0.1680 (mpp) REVERT: A 937 MET cc_start: 0.1880 (tmt) cc_final: 0.1377 (tpp) REVERT: A 1044 MET cc_start: 0.0448 (mtp) cc_final: -0.0370 (tpt) REVERT: A 1525 LYS cc_start: 0.6741 (mptt) cc_final: 0.6052 (pttt) REVERT: A 1530 LYS cc_start: 0.4225 (tppt) cc_final: 0.3908 (mtpp) REVERT: B 65 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7686 (mmtt) REVERT: B 221 GLU cc_start: 0.6508 (tt0) cc_final: 0.6192 (pt0) REVERT: B 227 LYS cc_start: 0.7519 (mmpt) cc_final: 0.7277 (mmmt) REVERT: B 332 TYR cc_start: 0.6654 (t80) cc_final: 0.5884 (m-80) REVERT: B 338 TYR cc_start: 0.4920 (t80) cc_final: 0.4689 (m-10) REVERT: B 401 ASP cc_start: 0.8437 (t0) cc_final: 0.8064 (t70) REVERT: B 1044 MET cc_start: 0.0011 (mtm) cc_final: -0.0636 (tpp) REVERT: B 1249 MET cc_start: 0.2402 (mmp) cc_final: 0.1483 (tmm) REVERT: B 1555 ARG cc_start: 0.6988 (mmm-85) cc_final: 0.6626 (mmt90) REVERT: B 1563 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6900 (mm-30) REVERT: C 140 LYS cc_start: 0.7143 (tttt) cc_final: 0.6470 (tttp) REVERT: C 177 GLU cc_start: 0.7144 (pt0) cc_final: 0.6616 (pp20) REVERT: C 474 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7908 (mt-10) REVERT: C 492 ASN cc_start: 0.6427 (m-40) cc_final: 0.5906 (m110) REVERT: C 537 SER cc_start: 0.7292 (m) cc_final: 0.6934 (t) REVERT: C 589 TYR cc_start: 0.3824 (m-80) cc_final: 0.3465 (m-80) REVERT: C 665 LYS cc_start: 0.6014 (mttm) cc_final: 0.5762 (tttt) REVERT: C 934 MET cc_start: 0.2574 (ttm) cc_final: 0.1657 (mpp) REVERT: C 937 MET cc_start: 0.1335 (tmt) cc_final: 0.0696 (tpp) REVERT: C 1044 MET cc_start: 0.0156 (mtp) cc_final: -0.0522 (tpt) REVERT: C 1525 LYS cc_start: 0.6820 (mptt) cc_final: 0.6043 (pttt) REVERT: C 1530 LYS cc_start: 0.4232 (tppt) cc_final: 0.3963 (mtpp) REVERT: D 3 LYS cc_start: 0.7799 (ptmt) cc_final: 0.7460 (mtmm) REVERT: D 65 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7620 (mmtt) REVERT: D 196 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7769 (mt-10) REVERT: D 221 GLU cc_start: 0.6529 (tt0) cc_final: 0.6245 (pt0) REVERT: D 227 LYS cc_start: 0.7591 (mmpt) cc_final: 0.7325 (mmmt) REVERT: D 338 TYR cc_start: 0.4874 (t80) cc_final: 0.4631 (m-10) REVERT: D 401 ASP cc_start: 0.8420 (t0) cc_final: 0.8055 (t70) REVERT: D 1044 MET cc_start: -0.0025 (mtm) cc_final: -0.0651 (tpp) REVERT: D 1249 MET cc_start: 0.2441 (mmp) cc_final: 0.1315 (tmm) REVERT: D 1555 ARG cc_start: 0.6934 (mmm-85) cc_final: 0.6657 (mmt90) REVERT: E 76 MET cc_start: 0.1883 (tpt) cc_final: 0.1395 (pp-130) REVERT: E 86 MET cc_start: 0.0880 (pmm) cc_final: 0.0527 (pp-130) REVERT: E 109 GLU cc_start: 0.1846 (mp0) cc_final: 0.1620 (pp20) REVERT: E 114 MET cc_start: 0.1612 (tpt) cc_final: 0.1367 (ttp) REVERT: E 120 MET cc_start: 0.0826 (mtt) cc_final: 0.0001 (mmm) REVERT: E 149 ILE cc_start: 0.2489 (mt) cc_final: 0.2238 (mp) REVERT: E 199 MET cc_start: -0.0124 (mtt) cc_final: -0.0404 (mmt) REVERT: E 437 GLN cc_start: 0.2561 (pm20) cc_final: 0.2336 (mp10) REVERT: E 455 MET cc_start: 0.0268 (ptm) cc_final: 0.0007 (mmp) REVERT: F 157 ASN cc_start: 0.3232 (m-40) cc_final: 0.1701 (p0) REVERT: F 215 THR cc_start: 0.0338 (m) cc_final: -0.0073 (m) REVERT: F 216 HIS cc_start: 0.3135 (t-170) cc_final: 0.2450 (t-90) REVERT: F 221 GLU cc_start: 0.2193 (mm-30) cc_final: 0.0805 (tt0) REVERT: F 250 PRO cc_start: 0.1568 (Cg_endo) cc_final: 0.0891 (Cg_exo) REVERT: F 259 ILE cc_start: 0.0358 (mt) cc_final: 0.0032 (tt) REVERT: F 430 MET cc_start: 0.0184 (ttt) cc_final: -0.0167 (mmt) REVERT: G 86 MET cc_start: 0.0810 (pmm) cc_final: 0.0502 (pp-130) REVERT: G 109 GLU cc_start: 0.1872 (mp0) cc_final: 0.1196 (pp20) REVERT: G 114 MET cc_start: 0.1671 (tpt) cc_final: 0.1442 (ttp) REVERT: G 120 MET cc_start: 0.0786 (mtt) cc_final: -0.0065 (mmm) REVERT: G 156 TYR cc_start: 0.1137 (t80) cc_final: 0.0899 (t80) REVERT: G 199 MET cc_start: -0.0136 (mtm) cc_final: -0.0498 (mmt) REVERT: H 109 GLU cc_start: 0.1924 (mt-10) cc_final: 0.1684 (tm-30) REVERT: H 114 MET cc_start: 0.3018 (mmm) cc_final: 0.2042 (ptt) REVERT: H 215 THR cc_start: 0.0312 (m) cc_final: 0.0039 (m) REVERT: H 216 HIS cc_start: 0.3178 (t-170) cc_final: 0.2450 (t-90) REVERT: H 221 GLU cc_start: 0.2234 (mm-30) cc_final: 0.0850 (tt0) REVERT: H 250 PRO cc_start: 0.1561 (Cg_endo) cc_final: 0.0861 (Cg_exo) REVERT: H 259 ILE cc_start: 0.0373 (mt) cc_final: -0.0453 (tt) REVERT: H 289 MET cc_start: 0.0106 (ttm) cc_final: -0.0797 (mmt) REVERT: H 310 ARG cc_start: 0.1300 (ptp-170) cc_final: 0.1021 (ptm160) REVERT: H 430 MET cc_start: 0.0149 (ttt) cc_final: -0.0152 (mmt) outliers start: 38 outliers final: 3 residues processed: 983 average time/residue: 1.7416 time to fit residues: 2214.1843 Evaluate side-chains 424 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 421 time to evaluate : 7.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 667 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 663 optimal weight: 10.0000 chunk 595 optimal weight: 6.9990 chunk 330 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 401 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 chunk 616 optimal weight: 40.0000 chunk 238 optimal weight: 6.9990 chunk 374 optimal weight: 6.9990 chunk 458 optimal weight: 2.9990 chunk 713 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN A 987 HIS ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 ASN B 139 GLN B 648 GLN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1523 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 HIS C1321 HIS ** D1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 ASN E 412 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 69 ASN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN G 281 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 66394 Z= 0.247 Angle : 0.674 14.284 89788 Z= 0.360 Chirality : 0.045 0.195 9842 Planarity : 0.005 0.064 11402 Dihedral : 5.991 54.264 8754 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.97 % Allowed : 11.55 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.09), residues: 7844 helix: 0.82 (0.07), residues: 4734 sheet: -0.02 (0.20), residues: 670 loop : 0.10 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 617 HIS 0.009 0.002 HIS B1272 PHE 0.030 0.002 PHE A 539 TYR 0.040 0.002 TYR E 156 ARG 0.011 0.001 ARG F 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 529 time to evaluate : 7.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7631 (mtpt) REVERT: A 177 GLU cc_start: 0.7175 (pt0) cc_final: 0.6817 (pp20) REVERT: A 492 ASN cc_start: 0.6652 (m110) cc_final: 0.6301 (m110) REVERT: A 594 GLN cc_start: 0.6356 (OUTLIER) cc_final: 0.5908 (mt0) REVERT: A 934 MET cc_start: 0.2731 (ttm) cc_final: 0.1789 (mpp) REVERT: A 937 MET cc_start: 0.1853 (tmt) cc_final: 0.1142 (tpp) REVERT: A 1039 MET cc_start: 0.1331 (pp-130) cc_final: -0.1086 (ttm) REVERT: A 1044 MET cc_start: 0.0544 (mtp) cc_final: -0.0281 (tpt) REVERT: A 1525 LYS cc_start: 0.6812 (mptt) cc_final: 0.6132 (pttt) REVERT: A 1540 GLU cc_start: 0.6611 (tm-30) cc_final: 0.6352 (mt-10) REVERT: B 65 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7432 (mmtt) REVERT: B 221 GLU cc_start: 0.6538 (tt0) cc_final: 0.6193 (pt0) REVERT: B 227 LYS cc_start: 0.7474 (mmpt) cc_final: 0.7217 (mmmt) REVERT: B 321 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.7001 (mmmt) REVERT: B 401 ASP cc_start: 0.8184 (t0) cc_final: 0.7804 (t70) REVERT: B 515 ARG cc_start: 0.7262 (mmm-85) cc_final: 0.6983 (mmt180) REVERT: B 521 GLN cc_start: 0.5365 (mm-40) cc_final: 0.4943 (pm20) REVERT: B 613 LYS cc_start: 0.3570 (mmmm) cc_final: 0.3344 (mmmm) REVERT: B 940 ASP cc_start: -0.0331 (OUTLIER) cc_final: -0.0549 (t0) REVERT: B 1044 MET cc_start: 0.0050 (mtm) cc_final: -0.0715 (tpp) REVERT: B 1076 LYS cc_start: 0.2892 (OUTLIER) cc_final: 0.2478 (tmtm) REVERT: B 1555 ARG cc_start: 0.7112 (mmm-85) cc_final: 0.6882 (mmm160) REVERT: C 49 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: C 65 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7644 (mtpt) REVERT: C 177 GLU cc_start: 0.7329 (pt0) cc_final: 0.6815 (pp20) REVERT: C 492 ASN cc_start: 0.6614 (m110) cc_final: 0.6218 (m110) REVERT: C 594 GLN cc_start: 0.6445 (OUTLIER) cc_final: 0.5994 (mt0) REVERT: C 742 GLU cc_start: 0.2469 (OUTLIER) cc_final: 0.2218 (pt0) REVERT: C 934 MET cc_start: 0.2907 (ttm) cc_final: 0.1854 (mpp) REVERT: C 937 MET cc_start: 0.1825 (tmt) cc_final: 0.1081 (tpp) REVERT: C 1039 MET cc_start: 0.1328 (pp-130) cc_final: -0.1107 (ttm) REVERT: C 1044 MET cc_start: 0.0182 (mtp) cc_final: -0.0503 (tpt) REVERT: C 1525 LYS cc_start: 0.6762 (mptt) cc_final: 0.6103 (pttt) REVERT: D 3 LYS cc_start: 0.7725 (ptmt) cc_final: 0.7358 (mtmm) REVERT: D 65 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7432 (mmtt) REVERT: D 196 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7836 (mt-10) REVERT: D 221 GLU cc_start: 0.6389 (tt0) cc_final: 0.6130 (pt0) REVERT: D 227 LYS cc_start: 0.7592 (mmpt) cc_final: 0.7295 (mmmt) REVERT: D 401 ASP cc_start: 0.8254 (t0) cc_final: 0.7916 (t70) REVERT: D 515 ARG cc_start: 0.7434 (mmm-85) cc_final: 0.7042 (mmt180) REVERT: D 934 MET cc_start: 0.2507 (OUTLIER) cc_final: 0.1834 (tmm) REVERT: D 940 ASP cc_start: -0.0285 (OUTLIER) cc_final: -0.0553 (t0) REVERT: D 1044 MET cc_start: -0.0023 (mtm) cc_final: -0.0621 (tpp) REVERT: E 109 GLU cc_start: 0.1847 (OUTLIER) cc_final: 0.1072 (pp20) REVERT: E 114 MET cc_start: 0.1529 (tpt) cc_final: 0.1272 (ttm) REVERT: E 120 MET cc_start: 0.1091 (mtt) cc_final: 0.0156 (mmm) REVERT: E 132 LEU cc_start: 0.2725 (pp) cc_final: 0.2221 (mm) REVERT: E 199 MET cc_start: -0.0097 (mtm) cc_final: -0.0346 (mmt) REVERT: E 407 GLN cc_start: 0.2167 (OUTLIER) cc_final: 0.1776 (tt0) REVERT: E 437 GLN cc_start: 0.1959 (OUTLIER) cc_final: 0.1232 (mt0) REVERT: E 455 MET cc_start: 0.0425 (ptm) cc_final: 0.0108 (mmp) REVERT: F 86 MET cc_start: 0.2795 (pmm) cc_final: 0.1653 (ppp) REVERT: F 114 MET cc_start: 0.2399 (ppp) cc_final: 0.2027 (tmm) REVERT: F 179 GLN cc_start: 0.1934 (OUTLIER) cc_final: 0.1552 (tt0) REVERT: F 216 HIS cc_start: 0.3297 (t-170) cc_final: 0.3090 (t-90) REVERT: F 289 MET cc_start: 0.0626 (ttm) cc_final: -0.0067 (mmt) REVERT: F 291 MET cc_start: 0.0332 (mmm) cc_final: -0.0014 (tmm) REVERT: F 307 GLN cc_start: 0.2733 (OUTLIER) cc_final: 0.2165 (pm20) REVERT: F 310 ARG cc_start: 0.1760 (ptp-170) cc_final: 0.1548 (ptm160) REVERT: F 430 MET cc_start: 0.0178 (ttt) cc_final: -0.0240 (mmt) REVERT: G 83 GLN cc_start: 0.1628 (pp30) cc_final: 0.0621 (pm20) REVERT: G 109 GLU cc_start: 0.1891 (OUTLIER) cc_final: 0.1093 (pp20) REVERT: G 114 MET cc_start: 0.1562 (tpt) cc_final: 0.1188 (ttm) REVERT: G 120 MET cc_start: 0.0921 (mtt) cc_final: 0.0290 (mmm) REVERT: G 124 GLU cc_start: 0.2498 (mm-30) cc_final: 0.2270 (tp30) REVERT: G 147 LEU cc_start: 0.4013 (OUTLIER) cc_final: 0.3791 (mm) REVERT: G 156 TYR cc_start: 0.1344 (t80) cc_final: 0.0174 (m-80) REVERT: G 199 MET cc_start: -0.0066 (mtm) cc_final: -0.0368 (mmt) REVERT: G 216 HIS cc_start: 0.2716 (t-90) cc_final: 0.2276 (t-90) REVERT: H 109 GLU cc_start: 0.2653 (mt-10) cc_final: 0.2294 (tm-30) REVERT: H 114 MET cc_start: 0.2687 (mmm) cc_final: 0.2219 (mmt) REVERT: H 259 ILE cc_start: -0.0183 (mt) cc_final: -0.0403 (tt) REVERT: H 289 MET cc_start: 0.0276 (ttm) cc_final: -0.0363 (mmt) REVERT: H 291 MET cc_start: 0.1845 (ptm) cc_final: 0.1177 (tpp) REVERT: H 307 GLN cc_start: 0.2612 (OUTLIER) cc_final: 0.2088 (pm20) REVERT: H 397 GLN cc_start: 0.1990 (mt0) cc_final: 0.1767 (mm110) REVERT: H 430 MET cc_start: 0.0161 (OUTLIER) cc_final: -0.0231 (mmt) outliers start: 213 outliers final: 34 residues processed: 698 average time/residue: 1.6563 time to fit residues: 1507.8347 Evaluate side-chains 436 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 382 time to evaluate : 7.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 1076 LYS Chi-restraints excluded: chain B residue 1297 HIS Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 594 GLN Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 742 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 934 MET Chi-restraints excluded: chain D residue 940 ASP Chi-restraints excluded: chain D residue 1297 HIS Chi-restraints excluded: chain D residue 1520 LEU Chi-restraints excluded: chain D residue 1526 LEU Chi-restraints excluded: chain D residue 1578 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 407 GLN Chi-restraints excluded: chain E residue 437 GLN Chi-restraints excluded: chain F residue 179 GLN Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 437 GLN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 185 LYS Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain H residue 430 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 396 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 594 optimal weight: 9.9990 chunk 486 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 715 optimal weight: 0.0870 chunk 772 optimal weight: 6.9990 chunk 636 optimal weight: 8.9990 chunk 709 optimal weight: 7.9990 chunk 243 optimal weight: 20.0000 chunk 573 optimal weight: 10.0000 overall best weight: 3.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 987 HIS ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN A1533 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 ASN B 648 GLN B 825 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 987 HIS C1137 ASN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 HIS ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5567 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 66394 Z= 0.260 Angle : 0.646 12.712 89788 Z= 0.340 Chirality : 0.044 0.199 9842 Planarity : 0.005 0.076 11402 Dihedral : 5.824 55.352 8752 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.14 % Allowed : 12.74 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.09), residues: 7844 helix: 1.00 (0.07), residues: 4742 sheet: -0.14 (0.20), residues: 626 loop : -0.19 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 888 HIS 0.008 0.001 HIS B 469 PHE 0.026 0.002 PHE C 539 TYR 0.032 0.002 TYR A1390 ARG 0.009 0.001 ARG B 657 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 435 time to evaluate : 7.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.7308 (pt0) cc_final: 0.6930 (pp20) REVERT: A 492 ASN cc_start: 0.6978 (m110) cc_final: 0.6772 (m110) REVERT: A 541 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6750 (mtpt) REVERT: A 594 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.5813 (mt0) REVERT: A 934 MET cc_start: 0.2526 (ttm) cc_final: 0.1599 (mpp) REVERT: A 1039 MET cc_start: 0.1359 (pp-130) cc_final: -0.0988 (ttm) REVERT: A 1044 MET cc_start: 0.0708 (mtp) cc_final: -0.0186 (tpt) REVERT: A 1225 MET cc_start: 0.1650 (ptm) cc_final: 0.1382 (ptp) REVERT: A 1263 TYR cc_start: 0.4026 (t80) cc_final: 0.3145 (t80) REVERT: A 1520 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7833 (mp) REVERT: A 1525 LYS cc_start: 0.6570 (mptt) cc_final: 0.5904 (pttt) REVERT: A 1559 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: B 32 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6679 (tp30) REVERT: B 65 LYS cc_start: 0.8379 (mmtt) cc_final: 0.7440 (mmtt) REVERT: B 227 LYS cc_start: 0.7570 (mmpt) cc_final: 0.7298 (mmpt) REVERT: B 321 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6888 (mmmt) REVERT: B 345 LYS cc_start: 0.6663 (tppt) cc_final: 0.6439 (mtmt) REVERT: B 515 ARG cc_start: 0.7333 (mmm-85) cc_final: 0.7030 (mmt180) REVERT: B 524 LYS cc_start: 0.6498 (OUTLIER) cc_final: 0.6149 (mptt) REVERT: B 613 LYS cc_start: 0.4183 (mmmm) cc_final: 0.3867 (mmmm) REVERT: B 792 TYR cc_start: 0.2963 (t80) cc_final: 0.2704 (t80) REVERT: B 1044 MET cc_start: -0.0340 (mtm) cc_final: -0.0557 (tpp) REVERT: B 1532 GLU cc_start: 0.6136 (mp0) cc_final: 0.5848 (mp0) REVERT: C 49 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: C 177 GLU cc_start: 0.7418 (pt0) cc_final: 0.6864 (pp20) REVERT: C 492 ASN cc_start: 0.6960 (m110) cc_final: 0.6744 (m110) REVERT: C 541 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6708 (mtpt) REVERT: C 594 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.6006 (mt0) REVERT: C 934 MET cc_start: 0.2534 (ttm) cc_final: 0.1577 (mpp) REVERT: C 937 MET cc_start: 0.1546 (OUTLIER) cc_final: 0.1306 (tpp) REVERT: C 1039 MET cc_start: 0.1363 (pp-130) cc_final: -0.1001 (ttm) REVERT: C 1044 MET cc_start: 0.0331 (mtp) cc_final: -0.0403 (tpt) REVERT: C 1225 MET cc_start: 0.1873 (ptm) cc_final: 0.1670 (ptp) REVERT: C 1520 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7944 (mp) REVERT: C 1525 LYS cc_start: 0.6590 (mptt) cc_final: 0.5916 (pttt) REVERT: D 32 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6739 (tp30) REVERT: D 65 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7439 (mmtt) REVERT: D 227 LYS cc_start: 0.7589 (mmpt) cc_final: 0.7281 (mmpt) REVERT: D 515 ARG cc_start: 0.7379 (mmm-85) cc_final: 0.6996 (mmt180) REVERT: D 575 ARG cc_start: 0.5879 (OUTLIER) cc_final: 0.5401 (mmt180) REVERT: D 613 LYS cc_start: 0.4167 (mmmm) cc_final: 0.3845 (mmmm) REVERT: D 792 TYR cc_start: 0.2987 (t80) cc_final: 0.2723 (t80) REVERT: D 1044 MET cc_start: -0.0041 (mtm) cc_final: -0.0548 (ttp) REVERT: D 1143 ASP cc_start: 0.3047 (OUTLIER) cc_final: 0.2768 (m-30) REVERT: D 1532 GLU cc_start: 0.6149 (mp0) cc_final: 0.5859 (mp0) REVERT: D 1555 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6936 (mmm160) REVERT: E 109 GLU cc_start: 0.2084 (OUTLIER) cc_final: 0.1217 (pp20) REVERT: E 114 MET cc_start: 0.1595 (tpt) cc_final: 0.1350 (ttm) REVERT: E 120 MET cc_start: 0.1023 (mtt) cc_final: 0.0231 (mmm) REVERT: E 216 HIS cc_start: 0.2846 (t-90) cc_final: 0.2627 (t-90) REVERT: E 437 GLN cc_start: 0.2229 (OUTLIER) cc_final: 0.1377 (mt0) REVERT: F 76 MET cc_start: 0.2051 (tpt) cc_final: 0.1519 (tmm) REVERT: F 86 MET cc_start: 0.2882 (pmm) cc_final: 0.1878 (ppp) REVERT: F 114 MET cc_start: 0.2557 (ppp) cc_final: 0.2191 (tmm) REVERT: F 148 TYR cc_start: 0.1672 (t80) cc_final: 0.1330 (t80) REVERT: F 216 HIS cc_start: 0.3382 (t-170) cc_final: 0.3003 (t70) REVERT: F 221 GLU cc_start: 0.2295 (mm-30) cc_final: 0.1044 (tt0) REVERT: F 291 MET cc_start: 0.1013 (mmm) cc_final: 0.0553 (tmm) REVERT: F 309 ARG cc_start: 0.0998 (OUTLIER) cc_final: 0.0646 (mmp-170) REVERT: F 430 MET cc_start: 0.0327 (ttt) cc_final: -0.0171 (mmt) REVERT: G 80 PHE cc_start: 0.1546 (m-10) cc_final: 0.1251 (m-10) REVERT: G 83 GLN cc_start: 0.1732 (pp30) cc_final: 0.1170 (pm20) REVERT: G 109 GLU cc_start: 0.2096 (OUTLIER) cc_final: 0.1225 (pp20) REVERT: G 114 MET cc_start: 0.1636 (tpt) cc_final: 0.1379 (ttm) REVERT: G 120 MET cc_start: 0.0933 (mtt) cc_final: 0.0269 (mmm) REVERT: G 124 GLU cc_start: 0.2457 (mm-30) cc_final: 0.1695 (mm-30) REVERT: G 156 TYR cc_start: 0.1386 (t80) cc_final: 0.0254 (m-80) REVERT: G 199 MET cc_start: -0.0172 (mtm) cc_final: -0.0421 (mmt) REVERT: G 216 HIS cc_start: 0.2829 (t-90) cc_final: 0.2626 (t-90) REVERT: G 407 GLN cc_start: 0.2034 (OUTLIER) cc_final: 0.1606 (tt0) REVERT: H 76 MET cc_start: 0.1886 (tpt) cc_final: 0.1483 (tmm) REVERT: H 109 GLU cc_start: 0.2674 (mt-10) cc_final: 0.2320 (tm-30) REVERT: H 114 MET cc_start: 0.2942 (mmm) cc_final: 0.2467 (mmt) REVERT: H 148 TYR cc_start: 0.1630 (t80) cc_final: 0.1336 (t80) REVERT: H 157 ASN cc_start: 0.4021 (OUTLIER) cc_final: 0.2517 (p0) REVERT: H 221 GLU cc_start: 0.2515 (mm-30) cc_final: 0.1160 (tt0) REVERT: H 259 ILE cc_start: -0.0070 (mt) cc_final: -0.0296 (tt) REVERT: H 291 MET cc_start: 0.1562 (ptm) cc_final: 0.1215 (pp-130) REVERT: H 307 GLN cc_start: 0.2801 (OUTLIER) cc_final: 0.2268 (pm20) REVERT: H 397 GLN cc_start: 0.2044 (mt0) cc_final: 0.1716 (mm110) REVERT: H 430 MET cc_start: 0.0315 (OUTLIER) cc_final: -0.0141 (mmt) outliers start: 225 outliers final: 66 residues processed: 622 average time/residue: 1.7117 time to fit residues: 1389.5264 Evaluate side-chains 454 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 364 time to evaluate : 8.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1559 GLN Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1239 HIS Chi-restraints excluded: chain B residue 1287 ILE Chi-restraints excluded: chain B residue 1297 HIS Chi-restraints excluded: chain B residue 1437 THR Chi-restraints excluded: chain B residue 1489 HIS Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain B residue 1574 LYS Chi-restraints excluded: chain B residue 1578 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 541 LYS Chi-restraints excluded: chain C residue 594 GLN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 937 MET Chi-restraints excluded: chain C residue 1520 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 575 ARG Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 1079 SER Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1239 HIS Chi-restraints excluded: chain D residue 1297 HIS Chi-restraints excluded: chain D residue 1489 HIS Chi-restraints excluded: chain D residue 1526 LEU Chi-restraints excluded: chain D residue 1555 ARG Chi-restraints excluded: chain D residue 1578 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 437 GLN Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 ARG Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 407 GLN Chi-restraints excluded: chain G residue 425 THR Chi-restraints excluded: chain G residue 437 GLN Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 185 LYS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain H residue 342 LYS Chi-restraints excluded: chain H residue 430 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 706 optimal weight: 20.0000 chunk 537 optimal weight: 0.0060 chunk 371 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 341 optimal weight: 0.7980 chunk 480 optimal weight: 1.9990 chunk 717 optimal weight: 1.9990 chunk 759 optimal weight: 7.9990 chunk 374 optimal weight: 0.0870 chunk 680 optimal weight: 0.5980 chunk 204 optimal weight: 5.9990 overall best weight: 0.6976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS A1533 ASN B1523 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 HIS C1533 ASN D 648 GLN D1523 ASN E 83 GLN E 121 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 66394 Z= 0.142 Angle : 0.524 13.545 89788 Z= 0.274 Chirality : 0.040 0.249 9842 Planarity : 0.004 0.048 11402 Dihedral : 5.357 56.591 8752 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.04 % Allowed : 14.36 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.10), residues: 7844 helix: 1.42 (0.08), residues: 4762 sheet: -0.02 (0.21), residues: 626 loop : -0.03 (0.13), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 646 HIS 0.004 0.001 HIS A 778 PHE 0.026 0.001 PHE C 539 TYR 0.018 0.001 TYR C 676 ARG 0.006 0.000 ARG A1417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 427 time to evaluate : 8.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.7664 (tppt) cc_final: 0.7323 (tppp) REVERT: A 206 ARG cc_start: 0.6554 (ttp-110) cc_final: 0.5809 (ttp-170) REVERT: A 934 MET cc_start: 0.2510 (ttm) cc_final: 0.1718 (mpp) REVERT: A 1039 MET cc_start: 0.1449 (pp-130) cc_final: -0.0846 (ttm) REVERT: A 1044 MET cc_start: 0.0544 (mtp) cc_final: -0.0328 (tpt) REVERT: A 1520 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.8003 (mp) REVERT: A 1525 LYS cc_start: 0.6546 (mptt) cc_final: 0.6019 (ptpt) REVERT: B 227 LYS cc_start: 0.7554 (mmpt) cc_final: 0.7284 (mmpt) REVERT: B 401 ASP cc_start: 0.7838 (t0) cc_final: 0.7497 (t70) REVERT: B 524 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6233 (mptt) REVERT: B 792 TYR cc_start: 0.2835 (t80) cc_final: 0.2599 (t80) REVERT: B 1044 MET cc_start: -0.0510 (mtm) cc_final: -0.0765 (tpp) REVERT: B 1417 ARG cc_start: 0.3520 (mmp80) cc_final: 0.3146 (tpm-80) REVERT: B 1428 TRP cc_start: 0.3875 (t-100) cc_final: 0.3670 (t-100) REVERT: C 65 LYS cc_start: 0.7652 (tppt) cc_final: 0.7304 (tppp) REVERT: C 135 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6646 (pp) REVERT: C 206 ARG cc_start: 0.6542 (ttp-110) cc_final: 0.5831 (ttp-170) REVERT: C 563 ARG cc_start: 0.5630 (pmt-80) cc_final: 0.5411 (pmt-80) REVERT: C 934 MET cc_start: 0.2667 (ttm) cc_final: 0.1727 (mpp) REVERT: C 990 ILE cc_start: -0.0531 (OUTLIER) cc_final: -0.0952 (mp) REVERT: C 1039 MET cc_start: 0.1376 (pp-130) cc_final: -0.0915 (ttm) REVERT: C 1044 MET cc_start: 0.0461 (mtp) cc_final: -0.0317 (tpt) REVERT: C 1419 ASN cc_start: 0.2141 (OUTLIER) cc_final: 0.1922 (m-40) REVERT: C 1520 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7994 (mp) REVERT: C 1525 LYS cc_start: 0.6595 (mptt) cc_final: 0.6075 (ptpt) REVERT: D 227 LYS cc_start: 0.7572 (mmpt) cc_final: 0.7260 (mmpt) REVERT: D 401 ASP cc_start: 0.7848 (t0) cc_final: 0.7505 (t70) REVERT: D 563 ARG cc_start: 0.6522 (ptm160) cc_final: 0.5614 (ttp80) REVERT: D 792 TYR cc_start: 0.2845 (t80) cc_final: 0.2623 (t80) REVERT: D 934 MET cc_start: 0.1658 (OUTLIER) cc_final: 0.1420 (tmm) REVERT: D 1417 ARG cc_start: 0.3591 (mmp80) cc_final: 0.3259 (tpm-80) REVERT: D 1428 TRP cc_start: 0.3772 (t-100) cc_final: 0.3563 (t-100) REVERT: E 83 GLN cc_start: 0.2222 (OUTLIER) cc_final: 0.0945 (pt0) REVERT: E 86 MET cc_start: 0.1752 (pmm) cc_final: 0.0977 (ppp) REVERT: E 109 GLU cc_start: 0.1717 (OUTLIER) cc_final: 0.1340 (pp20) REVERT: E 114 MET cc_start: 0.1667 (tpt) cc_final: 0.1444 (ttm) REVERT: E 120 MET cc_start: 0.1017 (mtt) cc_final: 0.0019 (mmm) REVERT: E 309 ARG cc_start: 0.1320 (OUTLIER) cc_final: 0.0474 (mmp-170) REVERT: E 437 GLN cc_start: 0.2173 (OUTLIER) cc_final: 0.1401 (mt0) REVERT: E 442 LEU cc_start: 0.3791 (OUTLIER) cc_final: 0.3539 (tp) REVERT: F 76 MET cc_start: 0.2060 (tpt) cc_final: 0.1490 (tmm) REVERT: F 86 MET cc_start: 0.2946 (pmm) cc_final: 0.1699 (ppp) REVERT: F 114 MET cc_start: 0.2532 (ppp) cc_final: 0.2173 (tmm) REVERT: F 148 TYR cc_start: 0.1629 (t80) cc_final: 0.1351 (t80) REVERT: F 185 LYS cc_start: 0.1184 (OUTLIER) cc_final: -0.0207 (tppp) REVERT: F 216 HIS cc_start: 0.3222 (t-170) cc_final: 0.2784 (t-90) REVERT: F 221 GLU cc_start: 0.2272 (mm-30) cc_final: 0.0995 (tt0) REVERT: F 291 MET cc_start: 0.1514 (mmm) cc_final: 0.0623 (tmm) REVERT: F 309 ARG cc_start: 0.0924 (OUTLIER) cc_final: 0.0203 (tpp-160) REVERT: F 430 MET cc_start: -0.0132 (ttt) cc_final: -0.0572 (mmt) REVERT: G 83 GLN cc_start: 0.1783 (pp30) cc_final: 0.1136 (pm20) REVERT: G 101 GLN cc_start: 0.2919 (pm20) cc_final: 0.1619 (pt0) REVERT: G 109 GLU cc_start: 0.1802 (OUTLIER) cc_final: 0.1416 (pp20) REVERT: G 114 MET cc_start: 0.1722 (tpt) cc_final: 0.1471 (ttm) REVERT: G 120 MET cc_start: 0.0975 (mtt) cc_final: 0.0373 (mmm) REVERT: G 122 TYR cc_start: 0.2855 (OUTLIER) cc_final: 0.2494 (t80) REVERT: G 156 TYR cc_start: 0.1468 (t80) cc_final: 0.0232 (m-80) REVERT: G 439 LEU cc_start: 0.2873 (OUTLIER) cc_final: 0.2523 (mp) REVERT: H 76 MET cc_start: 0.1846 (tpt) cc_final: 0.1435 (tmm) REVERT: H 109 GLU cc_start: 0.2524 (mt-10) cc_final: 0.2218 (tm-30) REVERT: H 114 MET cc_start: 0.2925 (mmm) cc_final: 0.2488 (mmt) REVERT: H 157 ASN cc_start: 0.3912 (OUTLIER) cc_final: 0.2426 (p0) REVERT: H 185 LYS cc_start: 0.1162 (OUTLIER) cc_final: -0.0347 (pptt) REVERT: H 210 MET cc_start: 0.1183 (mmt) cc_final: 0.0945 (mmp) REVERT: H 221 GLU cc_start: 0.2418 (mm-30) cc_final: 0.1022 (tt0) REVERT: H 259 ILE cc_start: -0.0221 (mt) cc_final: -0.0464 (tt) REVERT: H 289 MET cc_start: 0.0314 (ttm) cc_final: -0.0308 (mmt) REVERT: H 291 MET cc_start: 0.1314 (ptm) cc_final: 0.1024 (tmm) REVERT: H 307 GLN cc_start: 0.2724 (OUTLIER) cc_final: 0.2245 (pm20) REVERT: H 430 MET cc_start: -0.0058 (OUTLIER) cc_final: -0.0582 (mmt) outliers start: 146 outliers final: 30 residues processed: 545 average time/residue: 1.7092 time to fit residues: 1225.2457 Evaluate side-chains 412 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 361 time to evaluate : 7.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 1239 HIS Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1489 HIS Chi-restraints excluded: chain B residue 1526 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 990 ILE Chi-restraints excluded: chain C residue 1419 ASN Chi-restraints excluded: chain C residue 1520 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 538 ASN Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 934 MET Chi-restraints excluded: chain D residue 1239 HIS Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1489 HIS Chi-restraints excluded: chain D residue 1526 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 437 GLN Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 ARG Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 437 GLN Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 455 MET Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 185 LYS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain H residue 430 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 632 optimal weight: 30.0000 chunk 431 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 565 optimal weight: 20.0000 chunk 313 optimal weight: 3.9990 chunk 648 optimal weight: 4.9990 chunk 525 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 387 optimal weight: 20.0000 chunk 681 optimal weight: 40.0000 chunk 191 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 ASN B 648 GLN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C1533 ASN E 83 GLN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN ** H 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5586 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 66394 Z= 0.299 Angle : 0.637 14.573 89788 Z= 0.334 Chirality : 0.044 0.229 9842 Planarity : 0.005 0.056 11402 Dihedral : 5.673 55.999 8752 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.89 % Allowed : 14.39 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.09), residues: 7844 helix: 1.16 (0.08), residues: 4728 sheet: -0.16 (0.21), residues: 618 loop : -0.25 (0.13), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 449 HIS 0.013 0.001 HIS A 778 PHE 0.027 0.002 PHE A 539 TYR 0.026 0.002 TYR C 980 ARG 0.011 0.001 ARG A1268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 388 time to evaluate : 5.703 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: A 65 LYS cc_start: 0.8100 (tppt) cc_final: 0.7736 (tppp) REVERT: A 177 GLU cc_start: 0.7430 (pt0) cc_final: 0.7132 (pp20) REVERT: A 500 GLU cc_start: 0.7335 (pm20) cc_final: 0.6993 (pp20) REVERT: A 594 GLN cc_start: 0.6624 (OUTLIER) cc_final: 0.6228 (mt0) REVERT: A 934 MET cc_start: 0.2476 (ttm) cc_final: 0.1590 (mpp) REVERT: A 937 MET cc_start: 0.1593 (tpp) cc_final: 0.1133 (mtp) REVERT: A 1039 MET cc_start: 0.1356 (pp-130) cc_final: -0.0968 (ttm) REVERT: A 1044 MET cc_start: 0.0614 (mtp) cc_final: -0.0339 (tpt) REVERT: A 1263 TYR cc_start: 0.4057 (t80) cc_final: 0.3295 (t80) REVERT: A 1520 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7814 (mp) REVERT: A 1525 LYS cc_start: 0.6600 (mptt) cc_final: 0.5988 (ptpt) REVERT: A 1559 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: B 32 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6733 (tp30) REVERT: B 65 LYS cc_start: 0.8385 (mmtt) cc_final: 0.7431 (mmtt) REVERT: B 166 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: B 221 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: B 227 LYS cc_start: 0.7584 (mmpt) cc_final: 0.7181 (mmmt) REVERT: B 792 TYR cc_start: 0.2958 (t80) cc_final: 0.2734 (t80) REVERT: B 1044 MET cc_start: -0.0610 (mtm) cc_final: -0.0874 (tpp) REVERT: B 1421 TYR cc_start: 0.2886 (t80) cc_final: 0.2463 (t80) REVERT: B 1520 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7423 (mt) REVERT: C 49 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7659 (pt0) REVERT: C 65 LYS cc_start: 0.8102 (tppt) cc_final: 0.7779 (tppp) REVERT: C 177 GLU cc_start: 0.7319 (pt0) cc_final: 0.7026 (pp20) REVERT: C 594 GLN cc_start: 0.6338 (OUTLIER) cc_final: 0.6031 (mt0) REVERT: C 934 MET cc_start: 0.2286 (ttm) cc_final: 0.1508 (mpp) REVERT: C 1039 MET cc_start: 0.1361 (pp-130) cc_final: -0.0991 (ttm) REVERT: C 1044 MET cc_start: 0.0605 (mtp) cc_final: -0.0288 (tpt) REVERT: C 1520 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8070 (mp) REVERT: C 1525 LYS cc_start: 0.6585 (mptt) cc_final: 0.5953 (ptpt) REVERT: D 32 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6765 (tp30) REVERT: D 166 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: D 221 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: D 227 LYS cc_start: 0.7701 (mmpt) cc_final: 0.7221 (mmmt) REVERT: D 610 THR cc_start: 0.6259 (p) cc_final: 0.6002 (m) REVERT: D 654 GLU cc_start: 0.4810 (mt-10) cc_final: 0.4587 (mp0) REVERT: D 1225 MET cc_start: 0.0146 (tpp) cc_final: -0.0168 (mmt) REVERT: D 1417 ARG cc_start: 0.3534 (mmp80) cc_final: 0.3169 (tpm-80) REVERT: D 1487 MET cc_start: 0.5246 (mpt) cc_final: 0.4878 (mmt) REVERT: D 1520 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7427 (mt) REVERT: D 1555 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6906 (mmm160) REVERT: E 75 LEU cc_start: 0.4216 (OUTLIER) cc_final: 0.3928 (pp) REVERT: E 76 MET cc_start: 0.2495 (tpp) cc_final: 0.2235 (OUTLIER) REVERT: E 109 GLU cc_start: 0.1904 (OUTLIER) cc_final: 0.1568 (pp20) REVERT: E 114 MET cc_start: 0.1824 (tpt) cc_final: 0.1453 (ttm) REVERT: E 120 MET cc_start: 0.1381 (mtt) cc_final: 0.0417 (mmm) REVERT: E 309 ARG cc_start: 0.1608 (OUTLIER) cc_final: 0.0676 (mmp-170) REVERT: E 407 GLN cc_start: 0.2145 (OUTLIER) cc_final: 0.1740 (tt0) REVERT: E 437 GLN cc_start: 0.1947 (OUTLIER) cc_final: 0.1128 (mt0) REVERT: F 76 MET cc_start: 0.1729 (tpt) cc_final: 0.1260 (tmm) REVERT: F 83 GLN cc_start: 0.2423 (OUTLIER) cc_final: 0.2191 (tp40) REVERT: F 86 MET cc_start: 0.2929 (pmm) cc_final: 0.1949 (ppp) REVERT: F 114 MET cc_start: 0.2494 (ppp) cc_final: 0.2126 (tmm) REVERT: F 216 HIS cc_start: 0.3381 (t-170) cc_final: 0.3022 (t-90) REVERT: F 221 GLU cc_start: 0.2334 (mm-30) cc_final: 0.1095 (tt0) REVERT: F 291 MET cc_start: 0.1681 (mmm) cc_final: 0.0653 (tmm) REVERT: F 309 ARG cc_start: 0.1197 (OUTLIER) cc_final: 0.0633 (mmm160) REVERT: F 430 MET cc_start: 0.0089 (ttt) cc_final: -0.0453 (mmt) REVERT: G 83 GLN cc_start: 0.1707 (pp30) cc_final: 0.1109 (pm20) REVERT: G 86 MET cc_start: 0.1838 (pmm) cc_final: 0.1144 (tmm) REVERT: G 109 GLU cc_start: 0.1747 (OUTLIER) cc_final: 0.1464 (pp20) REVERT: G 114 MET cc_start: 0.1735 (tpt) cc_final: 0.1439 (ttm) REVERT: G 120 MET cc_start: 0.1324 (mtt) cc_final: 0.0341 (mmm) REVERT: G 122 TYR cc_start: 0.2811 (OUTLIER) cc_final: 0.2519 (t80) REVERT: G 124 GLU cc_start: 0.2100 (mm-30) cc_final: 0.1798 (mm-30) REVERT: G 332 LEU cc_start: 0.2276 (mm) cc_final: 0.1958 (mt) REVERT: G 439 LEU cc_start: 0.2866 (OUTLIER) cc_final: 0.2515 (mp) REVERT: H 76 MET cc_start: 0.1665 (tpt) cc_final: 0.1283 (tmm) REVERT: H 86 MET cc_start: 0.2969 (pmm) cc_final: 0.2056 (ppp) REVERT: H 109 GLU cc_start: 0.2362 (mt-10) cc_final: 0.2101 (tm-30) REVERT: H 114 MET cc_start: 0.3018 (mmm) cc_final: 0.2617 (mmt) REVERT: H 221 GLU cc_start: 0.2567 (mm-30) cc_final: 0.1215 (tt0) REVERT: H 307 GLN cc_start: 0.2463 (OUTLIER) cc_final: 0.2043 (pm20) REVERT: H 430 MET cc_start: 0.0137 (OUTLIER) cc_final: -0.0378 (mmt) outliers start: 207 outliers final: 72 residues processed: 557 average time/residue: 1.3688 time to fit residues: 997.1512 Evaluate side-chains 453 residues out of total 7160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 355 time to evaluate : 5.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 1082 MET Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1520 LEU Chi-restraints excluded: chain A residue 1559 GLN Chi-restraints excluded: chain A residue 1586 ILE Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1239 HIS Chi-restraints excluded: chain B residue 1287 ILE Chi-restraints excluded: chain B residue 1297 HIS Chi-restraints excluded: chain B residue 1386 ASP Chi-restraints excluded: chain B residue 1489 HIS Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 594 GLN Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 706 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1184 VAL Chi-restraints excluded: chain C residue 1504 ILE Chi-restraints excluded: chain C residue 1520 LEU Chi-restraints excluded: chain C residue 1586 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 538 ASN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 1239 HIS Chi-restraints excluded: chain D residue 1297 HIS Chi-restraints excluded: chain D residue 1386 ASP Chi-restraints excluded: chain D residue 1437 THR Chi-restraints excluded: chain D residue 1489 HIS Chi-restraints excluded: chain D residue 1520 LEU Chi-restraints excluded: chain D residue 1555 ARG Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 407 GLN Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 437 GLN Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 ARG Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 309 ARG Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 437 GLN Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain H residue 185 LYS Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain H residue 430 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 255 optimal weight: 3.9990 chunk 684 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 446 optimal weight: 20.0000 chunk 187 optimal weight: 0.2980 chunk 760 optimal weight: 30.0000 chunk 631 optimal weight: 4.9990 chunk 352 optimal weight: 0.0570 chunk 63 optimal weight: 20.0000 chunk 251 optimal weight: 1.9990 chunk 399 optimal weight: 9.9990 overall best weight: 1.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: