Starting phenix.real_space_refine on Tue Nov 19 05:47:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/11_2024/5ykg_6833.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/11_2024/5ykg_6833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/11_2024/5ykg_6833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/11_2024/5ykg_6833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/11_2024/5ykg_6833.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykg_6833/11_2024/5ykg_6833.cif" } resolution = 4.57 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= 0.005 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 24 5.49 5 S 284 5.16 5 Cl 4 4.86 5 C 33044 2.51 5 N 8608 2.21 5 O 8904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 50868 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2433 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 29} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 10189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10189 Classifications: {'peptide': 1309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 45, 'TRANS': 1263} Chain breaks: 11 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AGS': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 33.33, per 1000 atoms: 0.66 Number of scatterers: 50868 At special positions: 0 Unit cell: (209.945, 209.945, 142.425, 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) Cl 4 17.00 S 284 16.00 P 24 15.00 O 8904 8.00 N 8608 7.00 C 33044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 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: 12.78 Conformation dependent library (CDL) restraints added in 6.4 seconds 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12344 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 40 sheets defined 63.0% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.941A pdb=" N THR A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 98 removed outlier: 3.721A pdb=" N GLY A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.642A pdb=" N VAL A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.618A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 4.231A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 270 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'B' and resid 25 through 52 Proline residue: B 35 - end of helix removed outlier: 3.908A pdb=" N PHE B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 70 through 96 Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.549A pdb=" N LEU B 106 " --> pdb=" O HIS B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 107 through 130 removed outlier: 3.922A pdb=" N GLY B 111 " --> pdb=" O TYR B 107 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 159 removed outlier: 3.723A pdb=" N TYR B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 193 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.249A pdb=" N PHE B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 423 Processing helix chain 'B' and resid 423 through 457 Proline residue: B 436 - end of helix removed outlier: 3.535A pdb=" N TRP B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 3.594A pdb=" N GLU B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Proline residue: B 551 - end of helix removed outlier: 3.554A pdb=" N VAL B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Proline residue: B 589 - end of helix removed outlier: 4.446A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 593 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 783 through 790 Processing helix chain 'B' and resid 796 through 806 Processing helix chain 'B' and resid 808 through 815 removed outlier: 3.579A pdb=" N LEU B 815 " --> pdb=" O ASP B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 846 removed outlier: 3.543A pdb=" N GLN B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 872 Processing helix chain 'B' and resid 893 through 897 removed outlier: 3.652A pdb=" N ALA B 897 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 919 Processing helix chain 'B' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS B1001 " --> pdb=" O PRO B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1039 removed outlier: 3.532A pdb=" N LEU B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B1019 " --> pdb=" O LEU B1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP B1039 " --> pdb=" O ALA B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1107 removed outlier: 3.542A pdb=" N LEU B1107 " --> pdb=" O ASN B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1116 Processing helix chain 'B' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE B1121 " --> pdb=" O PRO B1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1161 Proline residue: B1137 - end of helix removed outlier: 3.577A pdb=" N THR B1161 " --> pdb=" O ILE B1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU B1165 " --> pdb=" O THR B1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B1166 " --> pdb=" O PRO B1162 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 3.539A pdb=" N PHE B1177 " --> pdb=" O VAL B1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1181 " --> pdb=" O PHE B1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B1188 " --> pdb=" O VAL B1184 " (cutoff:3.500A) Proline residue: B1199 - end of helix removed outlier: 3.524A pdb=" N GLY B1210 " --> pdb=" O GLU B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1218 Processing helix chain 'B' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA B1237 " --> pdb=" O SER B1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1242 " --> pdb=" O SER B1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B1260 " --> pdb=" O GLY B1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B1269 " --> pdb=" O ALA B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL B1281 " --> pdb=" O SER B1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B1282 " --> pdb=" O ALA B1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR B1294 " --> pdb=" O MET B1290 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG B1314 " --> pdb=" O GLY B1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B1315 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B1316 " --> pdb=" O VAL B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1384 through 1393 Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1435 through 1441 Processing helix chain 'B' and resid 1447 through 1458 Processing helix chain 'B' and resid 1460 through 1466 Processing helix chain 'B' and resid 1483 through 1499 removed outlier: 3.856A pdb=" N LYS B1499 " --> pdb=" O ALA B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1528 removed outlier: 4.096A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1539 through 1546 removed outlier: 3.674A pdb=" N ILE B1543 " --> pdb=" O ARG B1539 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B1546 " --> pdb=" O THR B1542 " (cutoff:3.500A) Processing helix chain 'B' and resid 1562 through 1570 removed outlier: 4.306A pdb=" N SER B1568 " --> pdb=" O GLU B1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B1570 " --> pdb=" O LEU B1566 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 65 removed outlier: 3.941A pdb=" N THR C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 98 removed outlier: 3.721A pdb=" N GLY C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.642A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.618A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 4.231A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 270 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'D' and resid 25 through 52 Proline residue: D 35 - end of helix removed outlier: 3.908A pdb=" N PHE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 70 through 96 Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.549A pdb=" N LEU D 106 " --> pdb=" O HIS D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 107 through 130 removed outlier: 3.922A pdb=" N GLY D 111 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 159 removed outlier: 3.723A pdb=" N TYR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 193 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 232 through 243 removed outlier: 4.249A pdb=" N PHE D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG D 297 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET D 400 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 Processing helix chain 'D' and resid 423 through 457 Proline residue: D 436 - end of helix removed outlier: 3.535A pdb=" N TRP D 439 " --> pdb=" O CYS D 435 " (cutoff:3.500A) Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Proline residue: D 472 - end of helix removed outlier: 3.594A pdb=" N GLU D 501 " --> pdb=" O LYS D 497 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG D 521 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D 535 " --> pdb=" O THR D 531 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 548 " --> pdb=" O ILE D 544 " (cutoff:3.500A) Proline residue: D 551 - end of helix removed outlier: 3.554A pdb=" N VAL D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA D 576 " --> pdb=" O SER D 572 " (cutoff:3.500A) Proline residue: D 589 - end of helix removed outlier: 4.446A pdb=" N LEU D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 783 through 790 Processing helix chain 'D' and resid 796 through 806 Processing helix chain 'D' and resid 808 through 815 removed outlier: 3.579A pdb=" N LEU D 815 " --> pdb=" O ASP D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 846 removed outlier: 3.543A pdb=" N GLN D 846 " --> pdb=" O ARG D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 872 Processing helix chain 'D' and resid 893 through 897 removed outlier: 3.652A pdb=" N ALA D 897 " --> pdb=" O LEU D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS D1001 " --> pdb=" O PRO D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1009 through 1039 removed outlier: 3.532A pdb=" N LEU D1013 " --> pdb=" O GLY D1009 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER D1014 " --> pdb=" O ILE D1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D1015 " --> pdb=" O LEU D1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D1019 " --> pdb=" O LEU D1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D1031 " --> pdb=" O LEU D1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D1036 " --> pdb=" O TYR D1032 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP D1039 " --> pdb=" O ALA D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1107 removed outlier: 3.542A pdb=" N LEU D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1116 Processing helix chain 'D' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE D1121 " --> pdb=" O PRO D1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1127 through 1161 Proline residue: D1137 - end of helix removed outlier: 3.577A pdb=" N THR D1161 " --> pdb=" O ILE D1157 " (cutoff:3.500A) Processing helix chain 'D' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU D1165 " --> pdb=" O THR D1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D1166 " --> pdb=" O PRO D1162 " (cutoff:3.500A) Proline residue: D1170 - end of helix removed outlier: 3.539A pdb=" N PHE D1177 " --> pdb=" O VAL D1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D1181 " --> pdb=" O PHE D1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D1182 " --> pdb=" O ILE D1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D1185 " --> pdb=" O TYR D1181 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP D1188 " --> pdb=" O VAL D1184 " (cutoff:3.500A) Proline residue: D1199 - end of helix removed outlier: 3.524A pdb=" N GLY D1210 " --> pdb=" O GLU D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1210 through 1218 Processing helix chain 'D' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA D1237 " --> pdb=" O SER D1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D1242 " --> pdb=" O SER D1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D1260 " --> pdb=" O GLY D1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D1269 " --> pdb=" O ALA D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL D1281 " --> pdb=" O SER D1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY D1282 " --> pdb=" O ALA D1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D1283 " --> pdb=" O GLY D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR D1294 " --> pdb=" O MET D1290 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG D1314 " --> pdb=" O GLY D1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE D1315 " --> pdb=" O ALA D1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS D1316 " --> pdb=" O VAL D1312 " (cutoff:3.500A) Processing helix chain 'D' and resid 1384 through 1393 Processing helix chain 'D' and resid 1414 through 1420 Processing helix chain 'D' and resid 1435 through 1441 Processing helix chain 'D' and resid 1447 through 1458 Processing helix chain 'D' and resid 1460 through 1466 Processing helix chain 'D' and resid 1483 through 1499 removed outlier: 3.856A pdb=" N LYS D1499 " --> pdb=" O ALA D1495 " (cutoff:3.500A) Processing helix chain 'D' and resid 1513 through 1528 removed outlier: 4.096A pdb=" N ILE D1519 " --> pdb=" O ALA D1515 " (cutoff:3.500A) Processing helix chain 'D' and resid 1539 through 1546 removed outlier: 3.674A pdb=" N ILE D1543 " --> pdb=" O ARG D1539 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D1546 " --> pdb=" O THR D1542 " (cutoff:3.500A) Processing helix chain 'D' and resid 1562 through 1570 removed outlier: 4.306A pdb=" N SER D1568 " --> pdb=" O GLU D1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS D1570 " --> pdb=" O LEU D1566 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 removed outlier: 3.941A pdb=" N THR E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 98 removed outlier: 3.721A pdb=" N GLY E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 129 removed outlier: 3.642A pdb=" N VAL E 129 " --> pdb=" O ILE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 172 removed outlier: 3.618A pdb=" N ILE E 146 " --> pdb=" O CYS E 142 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 270 removed outlier: 4.231A pdb=" N ASP E 269 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 270 " --> pdb=" O LEU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 356 Processing helix chain 'F' and resid 25 through 52 Proline residue: F 35 - end of helix removed outlier: 3.908A pdb=" N PHE F 44 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 70 through 96 Processing helix chain 'F' and resid 103 through 106 removed outlier: 3.549A pdb=" N LEU F 106 " --> pdb=" O HIS F 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 106' Processing helix chain 'F' and resid 107 through 130 removed outlier: 3.922A pdb=" N GLY F 111 " --> pdb=" O TYR F 107 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 159 removed outlier: 3.723A pdb=" N TYR F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 193 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 232 through 243 removed outlier: 4.249A pdb=" N PHE F 236 " --> pdb=" O TRP F 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN F 262 " --> pdb=" O ARG F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE F 300 " --> pdb=" O GLY F 296 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET F 400 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 402 " --> pdb=" O LYS F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 423 Processing helix chain 'F' and resid 423 through 457 Proline residue: F 436 - end of helix removed outlier: 3.535A pdb=" N TRP F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU F 461 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 471 " --> pdb=" O ILE F 467 " (cutoff:3.500A) Proline residue: F 472 - end of helix removed outlier: 3.594A pdb=" N GLU F 501 " --> pdb=" O LYS F 497 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG F 521 " --> pdb=" O ILE F 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS F 528 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA F 535 " --> pdb=" O THR F 531 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR F 548 " --> pdb=" O ILE F 544 " (cutoff:3.500A) Proline residue: F 551 - end of helix removed outlier: 3.554A pdb=" N VAL F 555 " --> pdb=" O PRO F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA F 576 " --> pdb=" O SER F 572 " (cutoff:3.500A) Proline residue: F 589 - end of helix removed outlier: 4.446A pdb=" N LEU F 592 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 593 " --> pdb=" O PRO F 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 727 Processing helix chain 'F' and resid 783 through 790 Processing helix chain 'F' and resid 796 through 806 Processing helix chain 'F' and resid 808 through 815 removed outlier: 3.579A pdb=" N LEU F 815 " --> pdb=" O ASP F 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 831 through 846 removed outlier: 3.543A pdb=" N GLN F 846 " --> pdb=" O ARG F 842 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 872 Processing helix chain 'F' and resid 893 through 897 removed outlier: 3.652A pdb=" N ALA F 897 " --> pdb=" O LEU F 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 914 through 919 Processing helix chain 'F' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS F1001 " --> pdb=" O PRO F 997 " (cutoff:3.500A) Processing helix chain 'F' and resid 1009 through 1039 removed outlier: 3.532A pdb=" N LEU F1013 " --> pdb=" O GLY F1009 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER F1014 " --> pdb=" O ILE F1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU F1015 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER F1019 " --> pdb=" O LEU F1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP F1031 " --> pdb=" O LEU F1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F1036 " --> pdb=" O TYR F1032 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP F1039 " --> pdb=" O ALA F1035 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1107 removed outlier: 3.542A pdb=" N LEU F1107 " --> pdb=" O ASN F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1109 through 1116 Processing helix chain 'F' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE F1121 " --> pdb=" O PRO F1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE F1125 " --> pdb=" O ILE F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1127 through 1161 Proline residue: F1137 - end of helix removed outlier: 3.577A pdb=" N THR F1161 " --> pdb=" O ILE F1157 " (cutoff:3.500A) Processing helix chain 'F' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU F1165 " --> pdb=" O THR F1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL F1166 " --> pdb=" O PRO F1162 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 3.539A pdb=" N PHE F1177 " --> pdb=" O VAL F1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR F1181 " --> pdb=" O PHE F1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE F1182 " --> pdb=" O ILE F1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA F1185 " --> pdb=" O TYR F1181 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP F1188 " --> pdb=" O VAL F1184 " (cutoff:3.500A) Proline residue: F1199 - end of helix removed outlier: 3.524A pdb=" N GLY F1210 " --> pdb=" O GLU F1206 " (cutoff:3.500A) Processing helix chain 'F' and resid 1210 through 1218 Processing helix chain 'F' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA F1237 " --> pdb=" O SER F1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR F1242 " --> pdb=" O SER F1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F1260 " --> pdb=" O GLY F1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER F1269 " --> pdb=" O ALA F1265 " (cutoff:3.500A) Processing helix chain 'F' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL F1281 " --> pdb=" O SER F1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY F1282 " --> pdb=" O ALA F1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU F1283 " --> pdb=" O GLY F1279 " (cutoff:3.500A) Processing helix chain 'F' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR F1294 " --> pdb=" O MET F1290 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG F1314 " --> pdb=" O GLY F1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F1315 " --> pdb=" O ALA F1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS F1316 " --> pdb=" O VAL F1312 " (cutoff:3.500A) Processing helix chain 'F' and resid 1384 through 1393 Processing helix chain 'F' and resid 1414 through 1420 Processing helix chain 'F' and resid 1435 through 1441 Processing helix chain 'F' and resid 1447 through 1458 Processing helix chain 'F' and resid 1460 through 1466 Processing helix chain 'F' and resid 1483 through 1499 removed outlier: 3.856A pdb=" N LYS F1499 " --> pdb=" O ALA F1495 " (cutoff:3.500A) Processing helix chain 'F' and resid 1513 through 1528 removed outlier: 4.096A pdb=" N ILE F1519 " --> pdb=" O ALA F1515 " (cutoff:3.500A) Processing helix chain 'F' and resid 1539 through 1546 removed outlier: 3.674A pdb=" N ILE F1543 " --> pdb=" O ARG F1539 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F1546 " --> pdb=" O THR F1542 " (cutoff:3.500A) Processing helix chain 'F' and resid 1562 through 1570 removed outlier: 4.306A pdb=" N SER F1568 " --> pdb=" O GLU F1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS F1570 " --> pdb=" O LEU F1566 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 65 removed outlier: 3.941A pdb=" N THR G 62 " --> pdb=" O ASP G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 98 removed outlier: 3.721A pdb=" N GLY G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 129 removed outlier: 3.642A pdb=" N VAL G 129 " --> pdb=" O ILE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 172 removed outlier: 3.618A pdb=" N ILE G 146 " --> pdb=" O CYS G 142 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 270 removed outlier: 4.231A pdb=" N ASP G 269 " --> pdb=" O PRO G 266 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU G 270 " --> pdb=" O LEU G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 356 Processing helix chain 'H' and resid 25 through 52 Proline residue: H 35 - end of helix removed outlier: 3.908A pdb=" N PHE H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 70 through 96 Processing helix chain 'H' and resid 103 through 106 removed outlier: 3.549A pdb=" N LEU H 106 " --> pdb=" O HIS H 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 103 through 106' Processing helix chain 'H' and resid 107 through 130 removed outlier: 3.922A pdb=" N GLY H 111 " --> pdb=" O TYR H 107 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 159 removed outlier: 3.723A pdb=" N TYR H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 193 Processing helix chain 'H' and resid 225 through 230 Processing helix chain 'H' and resid 232 through 243 removed outlier: 4.249A pdb=" N PHE H 236 " --> pdb=" O TRP H 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN H 262 " --> pdb=" O ARG H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE H 300 " --> pdb=" O GLY H 296 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET H 400 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU H 402 " --> pdb=" O LYS H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 423 Processing helix chain 'H' and resid 423 through 457 Proline residue: H 436 - end of helix removed outlier: 3.535A pdb=" N TRP H 439 " --> pdb=" O CYS H 435 " (cutoff:3.500A) Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE H 468 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix removed outlier: 3.594A pdb=" N GLU H 501 " --> pdb=" O LYS H 497 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR H 512 " --> pdb=" O LEU H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG H 521 " --> pdb=" O ILE H 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS H 528 " --> pdb=" O VAL H 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA H 535 " --> pdb=" O THR H 531 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR H 548 " --> pdb=" O ILE H 544 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 3.554A pdb=" N VAL H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA H 576 " --> pdb=" O SER H 572 " (cutoff:3.500A) Proline residue: H 589 - end of helix removed outlier: 4.446A pdb=" N LEU H 592 " --> pdb=" O THR H 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 593 " --> pdb=" O PRO H 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 718 through 727 Processing helix chain 'H' and resid 783 through 790 Processing helix chain 'H' and resid 796 through 806 Processing helix chain 'H' and resid 808 through 815 removed outlier: 3.579A pdb=" N LEU H 815 " --> pdb=" O ASP H 811 " (cutoff:3.500A) Processing helix chain 'H' and resid 831 through 846 removed outlier: 3.543A pdb=" N GLN H 846 " --> pdb=" O ARG H 842 " (cutoff:3.500A) Processing helix chain 'H' and resid 861 through 872 Processing helix chain 'H' and resid 893 through 897 removed outlier: 3.652A pdb=" N ALA H 897 " --> pdb=" O LEU H 894 " (cutoff:3.500A) Processing helix chain 'H' and resid 914 through 919 Processing helix chain 'H' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS H1001 " --> pdb=" O PRO H 997 " (cutoff:3.500A) Processing helix chain 'H' and resid 1009 through 1039 removed outlier: 3.532A pdb=" N LEU H1013 " --> pdb=" O GLY H1009 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER H1014 " --> pdb=" O ILE H1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU H1015 " --> pdb=" O LEU H1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER H1019 " --> pdb=" O LEU H1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP H1031 " --> pdb=" O LEU H1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS H1036 " --> pdb=" O TYR H1032 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP H1039 " --> pdb=" O ALA H1035 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1107 removed outlier: 3.542A pdb=" N LEU H1107 " --> pdb=" O ASN H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1109 through 1116 Processing helix chain 'H' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE H1121 " --> pdb=" O PRO H1117 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE H1125 " --> pdb=" O ILE H1121 " (cutoff:3.500A) Processing helix chain 'H' and resid 1127 through 1161 Proline residue: H1137 - end of helix removed outlier: 3.577A pdb=" N THR H1161 " --> pdb=" O ILE H1157 " (cutoff:3.500A) Processing helix chain 'H' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU H1165 " --> pdb=" O THR H1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL H1166 " --> pdb=" O PRO H1162 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 3.539A pdb=" N PHE H1177 " --> pdb=" O VAL H1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR H1181 " --> pdb=" O PHE H1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE H1182 " --> pdb=" O ILE H1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA H1185 " --> pdb=" O TYR H1181 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP H1188 " --> pdb=" O VAL H1184 " (cutoff:3.500A) Proline residue: H1199 - end of helix removed outlier: 3.524A pdb=" N GLY H1210 " --> pdb=" O GLU H1206 " (cutoff:3.500A) Processing helix chain 'H' and resid 1210 through 1218 Processing helix chain 'H' and resid 1219 through 1271 removed outlier: 3.725A pdb=" N ALA H1237 " --> pdb=" O SER H1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR H1242 " --> pdb=" O SER H1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL H1260 " --> pdb=" O GLY H1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER H1269 " --> pdb=" O ALA H1265 " (cutoff:3.500A) Processing helix chain 'H' and resid 1277 through 1289 removed outlier: 4.572A pdb=" N VAL H1281 " --> pdb=" O SER H1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY H1282 " --> pdb=" O ALA H1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU H1283 " --> pdb=" O GLY H1279 " (cutoff:3.500A) Processing helix chain 'H' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR H1294 " --> pdb=" O MET H1290 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG H1314 " --> pdb=" O GLY H1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE H1315 " --> pdb=" O ALA H1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS H1316 " --> pdb=" O VAL H1312 " (cutoff:3.500A) Processing helix chain 'H' and resid 1384 through 1393 Processing helix chain 'H' and resid 1414 through 1420 Processing helix chain 'H' and resid 1435 through 1441 Processing helix chain 'H' and resid 1447 through 1458 Processing helix chain 'H' and resid 1460 through 1466 Processing helix chain 'H' and resid 1483 through 1499 removed outlier: 3.856A pdb=" N LYS H1499 " --> pdb=" O ALA H1495 " (cutoff:3.500A) Processing helix chain 'H' and resid 1513 through 1528 removed outlier: 4.096A pdb=" N ILE H1519 " --> pdb=" O ALA H1515 " (cutoff:3.500A) Processing helix chain 'H' and resid 1539 through 1546 removed outlier: 3.674A pdb=" N ILE H1543 " --> pdb=" O ARG H1539 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA H1546 " --> pdb=" O THR H1542 " (cutoff:3.500A) Processing helix chain 'H' and resid 1562 through 1570 removed outlier: 4.306A pdb=" N SER H1568 " --> pdb=" O GLU H1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS H1570 " --> pdb=" O LEU H1566 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.698A pdb=" N ALA A 45 " --> pdb=" O TYR C 326 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL C 328 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.539A pdb=" N HIS A 259 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 200 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 238 removed outlier: 4.212A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 213 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A 288 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 215 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 286 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N MET A 217 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 284 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL A 219 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 321 removed outlier: 5.940A pdb=" N TYR A 326 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS G 47 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL A 328 " --> pdb=" O LYS G 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AA8, first strand: chain 'B' and resid 685 through 686 Processing sheet with id=AA9, first strand: chain 'B' and resid 771 through 773 removed outlier: 6.709A pdb=" N ALA B 771 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA B 773 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL B 851 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL B 887 " --> pdb=" O VAL B 851 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 853 " --> pdb=" O VAL B 887 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B 900 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU B 911 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA B 902 " --> pdb=" O GLN B 909 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1365 through 1369 removed outlier: 7.090A pdb=" N ALA B1367 " --> pdb=" O GLN B1348 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN B1348 " --> pdb=" O ALA B1367 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE B1369 " --> pdb=" O GLN B1346 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN B1346 " --> pdb=" O ILE B1369 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE B1347 " --> pdb=" O ILE B1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B1404 " --> pdb=" O ILE B1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN B1349 " --> pdb=" O ARG B1402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG B1402 " --> pdb=" O ASN B1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B1398 " --> pdb=" O ARG B1353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER B1423 " --> pdb=" O ILE B1504 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP B1506 " --> pdb=" O SER B1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B1425 " --> pdb=" O ASP B1506 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B1503 " --> pdb=" O VAL B1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE B1536 " --> pdb=" O PHE B1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET B1505 " --> pdb=" O ILE B1536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET B1550 " --> pdb=" O GLY B1376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.698A pdb=" N ALA C 45 " --> pdb=" O TYR E 326 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL E 328 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 188 through 192 removed outlier: 3.539A pdb=" N HIS C 259 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 200 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 236 through 238 removed outlier: 4.212A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 213 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU C 288 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE C 215 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 286 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N MET C 217 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE C 284 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL C 219 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU C 282 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AB7, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AB8, first strand: chain 'D' and resid 701 through 703 Processing sheet with id=AB9, first strand: chain 'D' and resid 685 through 686 Processing sheet with id=AC1, first strand: chain 'D' and resid 771 through 773 removed outlier: 6.709A pdb=" N ALA D 771 " --> pdb=" O PHE D 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP D 854 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA D 773 " --> pdb=" O ASP D 854 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL D 851 " --> pdb=" O VAL D 885 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL D 887 " --> pdb=" O VAL D 851 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU D 853 " --> pdb=" O VAL D 887 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE D 900 " --> pdb=" O GLU D 911 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU D 911 " --> pdb=" O ILE D 900 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA D 902 " --> pdb=" O GLN D 909 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1365 through 1369 removed outlier: 7.090A pdb=" N ALA D1367 " --> pdb=" O GLN D1348 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN D1348 " --> pdb=" O ALA D1367 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE D1369 " --> pdb=" O GLN D1346 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN D1346 " --> pdb=" O ILE D1369 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE D1347 " --> pdb=" O ILE D1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE D1404 " --> pdb=" O ILE D1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN D1349 " --> pdb=" O ARG D1402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG D1402 " --> pdb=" O ASN D1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D1398 " --> pdb=" O ARG D1353 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER D1423 " --> pdb=" O ILE D1504 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP D1506 " --> pdb=" O SER D1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE D1425 " --> pdb=" O ASP D1506 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE D1503 " --> pdb=" O VAL D1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE D1536 " --> pdb=" O PHE D1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET D1505 " --> pdb=" O ILE D1536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET D1550 " --> pdb=" O GLY D1376 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.698A pdb=" N ALA E 45 " --> pdb=" O TYR G 326 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL G 328 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 188 through 192 removed outlier: 3.539A pdb=" N HIS E 259 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 200 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 236 through 238 removed outlier: 4.212A pdb=" N MET E 217 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA E 213 " --> pdb=" O GLU E 288 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU E 288 " --> pdb=" O ALA E 213 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE E 215 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 286 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N MET E 217 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE E 284 " --> pdb=" O MET E 217 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL E 219 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU E 282 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 223 through 224 Processing sheet with id=AC8, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC9, first strand: chain 'F' and resid 701 through 703 Processing sheet with id=AD1, first strand: chain 'F' and resid 685 through 686 Processing sheet with id=AD2, first strand: chain 'F' and resid 771 through 773 removed outlier: 6.709A pdb=" N ALA F 771 " --> pdb=" O PHE F 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP F 854 " --> pdb=" O ALA F 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA F 773 " --> pdb=" O ASP F 854 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL F 851 " --> pdb=" O VAL F 885 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL F 887 " --> pdb=" O VAL F 851 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU F 853 " --> pdb=" O VAL F 887 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE F 900 " --> pdb=" O GLU F 911 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU F 911 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA F 902 " --> pdb=" O GLN F 909 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 1365 through 1369 removed outlier: 7.090A pdb=" N ALA F1367 " --> pdb=" O GLN F1348 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN F1348 " --> pdb=" O ALA F1367 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE F1369 " --> pdb=" O GLN F1346 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN F1346 " --> pdb=" O ILE F1369 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE F1347 " --> pdb=" O ILE F1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE F1404 " --> pdb=" O ILE F1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN F1349 " --> pdb=" O ARG F1402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG F1402 " --> pdb=" O ASN F1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET F1398 " --> pdb=" O ARG F1353 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER F1423 " --> pdb=" O ILE F1504 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP F1506 " --> pdb=" O SER F1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE F1425 " --> pdb=" O ASP F1506 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE F1503 " --> pdb=" O VAL F1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE F1536 " --> pdb=" O PHE F1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET F1505 " --> pdb=" O ILE F1536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET F1550 " --> pdb=" O GLY F1376 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 188 through 192 removed outlier: 3.539A pdb=" N HIS G 259 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 200 " --> pdb=" O ILE G 257 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 236 through 238 removed outlier: 4.212A pdb=" N MET G 217 " --> pdb=" O ILE G 238 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA G 213 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU G 288 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE G 215 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE G 286 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N MET G 217 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE G 284 " --> pdb=" O MET G 217 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL G 219 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU G 282 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 223 through 224 Processing sheet with id=AD8, first strand: chain 'G' and resid 313 through 315 Processing sheet with id=AD9, first strand: chain 'H' and resid 701 through 703 Processing sheet with id=AE1, first strand: chain 'H' and resid 685 through 686 Processing sheet with id=AE2, first strand: chain 'H' and resid 771 through 773 removed outlier: 6.709A pdb=" N ALA H 771 " --> pdb=" O PHE H 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP H 854 " --> pdb=" O ALA H 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA H 773 " --> pdb=" O ASP H 854 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL H 851 " --> pdb=" O VAL H 885 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL H 887 " --> pdb=" O VAL H 851 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU H 853 " --> pdb=" O VAL H 887 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE H 900 " --> pdb=" O GLU H 911 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU H 911 " --> pdb=" O ILE H 900 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA H 902 " --> pdb=" O GLN H 909 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 1365 through 1369 removed outlier: 7.090A pdb=" N ALA H1367 " --> pdb=" O GLN H1348 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN H1348 " --> pdb=" O ALA H1367 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE H1369 " --> pdb=" O GLN H1346 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN H1346 " --> pdb=" O ILE H1369 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE H1347 " --> pdb=" O ILE H1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE H1404 " --> pdb=" O ILE H1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN H1349 " --> pdb=" O ARG H1402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG H1402 " --> pdb=" O ASN H1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET H1398 " --> pdb=" O ARG H1353 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER H1423 " --> pdb=" O ILE H1504 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP H1506 " --> pdb=" O SER H1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE H1425 " --> pdb=" O ASP H1506 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE H1503 " --> pdb=" O VAL H1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE H1536 " --> pdb=" O PHE H1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET H1505 " --> pdb=" O ILE H1536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET H1550 " --> pdb=" O GLY H1376 " (cutoff:3.500A) 3099 hydrogen bonds defined for protein. 9117 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: 21.02 Time building geometry restraints manager: 14.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 19040 1.38 - 1.56: 32384 1.56 - 1.73: 56 1.73 - 1.90: 436 1.90 - 2.08: 8 Bond restraints: 51924 Sorted by residual: bond pdb=" C4 AGS A 401 " pdb=" C5 AGS A 401 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 AGS G 401 " pdb=" C5 AGS G 401 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 AGS C 401 " pdb=" C5 AGS C 401 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 AGS E 401 " pdb=" C5 AGS E 401 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 AGS H2002 " pdb=" C5 AGS H2002 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.10e+01 ... (remaining 51919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 69540 2.39 - 4.79: 888 4.79 - 7.18: 136 7.18 - 9.57: 48 9.57 - 11.97: 12 Bond angle restraints: 70624 Sorted by residual: angle pdb=" C5 AGS F2002 " pdb=" C4 AGS F2002 " pdb=" N3 AGS F2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS D2002 " pdb=" C4 AGS D2002 " pdb=" N3 AGS D2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS H2002 " pdb=" C4 AGS H2002 " pdb=" N3 AGS H2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS B2002 " pdb=" C4 AGS B2002 " pdb=" N3 AGS B2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS G 401 " pdb=" C4 AGS G 401 " pdb=" N3 AGS G 401 " ideal model delta sigma weight residual 126.80 118.58 8.22 7.41e-01 1.82e+00 1.23e+02 ... (remaining 70619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.39: 29851 30.39 - 60.77: 948 60.77 - 91.16: 32 91.16 - 121.55: 4 121.55 - 151.94: 8 Dihedral angle restraints: 30843 sinusoidal: 11863 harmonic: 18980 Sorted by residual: dihedral pdb=" CA PHE D 295 " pdb=" C PHE D 295 " pdb=" N GLY D 296 " pdb=" CA GLY D 296 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE F 295 " pdb=" C PHE F 295 " pdb=" N GLY F 296 " pdb=" CA GLY F 296 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE B 295 " pdb=" C PHE B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 30840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 7816 0.075 - 0.149: 660 0.149 - 0.224: 40 0.224 - 0.298: 16 0.298 - 0.373: 8 Chirality restraints: 8540 Sorted by residual: chirality pdb=" CA LYS F1444 " pdb=" N LYS F1444 " pdb=" C LYS F1444 " pdb=" CB LYS F1444 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA LYS H1444 " pdb=" N LYS H1444 " pdb=" C LYS H1444 " pdb=" CB LYS H1444 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA LYS D1444 " pdb=" N LYS D1444 " pdb=" C LYS D1444 " pdb=" CB LYS D1444 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 8537 not shown) Planarity restraints: 8640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C25 GBM B2001 " -0.322 2.00e-02 2.50e+03 2.73e-01 9.30e+02 pdb=" C26 GBM B2001 " 0.077 2.00e-02 2.50e+03 pdb=" C27 GBM B2001 " -0.172 2.00e-02 2.50e+03 pdb=" N10 GBM B2001 " 0.479 2.00e-02 2.50e+03 pdb=" O6 GBM B2001 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM H2001 " -0.322 2.00e-02 2.50e+03 2.73e-01 9.30e+02 pdb=" C26 GBM H2001 " 0.077 2.00e-02 2.50e+03 pdb=" C27 GBM H2001 " -0.172 2.00e-02 2.50e+03 pdb=" N10 GBM H2001 " 0.479 2.00e-02 2.50e+03 pdb=" O6 GBM H2001 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM F2001 " 0.322 2.00e-02 2.50e+03 2.73e-01 9.30e+02 pdb=" C26 GBM F2001 " -0.077 2.00e-02 2.50e+03 pdb=" C27 GBM F2001 " 0.172 2.00e-02 2.50e+03 pdb=" N10 GBM F2001 " -0.479 2.00e-02 2.50e+03 pdb=" O6 GBM F2001 " 0.062 2.00e-02 2.50e+03 ... (remaining 8637 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 355 2.60 - 3.18: 45086 3.18 - 3.75: 79622 3.75 - 4.33: 101750 4.33 - 4.90: 168258 Nonbonded interactions: 395071 Sorted by model distance: nonbonded pdb=" SG CYS G 110 " pdb=" SG CYS G 142 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 110 " pdb=" SG CYS C 142 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS E 110 " pdb=" SG CYS E 142 " model vdw 2.031 3.760 nonbonded pdb=" OD2 ASP D1031 " pdb=" OH TYR D1287 " model vdw 2.245 3.040 nonbonded pdb=" OD2 ASP F1031 " pdb=" OH TYR F1287 " model vdw 2.245 3.040 ... (remaining 395066 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' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.040 Extract box with map and model: 1.960 Check model and map are aligned: 0.320 Set scattering table: 0.470 Process input model: 109.920 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 : 0.005 0.162 51924 Z= 0.292 Angle : 0.707 11.965 70624 Z= 0.454 Chirality : 0.045 0.373 8540 Planarity : 0.008 0.273 8640 Dihedral : 13.815 151.936 18496 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.23 % Favored : 95.65 % Rotamer: Outliers : 7.90 % Allowed : 9.08 % Favored : 83.03 % Cbeta Deviations : 0.06 % 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: -2.42 (0.09), residues: 6432 helix: -0.86 (0.07), residues: 3892 sheet: -2.00 (0.19), residues: 540 loop : -2.80 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F1339 HIS 0.004 0.001 HIS G 259 PHE 0.016 0.001 PHE B 305 TYR 0.015 0.001 TYR H 378 ARG 0.002 0.000 ARG D1494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8840 (tmm) REVERT: A 170 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8114 (ptmt) REVERT: A 218 GLN cc_start: 0.9079 (mt0) cc_final: 0.8808 (mp10) REVERT: A 331 SER cc_start: 0.8650 (m) cc_final: 0.8269 (t) REVERT: A 348 GLN cc_start: 0.9363 (mm-40) cc_final: 0.9065 (mm-40) outliers start: 34 outliers final: 4 residues processed: 106 average time/residue: 0.1350 time to fit residues: 16.8420 Evaluate side-chains 50 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.298 Evaluate side-chains 272 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 199 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 TRP cc_start: 0.9179 (m100) cc_final: 0.8875 (m100) REVERT: B 78 THR cc_start: 0.9197 (m) cc_final: 0.8887 (p) REVERT: B 82 LEU cc_start: 0.8809 (tp) cc_final: 0.8518 (tp) REVERT: B 104 LEU cc_start: 0.8260 (mt) cc_final: 0.8022 (tp) REVERT: B 108 MET cc_start: 0.8914 (mmm) cc_final: 0.8669 (mmp) REVERT: B 126 ASN cc_start: 0.8778 (m-40) cc_final: 0.8459 (t0) REVERT: B 137 ILE cc_start: 0.8716 (mt) cc_final: 0.8462 (mt) REVERT: B 140 LEU cc_start: 0.9506 (tp) cc_final: 0.8700 (tt) REVERT: B 156 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7966 (tptt) REVERT: B 223 ASN cc_start: 0.6191 (OUTLIER) cc_final: 0.5872 (m-40) REVERT: B 262 ASN cc_start: 0.7724 (m-40) cc_final: 0.7388 (m110) REVERT: B 374 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8776 (mm-40) REVERT: B 456 LEU cc_start: 0.9130 (mp) cc_final: 0.8430 (tt) REVERT: B 470 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8530 (pp) REVERT: B 530 MET cc_start: 0.8524 (mmt) cc_final: 0.8211 (mmt) REVERT: B 598 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.9104 (tpt90) REVERT: B 869 MET cc_start: 0.7677 (tmm) cc_final: 0.7245 (tpt) REVERT: B 903 MET cc_start: 0.6639 (mmm) cc_final: 0.5632 (mmm) REVERT: B 1031 ASP cc_start: 0.8942 (m-30) cc_final: 0.8535 (p0) REVERT: B 1068 PHE cc_start: 0.7986 (t80) cc_final: 0.7485 (t80) REVERT: B 1114 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8149 (pp20) REVERT: B 1171 LEU cc_start: 0.9048 (mt) cc_final: 0.8668 (pp) REVERT: B 1252 MET cc_start: 0.9178 (ttm) cc_final: 0.8688 (tpt) REVERT: B 1254 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8603 (t80) REVERT: B 1287 TYR cc_start: 0.9044 (m-80) cc_final: 0.8736 (m-10) REVERT: B 1305 MET cc_start: 0.7504 (tpt) cc_final: 0.7142 (mmm) REVERT: B 1514 MET cc_start: 0.7183 (mtm) cc_final: 0.6870 (tpt) outliers start: 73 outliers final: 18 residues processed: 258 average time/residue: 0.2222 time to fit residues: 81.5849 Evaluate side-chains 127 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 3.9990 chunk 491 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 331 optimal weight: 20.0000 chunk 262 optimal weight: 0.4980 chunk 507 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 308 optimal weight: 30.0000 chunk 378 optimal weight: 6.9990 chunk 588 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 186 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 485 GLN F1135 HIS F1225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 51924 Z= 0.237 Angle : 0.723 13.347 70624 Z= 0.366 Chirality : 0.045 0.211 8540 Planarity : 0.005 0.058 8640 Dihedral : 8.998 147.767 7168 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 0.30 % Allowed : 3.62 % Favored : 96.09 % 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: -1.05 (0.10), residues: 6432 helix: 0.29 (0.08), residues: 3932 sheet: -1.66 (0.19), residues: 564 loop : -2.35 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 439 HIS 0.004 0.001 HIS E 46 PHE 0.038 0.002 PHE B1223 TYR 0.020 0.001 TYR B 512 ARG 0.008 0.001 ARG F1498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.8227 (mmp) cc_final: 0.7940 (tmm) REVERT: C 88 MET cc_start: 0.9436 (tpt) cc_final: 0.8960 (tmm) REVERT: C 158 MET cc_start: 0.8289 (mmt) cc_final: 0.7978 (mmm) REVERT: C 163 MET cc_start: 0.8530 (ttp) cc_final: 0.8223 (ppp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1441 time to fit residues: 9.4286 Evaluate side-chains 31 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.239 Evaluate side-chains 119 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 82 LEU cc_start: 0.8712 (tp) cc_final: 0.8390 (tp) REVERT: F 104 LEU cc_start: 0.8293 (mt) cc_final: 0.7849 (tp) REVERT: F 108 MET cc_start: 0.8968 (mmm) cc_final: 0.8339 (mmm) REVERT: F 115 MET cc_start: 0.8809 (mmm) cc_final: 0.8554 (mmp) REVERT: F 126 ASN cc_start: 0.8596 (m-40) cc_final: 0.8387 (t0) REVERT: F 257 MET cc_start: 0.8489 (pmm) cc_final: 0.8227 (mpp) REVERT: F 400 MET cc_start: 0.8401 (mtt) cc_final: 0.8098 (mtt) REVERT: F 456 LEU cc_start: 0.8937 (mp) cc_final: 0.8665 (tp) REVERT: F 530 MET cc_start: 0.8179 (mmt) cc_final: 0.7921 (mmt) REVERT: F 869 MET cc_start: 0.7310 (tmm) cc_final: 0.6999 (tpp) REVERT: F 1031 ASP cc_start: 0.9095 (m-30) cc_final: 0.8750 (p0) REVERT: F 1068 PHE cc_start: 0.7968 (t80) cc_final: 0.7454 (t80) REVERT: F 1252 MET cc_start: 0.9060 (ttm) cc_final: 0.8756 (tpt) REVERT: F 1287 TYR cc_start: 0.9267 (m-80) cc_final: 0.8766 (m-10) REVERT: F 1514 MET cc_start: 0.7245 (mtm) cc_final: 0.6916 (tpt) outliers start: 4 outliers final: 0 residues processed: 119 average time/residue: 0.2026 time to fit residues: 36.3411 Evaluate side-chains 80 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 489 optimal weight: 4.9990 chunk 400 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 589 optimal weight: 4.9990 chunk 636 optimal weight: 4.9990 chunk 525 optimal weight: 0.2980 chunk 584 optimal weight: 0.0000 chunk 200 optimal weight: 8.9990 chunk 472 optimal weight: 0.7980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 247 ASN C 259 HIS C 348 GLN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 219 GLN F 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 51924 Z= 0.384 Angle : 0.931 18.962 70624 Z= 0.480 Chirality : 0.055 0.471 8540 Planarity : 0.008 0.158 8640 Dihedral : 9.066 143.340 7168 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.74 % Allowed : 4.06 % Favored : 95.20 % 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: -1.32 (0.10), residues: 6432 helix: 0.03 (0.08), residues: 3932 sheet: -1.60 (0.19), residues: 556 loop : -2.41 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP D 430 HIS 0.030 0.003 HIS F 241 PHE 0.151 0.005 PHE D 363 TYR 0.050 0.005 TYR E 258 ARG 0.033 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12212 Ramachandran restraints generated. 6106 Oldfield, 0 Emsley, 6106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 MET cc_start: 0.8257 (mmp) cc_final: 0.7902 (tmm) REVERT: C 88 MET cc_start: 0.9430 (tpt) cc_final: 0.9000 (tmm) REVERT: C 91 TRP cc_start: 0.8992 (t60) cc_final: 0.8711 (t-100) REVERT: C 163 MET cc_start: 0.8330 (ttt) cc_final: 0.8077 (ppp) REVERT: C 169 MET cc_start: 0.7163 (mtt) cc_final: 0.6951 (mtt) REVERT: C 350 ASP cc_start: 0.8696 (t0) cc_final: 0.8467 (t0) outliers start: 3 outliers final: 1 residues processed: 49 average time/residue: 0.1290 time to fit residues: 7.7400 Evaluate side-chains 30 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.293 Evaluate side-chains 104 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 82 LEU cc_start: 0.8782 (tp) cc_final: 0.8533 (tp) REVERT: F 104 LEU cc_start: 0.8484 (mt) cc_final: 0.8098 (tp) REVERT: F 108 MET cc_start: 0.8882 (mmm) cc_final: 0.8444 (mmm) REVERT: F 257 MET cc_start: 0.8488 (pmm) cc_final: 0.8039 (mpp) REVERT: F 400 MET cc_start: 0.8389 (mtt) cc_final: 0.8018 (mtt) REVERT: F 429 MET cc_start: 0.8932 (ppp) cc_final: 0.8581 (ppp) REVERT: F 456 LEU cc_start: 0.8974 (mp) cc_final: 0.8567 (tp) REVERT: F 530 MET cc_start: 0.8147 (mmt) cc_final: 0.7918 (mmt) REVERT: F 869 MET cc_start: 0.7449 (tmm) cc_final: 0.7113 (tpp) REVERT: F 1031 ASP cc_start: 0.9001 (m-30) cc_final: 0.8682 (p0) REVERT: F 1068 PHE cc_start: 0.8004 (t80) cc_final: 0.7532 (t80) REVERT: F 1252 MET cc_start: 0.9223 (ttm) cc_final: 0.8905 (tpt) REVERT: F 1287 TYR cc_start: 0.9294 (m-80) cc_final: 0.8787 (m-10) REVERT: F 1514 MET cc_start: 0.7245 (mtm) cc_final: 0.6902 (tpt) REVERT: F 1550 MET cc_start: 0.5814 (ptp) cc_final: 0.5555 (ppp) outliers start: 7 outliers final: 0 residues processed: 102 average time/residue: 0.1945 time to fit residues: 30.5666 Evaluate side-chains 74 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9986 > 50: distance: 0 - 1: 32.626 distance: 0 - 4: 13.268 distance: 2 - 3: 40.545 distance: 4 - 5: 28.833 distance: 5 - 6: 24.721 distance: 5 - 8: 22.892 distance: 6 - 7: 34.312 distance: 6 - 12: 48.844 distance: 8 - 9: 9.397 distance: 9 - 10: 11.284 distance: 9 - 11: 48.629 distance: 12 - 13: 34.860 distance: 13 - 14: 31.146 distance: 13 - 16: 37.773 distance: 14 - 15: 33.388 distance: 14 - 20: 43.130 distance: 16 - 17: 20.949 distance: 16 - 18: 18.731 distance: 17 - 19: 40.419 distance: 20 - 21: 64.063 distance: 21 - 22: 29.916 distance: 21 - 24: 34.457 distance: 22 - 23: 32.139 distance: 22 - 27: 30.810 distance: 24 - 25: 36.569 distance: 24 - 26: 52.119 distance: 27 - 28: 9.684 distance: 28 - 29: 15.908 distance: 28 - 31: 16.266 distance: 29 - 30: 40.324 distance: 29 - 35: 36.013 distance: 31 - 32: 33.494 distance: 31 - 33: 28.499 distance: 32 - 34: 57.236 distance: 35 - 36: 12.005 distance: 36 - 37: 27.850 distance: 36 - 39: 27.694 distance: 37 - 38: 40.376 distance: 37 - 46: 44.737 distance: 39 - 40: 21.264 distance: 40 - 41: 7.382 distance: 41 - 42: 9.148 distance: 42 - 43: 24.338 distance: 43 - 44: 53.381 distance: 43 - 45: 34.565 distance: 46 - 47: 12.807 distance: 47 - 48: 19.322 distance: 47 - 50: 25.457 distance: 48 - 49: 11.259 distance: 48 - 54: 24.736 distance: 50 - 51: 41.924 distance: 50 - 52: 13.352 distance: 51 - 53: 16.051 distance: 54 - 55: 19.763 distance: 54 - 60: 3.049 distance: 55 - 56: 24.800 distance: 55 - 58: 18.474 distance: 56 - 57: 34.998 distance: 56 - 61: 27.533 distance: 58 - 59: 32.268 distance: 59 - 60: 32.361 distance: 61 - 62: 27.032 distance: 62 - 63: 37.572 distance: 62 - 65: 44.323 distance: 63 - 64: 25.669 distance: 63 - 72: 41.412 distance: 65 - 66: 26.976 distance: 66 - 67: 42.897 distance: 67 - 68: 18.428 distance: 68 - 69: 29.804 distance: 69 - 70: 22.338 distance: 69 - 71: 27.252 distance: 72 - 73: 33.883 distance: 73 - 74: 33.568 distance: 74 - 75: 25.970 distance: 74 - 76: 26.056