Starting phenix.real_space_refine on Wed Sep 25 05:04:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/09_2024/6rd9_4810.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/09_2024/6rd9_4810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/09_2024/6rd9_4810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/09_2024/6rd9_4810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/09_2024/6rd9_4810.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd9_4810/09_2024/6rd9_4810.cif" } resolution = 3.0 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= -0.000 sd= 1.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34297 2.51 5 N 9112 2.21 5 O 10199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 408 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 53776 Number of models: 1 Model: "" Number of chains: 41 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 24.60, per 1000 atoms: 0.46 Number of scatterers: 53776 At special positions: 0 Unit cell: (210.6, 132.678, 264.303, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10199 8.00 N 9112 7.00 C 34297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.56 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13086 Finding SS restraints... Secondary structure from input PDB file: 329 helices and 35 sheets defined 57.5% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.688A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 30 removed outlier: 3.623A pdb=" N LEU 0 21 " --> pdb=" O GLY 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 removed outlier: 3.526A pdb=" N ALA 0 49 " --> pdb=" O ALA 0 45 " (cutoff:3.500A) Processing helix chain '0' and resid 51 through 56 removed outlier: 3.793A pdb=" N GLN 0 56 " --> pdb=" O ILE 0 52 " (cutoff:3.500A) Processing helix chain '1' and resid 46 through 71 removed outlier: 3.643A pdb=" N ASN 1 52 " --> pdb=" O ASN 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 83 through 88 Processing helix chain '1' and resid 96 through 100 removed outlier: 3.712A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) Processing helix chain '1' and resid 103 through 105 No H-bonds generated for 'chain '1' and resid 103 through 105' Processing helix chain '1' and resid 106 through 142 removed outlier: 3.874A pdb=" N THR 1 135 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 175 removed outlier: 3.957A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 195 Processing helix chain '1' and resid 197 through 205 removed outlier: 3.537A pdb=" N ALA 1 201 " --> pdb=" O VAL 1 197 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 211 through 224 removed outlier: 3.632A pdb=" N GLU 1 215 " --> pdb=" O SER 1 211 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU 1 217 " --> pdb=" O VAL 1 213 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU 1 221 " --> pdb=" O LEU 1 217 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 244 through 271 removed outlier: 4.032A pdb=" N ARG 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.537A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL 1 277 " --> pdb=" O LEU 1 274 " (cutoff:3.500A) Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 removed outlier: 3.542A pdb=" N ALA 1 303 " --> pdb=" O GLU 1 299 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 317 removed outlier: 3.910A pdb=" N SER 1 317 " --> pdb=" O GLN 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 323 through 327 removed outlier: 3.542A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 362 Processing helix chain '1' and resid 363 through 367 removed outlier: 3.906A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.568A pdb=" N ARG 1 381 " --> pdb=" O SER 1 377 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS 1 386 " --> pdb=" O VAL 1 382 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 400 removed outlier: 3.652A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) Processing helix chain '1' and resid 400 through 421 removed outlier: 4.335A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY 1 421 " --> pdb=" O LYS 1 417 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.941A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 444 Processing helix chain '1' and resid 446 through 460 removed outlier: 3.664A pdb=" N ALA 1 460 " --> pdb=" O LYS 1 456 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 removed outlier: 3.711A pdb=" N TYR 1 468 " --> pdb=" O PRO 1 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR 1 471 " --> pdb=" O ALA 1 467 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN 1 474 " --> pdb=" O VAL 1 470 " (cutoff:3.500A) Processing helix chain '1' and resid 479 through 483 Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 497 Processing helix chain '1' and resid 500 through 515 removed outlier: 3.579A pdb=" N ASP 1 508 " --> pdb=" O ASP 1 504 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU 1 512 " --> pdb=" O ASP 1 508 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 Processing helix chain '1' and resid 541 through 549 removed outlier: 3.505A pdb=" N VAL 1 545 " --> pdb=" O PRO 1 541 " (cutoff:3.500A) Processing helix chain '1' and resid 549 through 562 removed outlier: 3.510A pdb=" N ILE 1 553 " --> pdb=" O ASP 1 549 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU 1 559 " --> pdb=" O LYS 1 555 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 586 Processing helix chain '1' and resid 588 through 591 Processing helix chain '1' and resid 592 through 597 Processing helix chain '1' and resid 597 through 606 removed outlier: 3.646A pdb=" N LYS 1 605 " --> pdb=" O ASP 1 601 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 20 removed outlier: 3.519A pdb=" N LYS 2 13 " --> pdb=" O PRO 2 9 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU 2 14 " --> pdb=" O ALA 2 10 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU 2 18 " --> pdb=" O GLU 2 14 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 39 Processing helix chain '2' and resid 44 through 58 removed outlier: 3.705A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 77 removed outlier: 3.514A pdb=" N THR 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 removed outlier: 3.531A pdb=" N ALA 2 91 " --> pdb=" O LEU 2 87 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER 2 93 " --> pdb=" O GLY 2 89 " (cutoff:3.500A) Processing helix chain '2' and resid 99 through 113 removed outlier: 3.714A pdb=" N SER 2 104 " --> pdb=" O PRO 2 100 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 131 removed outlier: 3.653A pdb=" N VAL 2 128 " --> pdb=" O ALA 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 Processing helix chain '2' and resid 154 through 168 removed outlier: 3.524A pdb=" N ALA 2 158 " --> pdb=" O ASP 2 154 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 198 removed outlier: 3.577A pdb=" N ASP 2 194 " --> pdb=" O LYS 2 190 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 201 No H-bonds generated for 'chain '2' and resid 199 through 201' Processing helix chain '2' and resid 207 through 221 Processing helix chain '2' and resid 227 through 233 Processing helix chain '2' and resid 240 through 255 removed outlier: 3.540A pdb=" N VAL 2 245 " --> pdb=" O PRO 2 241 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY 2 250 " --> pdb=" O GLU 2 246 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER 2 254 " --> pdb=" O GLY 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.703A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 277 through 280 removed outlier: 4.249A pdb=" N LEU 2 280 " --> pdb=" O PRO 2 277 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 277 through 280' Processing helix chain '2' and resid 281 through 295 removed outlier: 3.548A pdb=" N THR 2 293 " --> pdb=" O HIS 2 289 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 305 through 321 removed outlier: 3.685A pdb=" N LYS 2 309 " --> pdb=" O SER 2 305 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 341 removed outlier: 3.573A pdb=" N LEU 2 329 " --> pdb=" O ALA 2 325 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA 2 335 " --> pdb=" O ALA 2 331 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 353 removed outlier: 3.501A pdb=" N SER 2 351 " --> pdb=" O PRO 2 347 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 408 removed outlier: 4.160A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 Processing helix chain '2' and resid 426 through 440 Processing helix chain '3' and resid 78 through 87 Processing helix chain '3' and resid 91 through 99 removed outlier: 3.620A pdb=" N ASN 3 97 " --> pdb=" O GLU 3 93 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 113 removed outlier: 3.701A pdb=" N TRP 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 120 through 128 Processing helix chain '3' and resid 131 through 135 removed outlier: 3.507A pdb=" N LEU 3 135 " --> pdb=" O VAL 3 132 " (cutoff:3.500A) Processing helix chain '3' and resid 136 through 150 Processing helix chain '3' and resid 157 through 166 Processing helix chain '3' and resid 168 through 172 removed outlier: 3.636A pdb=" N PHE 3 172 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) Processing helix chain '3' and resid 173 through 187 removed outlier: 4.003A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA 3 182 " --> pdb=" O LEU 3 178 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 removed outlier: 3.566A pdb=" N SER 3 201 " --> pdb=" O ASP 3 197 " (cutoff:3.500A) Processing helix chain '3' and resid 215 through 229 removed outlier: 3.582A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 removed outlier: 3.533A pdb=" N ALA 3 238 " --> pdb=" O ALA 3 234 " (cutoff:3.500A) Processing helix chain '3' and resid 242 through 244 No H-bonds generated for 'chain '3' and resid 242 through 244' Processing helix chain '3' and resid 245 through 251 Processing helix chain '3' and resid 253 through 272 removed outlier: 3.733A pdb=" N SER 3 263 " --> pdb=" O ASP 3 259 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA 3 267 " --> pdb=" O SER 3 263 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR 3 270 " --> pdb=" O LYS 3 266 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 275 through 279 removed outlier: 3.931A pdb=" N GLU 3 279 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) Processing helix chain '3' and resid 282 through 287 Processing helix chain '3' and resid 288 through 292 removed outlier: 3.752A pdb=" N GLU 3 291 " --> pdb=" O SER 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 312 removed outlier: 3.728A pdb=" N ASN 3 309 " --> pdb=" O VAL 3 305 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA 3 310 " --> pdb=" O ALA 3 306 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 14 removed outlier: 3.525A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 33 Processing helix chain '4' and resid 47 through 68 removed outlier: 4.153A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.829A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 removed outlier: 3.536A pdb=" N LYS 4 107 " --> pdb=" O ILE 4 103 " (cutoff:3.500A) Processing helix chain '4' and resid 118 through 126 removed outlier: 3.653A pdb=" N ASN 4 124 " --> pdb=" O LYS 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 131 through 146 removed outlier: 3.641A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 4.122A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 188 Processing helix chain '4' and resid 196 through 234 removed outlier: 3.747A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA 4 213 " --> pdb=" O SER 4 209 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA 4 224 " --> pdb=" O LYS 4 220 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 258 removed outlier: 3.603A pdb=" N LYS 4 243 " --> pdb=" O ALA 4 239 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.803A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 29 Processing helix chain '5' and resid 29 through 57 removed outlier: 3.873A pdb=" N THR 5 33 " --> pdb=" O GLN 5 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 68 Processing helix chain '5' and resid 72 through 78 Processing helix chain '5' and resid 91 through 107 removed outlier: 4.067A pdb=" N SER 5 97 " --> pdb=" O GLU 5 93 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA 5 98 " --> pdb=" O LYS 5 94 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 5 102 " --> pdb=" O ALA 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 46 through 56 removed outlier: 5.438A pdb=" N LYS 6 52 " --> pdb=" O LEU 6 48 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR 6 53 " --> pdb=" O SER 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 74 through 94 removed outlier: 3.542A pdb=" N TYR 6 88 " --> pdb=" O SER 6 84 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 104 through 118 removed outlier: 3.925A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 130 Processing helix chain '7' and resid 83 through 105 removed outlier: 3.711A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 114 removed outlier: 3.689A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 120 removed outlier: 3.516A pdb=" N TYR 7 120 " --> pdb=" O LYS 7 116 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 145 removed outlier: 3.574A pdb=" N LYS 7 128 " --> pdb=" O PRO 7 124 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR 7 137 " --> pdb=" O ALA 7 133 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 154 Processing helix chain '7' and resid 157 through 165 Processing helix chain '7' and resid 174 through 187 removed outlier: 3.633A pdb=" N ASN 7 184 " --> pdb=" O GLY 7 180 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 removed outlier: 3.520A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 39 Processing helix chain '8' and resid 39 through 78 removed outlier: 3.727A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 16 removed outlier: 3.900A pdb=" N LYS 9 9 " --> pdb=" O SER 9 5 " (cutoff:3.500A) Processing helix chain '9' and resid 36 through 55 removed outlier: 4.170A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 97 removed outlier: 3.637A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 3.907A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.564A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 99 through 126 removed outlier: 3.582A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.921A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 70 through 92 removed outlier: 3.850A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 126 removed outlier: 4.173A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 67 removed outlier: 3.628A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 90 removed outlier: 3.677A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 126 removed outlier: 3.751A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 4.021A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 90 removed outlier: 3.764A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 125 removed outlier: 3.671A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 3.995A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS E 66 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 90 removed outlier: 4.319A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 124 removed outlier: 4.208A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.986A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.145A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY F 79 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 96 Processing helix chain 'F' and resid 99 through 124 removed outlier: 4.105A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE F 124 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.958A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.283A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY G 79 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 124 removed outlier: 3.640A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.787A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.517A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU H 85 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 126 removed outlier: 4.531A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 4.072A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.310A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 119 removed outlier: 3.799A pdb=" N GLY I 101 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 124 Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.818A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 92 removed outlier: 3.872A pdb=" N GLY J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN J 92 " --> pdb=" O GLY J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 126 removed outlier: 3.749A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE J 126 " --> pdb=" O PHE J 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 144 Processing helix chain 'M' and resid 147 through 164 removed outlier: 3.697A pdb=" N THR M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER M 161 " --> pdb=" O CYS M 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 168 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 199 removed outlier: 3.579A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 265 removed outlier: 3.591A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 308 removed outlier: 4.072A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY M 276 " --> pdb=" O PRO M 272 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU M 290 " --> pdb=" O GLY M 286 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL M 293 " --> pdb=" O TYR M 289 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER M 300 " --> pdb=" O SER M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 311 No H-bonds generated for 'chain 'M' and resid 309 through 311' Processing helix chain 'P' and resid 50 through 64 removed outlier: 3.510A pdb=" N THR P 55 " --> pdb=" O ALA P 51 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU P 64 " --> pdb=" O VAL P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 84 removed outlier: 3.563A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 97 through 109 removed outlier: 3.701A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 128 removed outlier: 3.617A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 147 Processing helix chain 'P' and resid 163 through 175 removed outlier: 3.595A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU P 170 " --> pdb=" O GLU P 166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 226 removed outlier: 3.767A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE P 221 " --> pdb=" O GLU P 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL P 226 " --> pdb=" O VAL P 222 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 removed outlier: 3.503A pdb=" N LEU Q 27 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 40 removed outlier: 3.872A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 41 removed outlier: 3.915A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 54 removed outlier: 3.510A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 158 through 168 removed outlier: 3.664A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 194 removed outlier: 3.790A pdb=" N ALA R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 70 removed outlier: 3.538A pdb=" N ILE S 47 " --> pdb=" O VAL S 43 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 76 Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.437A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 128 removed outlier: 3.519A pdb=" N ILE S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 151 removed outlier: 3.814A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 185 removed outlier: 4.452A pdb=" N HIS S 185 " --> pdb=" O GLU S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 216 through 222 removed outlier: 3.725A pdb=" N GLU S 221 " --> pdb=" O GLU S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.700A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA S 268 " --> pdb=" O CYS S 264 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 76 removed outlier: 4.094A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.853A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 191 through 195 Processing helix chain 'T' and resid 206 through 213 removed outlier: 3.580A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.575A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 250 through 253 Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 3.600A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.542A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 352 No H-bonds generated for 'chain 'T' and resid 351 through 352' Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.667A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 415 Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.891A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 430 through 435' Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.757A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 460 removed outlier: 4.438A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA T 460 " --> pdb=" O VAL T 456 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 4.149A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 Processing helix chain 'T' and resid 513 through 515 No H-bonds generated for 'chain 'T' and resid 513 through 515' Processing helix chain 'T' and resid 516 through 528 removed outlier: 3.733A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 540 removed outlier: 3.636A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 552 removed outlier: 4.217A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 46 Processing helix chain 'U' and resid 47 through 49 No H-bonds generated for 'chain 'U' and resid 47 through 49' Processing helix chain 'U' and resid 58 through 63 Processing helix chain 'U' and resid 65 through 72 removed outlier: 3.657A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.774A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.788A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.584A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS U 243 " --> pdb=" O ILE U 239 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 284 removed outlier: 3.519A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.599A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 329 through 341 Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.647A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 400 Processing helix chain 'U' and resid 409 through 415 Processing helix chain 'U' and resid 436 through 460 removed outlier: 3.565A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA U 460 " --> pdb=" O VAL U 456 " (cutoff:3.500A) Processing helix chain 'U' and resid 469 through 485 Processing helix chain 'U' and resid 493 through 506 removed outlier: 3.520A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS U 506 " --> pdb=" O TYR U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.939A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN U 527 " --> pdb=" O ALA U 523 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 540 Processing helix chain 'U' and resid 543 through 554 removed outlier: 3.727A pdb=" N ALA U 548 " --> pdb=" O PRO U 544 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.951A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 134 through 138 removed outlier: 4.054A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.888A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 283 removed outlier: 3.588A pdb=" N ARG V 283 " --> pdb=" O GLY V 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 280 through 283' Processing helix chain 'V' and resid 295 through 301 Processing helix chain 'V' and resid 301 through 316 removed outlier: 3.523A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 341 removed outlier: 3.544A pdb=" N VAL V 332 " --> pdb=" O SER V 328 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.591A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.686A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 415 removed outlier: 3.566A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS V 415 " --> pdb=" O GLU V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 435 removed outlier: 3.973A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 457 removed outlier: 3.887A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 3.543A pdb=" N VAL V 473 " --> pdb=" O ALA V 469 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 3.736A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 517 removed outlier: 3.957A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) Processing helix chain 'V' and resid 519 through 524 Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.624A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 554 removed outlier: 3.794A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.581A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU X 118 " --> pdb=" O ARG X 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 114 through 118' Processing helix chain 'X' and resid 149 through 153 removed outlier: 3.547A pdb=" N GLN X 153 " --> pdb=" O PHE X 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 200 removed outlier: 3.528A pdb=" N ILE X 193 " --> pdb=" O LYS X 189 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 229 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.066A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.672A pdb=" N VAL X 268 " --> pdb=" O THR X 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 299 removed outlier: 3.772A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 removed outlier: 3.549A pdb=" N LEU X 321 " --> pdb=" O ASP X 317 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 345 Processing helix chain 'X' and resid 348 through 355 removed outlier: 3.654A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE X 355 " --> pdb=" O PRO X 351 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 365 through 371 removed outlier: 3.559A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 412 Processing helix chain 'X' and resid 413 through 420 Processing helix chain 'X' and resid 421 through 425 removed outlier: 3.727A pdb=" N GLU X 424 " --> pdb=" O GLY X 421 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 491 through 506 removed outlier: 3.803A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS X 501 " --> pdb=" O GLU X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 528 through 533 removed outlier: 3.879A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 528 through 533' Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 201 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 4.010A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 Processing helix chain 'Y' and resid 287 through 298 removed outlier: 3.812A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL Y 297 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 removed outlier: 3.560A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 345 Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.672A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) Processing helix chain 'Y' and resid 356 through 358 No H-bonds generated for 'chain 'Y' and resid 356 through 358' Processing helix chain 'Y' and resid 365 through 370 Processing helix chain 'Y' and resid 388 through 393 Processing helix chain 'Y' and resid 393 through 418 removed outlier: 4.226A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 443 Processing helix chain 'Y' and resid 462 through 475 Processing helix chain 'Y' and resid 491 through 507 removed outlier: 3.775A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA Y 507 " --> pdb=" O ALA Y 503 " (cutoff:3.500A) Processing helix chain 'Y' and resid 526 through 532 removed outlier: 3.580A pdb=" N LEU Y 530 " --> pdb=" O SER Y 526 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 555 Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 164 through 171 removed outlier: 3.665A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 203 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.147A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 4.477A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 removed outlier: 3.589A pdb=" N PHE Z 290 " --> pdb=" O ASN Z 286 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 removed outlier: 3.859A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 345 Processing helix chain 'Z' and resid 348 through 355 Processing helix chain 'Z' and resid 365 through 370 Processing helix chain 'Z' and resid 393 through 412 removed outlier: 3.816A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 418 removed outlier: 3.747A pdb=" N ALA Z 418 " --> pdb=" O GLN Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 426 through 441 removed outlier: 3.501A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 450 through 455 removed outlier: 3.523A pdb=" N GLY Z 455 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.686A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 486 Processing helix chain 'Z' and resid 495 through 505 removed outlier: 4.177A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) Processing helix chain 'Z' and resid 506 through 509 removed outlier: 3.777A pdb=" N ARG Z 509 " --> pdb=" O ILE Z 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 506 through 509' Processing helix chain 'Z' and resid 526 through 532 removed outlier: 3.888A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain '2' and resid 369 through 372 removed outlier: 7.968A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 314 through 317 removed outlier: 3.644A pdb=" N GLU 3 314 " --> pdb=" O VAL M 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '5' and resid 121 through 123 removed outlier: 3.596A pdb=" N ALA 5 121 " --> pdb=" O VAL 7 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '7' and resid 35 through 41 Processing sheet with id=AA6, first strand: chain '7' and resid 35 through 41 Processing sheet with id=AA7, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.235A pdb=" N VAL P 156 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 61 through 65 removed outlier: 3.520A pdb=" N PHE Q 47 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N VAL S 137 " --> pdb=" O TYR S 158 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU S 160 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL S 139 " --> pdb=" O LEU S 160 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ILE S 162 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N SER S 141 " --> pdb=" O ILE S 162 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER S 100 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL S 140 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL S 102 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE S 142 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA S 104 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS S 99 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN S 191 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL S 101 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU S 193 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL S 103 " --> pdb=" O LEU S 193 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ASN S 195 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N VAL S 105 " --> pdb=" O ASN S 195 " (cutoff:3.500A) removed outlier: 10.583A pdb=" N PHE S 197 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 80 through 82 Processing sheet with id=AB1, first strand: chain 'R' and resid 80 through 82 Processing sheet with id=AB2, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.793A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 85 through 91 removed outlier: 6.641A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 38 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AB4, first strand: chain 'T' and resid 85 through 91 removed outlier: 6.641A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 116 through 122 current: chain 'Y' and resid 62 through 65 removed outlier: 4.671A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 38 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AB5, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'T' and resid 163 through 164 removed outlier: 6.374A pdb=" N THR T 164 " --> pdb=" O SER T 289 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU T 222 " --> pdb=" O ILE T 406 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU T 408 " --> pdb=" O LEU T 222 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE T 224 " --> pdb=" O LEU T 408 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 201 through 202 removed outlier: 4.372A pdb=" N ILE T 215 " --> pdb=" O LEU T 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 116 through 122 removed outlier: 4.243A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AC1, first strand: chain 'U' and resid 163 through 164 removed outlier: 6.342A pdb=" N THR U 164 " --> pdb=" O SER U 289 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 201 through 202 removed outlier: 4.461A pdb=" N ILE U 215 " --> pdb=" O LEU U 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 116 through 122 removed outlier: 3.872A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG Z 86 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N HIS Z 79 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR Z 84 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AC5, first strand: chain 'V' and resid 163 through 164 removed outlier: 6.496A pdb=" N LEU V 222 " --> pdb=" O ILE V 406 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU V 408 " --> pdb=" O LEU V 222 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE V 224 " --> pdb=" O LEU V 408 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 201 through 202 removed outlier: 4.431A pdb=" N ILE V 215 " --> pdb=" O LEU V 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 110 through 113 Processing sheet with id=AC8, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.358A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL X 280 " --> pdb=" O THR X 334 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL X 336 " --> pdb=" O VAL X 280 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU X 282 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ALA X 338 " --> pdb=" O LEU X 282 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL X 284 " --> pdb=" O ALA X 338 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N TYR X 340 " --> pdb=" O VAL X 284 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL X 339 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU X 181 " --> pdb=" O VAL X 339 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS X 178 " --> pdb=" O ALA X 360 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR X 362 " --> pdb=" O LYS X 178 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY X 180 " --> pdb=" O THR X 362 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.215A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AD2, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id=AD3, first strand: chain 'Y' and resid 121 through 122 removed outlier: 3.518A pdb=" N VAL Y 213 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE Y 179 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL Y 339 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU Y 181 " --> pdb=" O VAL Y 339 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.207A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id=AD6, first strand: chain 'Z' and resid 121 through 122 removed outlier: 6.036A pdb=" N MET Z 122 " --> pdb=" O TYR Z 248 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLN Z 250 " --> pdb=" O MET Z 122 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL Z 280 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL Z 336 " --> pdb=" O VAL Z 280 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU Z 282 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA Z 338 " --> pdb=" O LEU Z 282 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL Z 284 " --> pdb=" O ALA Z 338 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS Z 178 " --> pdb=" O ALA Z 360 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR Z 362 " --> pdb=" O LYS Z 178 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY Z 180 " --> pdb=" O THR Z 362 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 159 through 160 removed outlier: 4.304A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 559 through 561 2748 hydrogen bonds defined for protein. 7929 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: 21.94 Time building geometry restraints manager: 11.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11679 1.32 - 1.45: 11563 1.45 - 1.57: 31169 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54686 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.56e+01 bond pdb=" C4 ATP V1000 " pdb=" C5 ATP V1000 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.53e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.06e+01 bond pdb=" C5 ATP U1001 " pdb=" N7 ATP U1001 " ideal model delta sigma weight residual 1.387 1.327 0.060 1.00e-02 1.00e+04 3.64e+01 bond pdb=" C4 ATP V1000 " pdb=" N9 ATP V1000 " ideal model delta sigma weight residual 1.374 1.314 0.060 1.00e-02 1.00e+04 3.57e+01 ... (remaining 54681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 72757 3.31 - 6.61: 1235 6.61 - 9.92: 145 9.92 - 13.22: 20 13.22 - 16.53: 4 Bond angle restraints: 74161 Sorted by residual: angle pdb=" PB ATP V1000 " pdb=" O3B ATP V1000 " pdb=" PG ATP V1000 " ideal model delta sigma weight residual 139.87 123.34 16.53 1.00e+00 1.00e+00 2.73e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 126.36 13.51 1.00e+00 1.00e+00 1.83e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 123.71 13.12 1.00e+00 1.00e+00 1.72e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 124.75 12.08 1.00e+00 1.00e+00 1.46e+02 angle pdb=" PA ATP V1000 " pdb=" O3A ATP V1000 " pdb=" PB ATP V1000 " ideal model delta sigma weight residual 136.83 126.28 10.55 1.00e+00 1.00e+00 1.11e+02 ... (remaining 74156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.43: 32195 32.43 - 64.86: 767 64.86 - 97.29: 60 97.29 - 129.72: 1 129.72 - 162.15: 2 Dihedral angle restraints: 33025 sinusoidal: 12667 harmonic: 20358 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -122.78 -57.22 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -123.40 -56.60 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -124.58 -55.42 0 5.00e+00 4.00e-02 1.23e+02 ... (remaining 33022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 7203 0.088 - 0.177: 1356 0.177 - 0.265: 115 0.265 - 0.354: 11 0.354 - 0.442: 4 Chirality restraints: 8689 Sorted by residual: chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CB VAL T 180 " pdb=" CA VAL T 180 " pdb=" CG1 VAL T 180 " pdb=" CG2 VAL T 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CB VAL U 81 " pdb=" CA VAL U 81 " pdb=" CG1 VAL U 81 " pdb=" CG2 VAL U 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 8686 not shown) Planarity restraints: 9510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.031 2.00e-02 2.50e+03 5.94e-02 3.52e+01 pdb=" C ALA Y 503 " -0.103 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU 5 31 " -0.058 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO 5 32 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO 5 32 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO 5 32 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 307 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ALA Z 307 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA Z 307 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL Z 308 " -0.020 2.00e-02 2.50e+03 ... (remaining 9507 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 281 2.48 - 3.09: 34323 3.09 - 3.69: 84788 3.69 - 4.30: 131125 4.30 - 4.90: 212970 Nonbonded interactions: 463487 Sorted by model distance: nonbonded pdb=" O LYS P 149 " pdb=" N GLU P 151 " model vdw 1.876 3.120 nonbonded pdb=" O LYS Q 56 " pdb=" O ALA Q 57 " model vdw 1.904 3.040 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 1.990 2.170 nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1001 " model vdw 1.992 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.016 2.170 ... (remaining 463482 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1000 through 1001)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 1.730 Check model and map are aligned: 0.400 Set scattering table: 0.710 Process input model: 107.310 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.014 0.143 54686 Z= 0.931 Angle : 1.114 16.530 74161 Z= 0.619 Chirality : 0.069 0.442 8689 Planarity : 0.008 0.086 9510 Dihedral : 14.327 162.148 19939 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.75 % Favored : 95.01 % Rotamer: Outliers : 0.69 % Allowed : 6.70 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.13 (0.07), residues: 7038 helix: -4.32 (0.04), residues: 3851 sheet: -1.38 (0.19), residues: 657 loop : -1.98 (0.11), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP R 37 HIS 0.017 0.003 HIS Y 79 PHE 0.042 0.003 PHE R 74 TYR 0.027 0.003 TYR 4 211 ARG 0.019 0.001 ARG 3 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 826 time to evaluate : 4.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7017 (pm20) REVERT: 0 46 GLU cc_start: 0.8527 (tt0) cc_final: 0.8297 (tt0) REVERT: 1 143 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7969 (mttm) REVERT: 1 181 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7735 (tppt) REVERT: 1 572 ASP cc_start: 0.8219 (m-30) cc_final: 0.7848 (m-30) REVERT: 4 13 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8738 (m-80) REVERT: 4 194 ASP cc_start: 0.8059 (m-30) cc_final: 0.7858 (m-30) REVERT: 4 198 LYS cc_start: 0.8773 (mptt) cc_final: 0.8434 (mmmt) REVERT: 4 214 ASP cc_start: 0.8032 (m-30) cc_final: 0.7800 (m-30) REVERT: 5 11 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8068 (mt-10) REVERT: 7 135 ASP cc_start: 0.8300 (m-30) cc_final: 0.8063 (m-30) REVERT: 9 9 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7556 (tttm) REVERT: 9 80 GLN cc_start: 0.8733 (tp40) cc_final: 0.8487 (tp40) REVERT: A 81 MET cc_start: 0.8611 (ttp) cc_final: 0.8364 (ttm) REVERT: A 119 LEU cc_start: 0.7606 (mp) cc_final: 0.7396 (tt) REVERT: B 84 SER cc_start: 0.8238 (m) cc_final: 0.7975 (p) REVERT: F 81 MET cc_start: 0.8337 (ttp) cc_final: 0.8118 (ttp) REVERT: G 81 MET cc_start: 0.7898 (ttp) cc_final: 0.7630 (ttp) REVERT: G 115 LEU cc_start: 0.6953 (pp) cc_final: 0.6630 (mt) REVERT: J 81 MET cc_start: 0.8576 (ttp) cc_final: 0.7962 (ttp) REVERT: J 84 SER cc_start: 0.8359 (m) cc_final: 0.7774 (p) REVERT: P 145 MET cc_start: 0.8649 (mmm) cc_final: 0.8299 (mmm) REVERT: Q 18 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8179 (tpp80) REVERT: Q 40 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7660 (tp-100) REVERT: Q 48 ARG cc_start: 0.7845 (ptt180) cc_final: 0.7611 (ptt-90) REVERT: Q 49 GLN cc_start: 0.8339 (pt0) cc_final: 0.8092 (pt0) REVERT: Q 52 TYR cc_start: 0.6425 (m-80) cc_final: 0.6103 (m-10) REVERT: R 126 LYS cc_start: 0.7905 (mttm) cc_final: 0.7683 (mttp) REVERT: R 127 PHE cc_start: 0.8067 (m-80) cc_final: 0.7673 (m-80) REVERT: S 62 MET cc_start: 0.7379 (ptp) cc_final: 0.7006 (ptt) REVERT: S 186 ASN cc_start: 0.8074 (p0) cc_final: 0.7739 (p0) REVERT: S 206 THR cc_start: 0.8207 (m) cc_final: 0.7945 (p) REVERT: S 218 LYS cc_start: 0.7469 (tmtt) cc_final: 0.7245 (tptp) REVERT: S 229 ASP cc_start: 0.7304 (m-30) cc_final: 0.6927 (m-30) REVERT: S 234 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7959 (tm-30) REVERT: S 244 ARG cc_start: 0.8097 (tpp-160) cc_final: 0.7742 (ttp-110) REVERT: T 101 LYS cc_start: 0.8208 (tptt) cc_final: 0.7969 (mmmt) REVERT: T 199 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7220 (ptp90) REVERT: T 487 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7668 (ttmt) REVERT: T 496 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7678 (mtt90) REVERT: T 556 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7339 (mtmm) REVERT: U 71 LYS cc_start: 0.8492 (tppt) cc_final: 0.8145 (tppp) REVERT: U 75 LYS cc_start: 0.8298 (mtmt) cc_final: 0.8017 (mmpt) REVERT: U 96 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7902 (mtm-85) REVERT: U 149 GLN cc_start: 0.7857 (mt0) cc_final: 0.7345 (mm110) REVERT: U 200 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7610 (mt-10) REVERT: U 326 ASP cc_start: 0.7990 (m-30) cc_final: 0.7600 (m-30) REVERT: U 474 LEU cc_start: 0.8207 (mp) cc_final: 0.7961 (mm) REVERT: U 511 LYS cc_start: 0.8152 (mmmm) cc_final: 0.7905 (mmpt) REVERT: U 550 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8277 (tm) REVERT: V 50 LYS cc_start: 0.8477 (ttmt) cc_final: 0.7971 (tmmt) REVERT: V 61 HIS cc_start: 0.8042 (t70) cc_final: 0.7497 (m170) REVERT: V 283 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.7582 (ttt90) REVERT: V 515 GLN cc_start: 0.7190 (pp30) cc_final: 0.6882 (tm130) REVERT: V 534 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8282 (mtpm) REVERT: X 131 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8061 (mt-10) REVERT: X 215 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6930 (mm-30) REVERT: X 227 MET cc_start: 0.8172 (mtt) cc_final: 0.7970 (mtt) REVERT: X 415 ASP cc_start: 0.8151 (t70) cc_final: 0.7888 (t0) REVERT: X 448 GLN cc_start: 0.7837 (mt0) cc_final: 0.7533 (mp10) REVERT: X 550 LYS cc_start: 0.8046 (ptpp) cc_final: 0.7450 (pptt) REVERT: X 573 LYS cc_start: 0.7732 (mtmt) cc_final: 0.7414 (mmmt) REVERT: Y 251 MET cc_start: 0.8762 (mtm) cc_final: 0.8513 (mtt) REVERT: Y 359 ASP cc_start: 0.8069 (m-30) cc_final: 0.7790 (m-30) REVERT: Y 427 GLU cc_start: 0.6094 (mt-10) cc_final: 0.5857 (mp0) REVERT: Y 437 ARG cc_start: 0.7458 (mtt-85) cc_final: 0.7024 (mtp85) REVERT: Y 441 ARG cc_start: 0.7847 (mmt-90) cc_final: 0.7516 (mmt90) REVERT: Y 497 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6484 (mt-10) REVERT: Y 539 ILE cc_start: 0.7089 (pt) cc_final: 0.6759 (mt) REVERT: Y 547 GLU cc_start: 0.7191 (mp0) cc_final: 0.6967 (mp0) REVERT: Z 88 ILE cc_start: 0.9060 (tp) cc_final: 0.8774 (tp) REVERT: Z 292 GLN cc_start: 0.7917 (tt0) cc_final: 0.7582 (tt0) REVERT: Z 411 LYS cc_start: 0.8741 (mttp) cc_final: 0.8187 (tmmt) REVERT: Z 427 GLU cc_start: 0.7395 (tp30) cc_final: 0.7115 (pp20) REVERT: Z 441 ARG cc_start: 0.7557 (mmt-90) cc_final: 0.7167 (mmt-90) REVERT: Z 484 MET cc_start: 0.6921 (mmm) cc_final: 0.6370 (tmt) REVERT: Z 566 LYS cc_start: 0.8257 (tttm) cc_final: 0.7908 (tptp) outliers start: 39 outliers final: 21 residues processed: 855 average time/residue: 1.5110 time to fit residues: 1605.8768 Evaluate side-chains 611 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 588 time to evaluate : 4.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 5 residue 32 PRO Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 406 VAL Chi-restraints excluded: chain Y residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 7.9990 chunk 529 optimal weight: 7.9990 chunk 293 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 356 optimal weight: 0.8980 chunk 282 optimal weight: 0.0770 chunk 547 optimal weight: 0.5980 chunk 211 optimal weight: 0.8980 chunk 332 optimal weight: 0.9990 chunk 407 optimal weight: 0.9980 chunk 633 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 1 100 GLN 1 257 HIS 1 298 GLN 1 316 ASN 1 346 GLN 1 365 GLN 1 482 ASN 1 527 GLN 1 562 ASN 1 587 ASN 1 590 HIS 2 74 ASN 2 122 ASN 2 243 GLN 2 289 HIS ** 2 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 179 GLN 3 206 ASN 3 229 ASN 3 269 GLN 4 240 GLN 5 29 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 40 ASN 6 74 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 86 HIS 7 98 ASN 7 123 HIS 7 170 HIS 7 184 ASN 8 26 HIS 8 78 HIS 9 35 GLN A 94 ASN C 98 GLN D 94 ASN D 98 GLN G 87 ASN G 94 ASN H 94 ASN J 98 GLN M 108 ASN M 131 ASN M 163 ASN P 223 ASN Q 46 HIS R 73 ASN R 104 HIS R 137 HIS ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN S 96 ASN ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 GLN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 64 GLN T 104 GLN T 241 HIS T 264 GLN T 386 GLN T 405 GLN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 61 HIS U 121 ASN U 196 GLN U 246 ASN U 248 GLN U 264 GLN U 319 HIS U 386 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN U 539 ASN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS V 152 ASN V 244 ASN V 264 GLN V 278 GLN ** V 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN V 497 GLN V 529 ASN X 199 ASN X 278 GLN X 311 GLN X 337 GLN X 396 HIS X 408 GLN X 471 GLN Y 174 GLN Y 241 ASN Y 448 GLN Z 144 HIS Z 198 ASN Z 199 ASN Z 241 ASN Z 278 GLN Z 286 ASN Z 294 ASN Z 337 GLN Z 574 ASN Total number of N/Q/H flips: 95 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54686 Z= 0.199 Angle : 0.621 10.157 74161 Z= 0.327 Chirality : 0.043 0.159 8689 Planarity : 0.006 0.067 9510 Dihedral : 7.412 157.030 7700 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.17 % Favored : 96.68 % Rotamer: Outliers : 2.29 % Allowed : 11.69 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.79 (0.09), residues: 7038 helix: -2.06 (0.07), residues: 3875 sheet: -1.18 (0.20), residues: 630 loop : -1.32 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 4 206 HIS 0.018 0.001 HIS 8 78 PHE 0.024 0.001 PHE G 107 TYR 0.023 0.001 TYR 4 211 ARG 0.010 0.001 ARG P 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 731 time to evaluate : 4.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7025 (pm20) REVERT: 1 143 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7838 (mttm) REVERT: 1 181 LYS cc_start: 0.8031 (mmtp) cc_final: 0.7616 (tppt) REVERT: 1 347 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8206 (tppt) REVERT: 1 352 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7365 (mm-30) REVERT: 1 572 ASP cc_start: 0.8201 (m-30) cc_final: 0.7826 (m-30) REVERT: 2 13 LYS cc_start: 0.7686 (mtpm) cc_final: 0.7270 (ptmm) REVERT: 3 185 ASP cc_start: 0.8250 (t70) cc_final: 0.7896 (t70) REVERT: 3 274 TYR cc_start: 0.8410 (m-80) cc_final: 0.8173 (m-80) REVERT: 4 13 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: 4 156 ASP cc_start: 0.7232 (t70) cc_final: 0.6978 (t0) REVERT: 4 198 LYS cc_start: 0.8753 (mptt) cc_final: 0.8483 (mmmt) REVERT: 5 11 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8073 (mt-10) REVERT: 7 47 GLU cc_start: 0.7039 (pm20) cc_final: 0.6723 (mp0) REVERT: 9 9 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7232 (pttm) REVERT: 9 80 GLN cc_start: 0.8654 (tp40) cc_final: 0.8388 (tp40) REVERT: C 97 LYS cc_start: 0.8407 (mptt) cc_final: 0.8183 (mmpt) REVERT: E 60 LYS cc_start: 0.7959 (mtmt) cc_final: 0.7744 (mttm) REVERT: E 81 MET cc_start: 0.7674 (ttp) cc_final: 0.7419 (ttm) REVERT: E 115 LEU cc_start: 0.7156 (pp) cc_final: 0.6778 (mm) REVERT: G 95 ILE cc_start: 0.7883 (mm) cc_final: 0.7672 (mm) REVERT: H 61 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8052 (mpp) REVERT: H 109 LEU cc_start: 0.7845 (mm) cc_final: 0.7613 (mt) REVERT: J 81 MET cc_start: 0.8177 (ttp) cc_final: 0.7675 (ttp) REVERT: M 232 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7158 (mtp180) REVERT: P 99 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7852 (tp) REVERT: P 145 MET cc_start: 0.8419 (mmm) cc_final: 0.8206 (mmm) REVERT: P 151 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7223 (tm-30) REVERT: P 175 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: Q 40 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7415 (tp-100) REVERT: Q 42 ARG cc_start: 0.7888 (ptp90) cc_final: 0.7606 (ptp90) REVERT: Q 49 GLN cc_start: 0.8199 (pt0) cc_final: 0.7928 (pt0) REVERT: Q 52 TYR cc_start: 0.6258 (m-80) cc_final: 0.5724 (m-10) REVERT: R 86 LYS cc_start: 0.7738 (mptp) cc_final: 0.7518 (mmtm) REVERT: R 127 PHE cc_start: 0.7959 (m-80) cc_final: 0.7609 (m-80) REVERT: S 48 ARG cc_start: 0.6955 (tpp-160) cc_final: 0.6272 (ttm110) REVERT: S 62 MET cc_start: 0.7469 (ptp) cc_final: 0.7153 (mtp) REVERT: S 68 MET cc_start: 0.7876 (ttp) cc_final: 0.7577 (ttp) REVERT: S 206 THR cc_start: 0.7933 (m) cc_final: 0.7643 (p) REVERT: S 229 ASP cc_start: 0.7442 (m-30) cc_final: 0.7022 (m-30) REVERT: S 234 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7755 (tm-30) REVERT: S 244 ARG cc_start: 0.8035 (tpp-160) cc_final: 0.7551 (ttp-110) REVERT: T 72 GLU cc_start: 0.6960 (tp30) cc_final: 0.6695 (tp30) REVERT: T 199 ARG cc_start: 0.7598 (mmm160) cc_final: 0.7251 (ptp90) REVERT: T 237 ASP cc_start: 0.7682 (m-30) cc_final: 0.7357 (m-30) REVERT: T 447 LYS cc_start: 0.7697 (mtpm) cc_final: 0.7362 (tppt) REVERT: T 471 GLN cc_start: 0.7367 (tm-30) cc_final: 0.7075 (tm-30) REVERT: T 487 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7642 (ttmt) REVERT: T 496 ARG cc_start: 0.7609 (mtt-85) cc_final: 0.7295 (mtt90) REVERT: T 509 LEU cc_start: 0.8157 (mp) cc_final: 0.7941 (mm) REVERT: T 522 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7175 (tp30) REVERT: T 551 LYS cc_start: 0.7669 (ptpp) cc_final: 0.6978 (pttp) REVERT: T 553 GLU cc_start: 0.7534 (tp30) cc_final: 0.7296 (tp30) REVERT: U 71 LYS cc_start: 0.8531 (tppt) cc_final: 0.8157 (tppp) REVERT: U 75 LYS cc_start: 0.8150 (mtmt) cc_final: 0.7914 (mmpt) REVERT: U 84 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8803 (mp) REVERT: U 149 GLN cc_start: 0.7659 (mt0) cc_final: 0.7206 (mm110) REVERT: U 511 LYS cc_start: 0.7894 (mmmm) cc_final: 0.7692 (mmpt) REVERT: U 522 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: U 550 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8133 (tm) REVERT: V 50 LYS cc_start: 0.8409 (ttmt) cc_final: 0.7911 (tmmt) REVERT: V 61 HIS cc_start: 0.8019 (t70) cc_final: 0.7671 (m-70) REVERT: V 278 GLN cc_start: 0.7872 (mt0) cc_final: 0.7523 (mm-40) REVERT: V 370 LYS cc_start: 0.8453 (tppt) cc_final: 0.8232 (mptt) REVERT: V 535 ILE cc_start: 0.8510 (mm) cc_final: 0.8074 (mp) REVERT: V 539 ASN cc_start: 0.8602 (m-40) cc_final: 0.8311 (m-40) REVERT: X 359 ASP cc_start: 0.7877 (m-30) cc_final: 0.7648 (m-30) REVERT: X 385 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7110 (tpt90) REVERT: X 471 GLN cc_start: 0.7683 (tt0) cc_final: 0.7388 (tt0) REVERT: X 550 LYS cc_start: 0.8111 (ptpp) cc_final: 0.7571 (pptt) REVERT: Y 359 ASP cc_start: 0.7895 (m-30) cc_final: 0.7557 (m-30) REVERT: Y 411 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7962 (ttpt) REVERT: Y 414 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: Y 437 ARG cc_start: 0.6848 (mtt-85) cc_final: 0.6355 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7471 (mmt-90) cc_final: 0.7166 (mmt90) REVERT: Y 497 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6301 (tt0) REVERT: Y 539 ILE cc_start: 0.7305 (pt) cc_final: 0.6955 (mm) REVERT: Z 82 ASP cc_start: 0.7567 (t0) cc_final: 0.7014 (t0) REVERT: Z 88 ILE cc_start: 0.8922 (tp) cc_final: 0.8712 (pt) REVERT: Z 292 GLN cc_start: 0.7618 (tt0) cc_final: 0.7230 (tt0) REVERT: Z 411 LYS cc_start: 0.8326 (mttp) cc_final: 0.8125 (tmmt) REVERT: Z 427 GLU cc_start: 0.7417 (tp30) cc_final: 0.7169 (pp20) REVERT: Z 437 ARG cc_start: 0.7929 (mtp85) cc_final: 0.7636 (mmm160) REVERT: Z 566 LYS cc_start: 0.8264 (tttm) cc_final: 0.8007 (mppt) outliers start: 129 outliers final: 40 residues processed: 819 average time/residue: 1.3871 time to fit residues: 1434.1346 Evaluate side-chains 662 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 611 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 347 LYS Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 232 ARG Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 149 LYS Chi-restraints excluded: chain P residue 175 GLU Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 517 ILE Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 517 ILE Chi-restraints excluded: chain V residue 529 ASN Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 385 ARG Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 532 SER Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 568 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 527 optimal weight: 0.8980 chunk 431 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 635 optimal weight: 0.0470 chunk 685 optimal weight: 2.9990 chunk 565 optimal weight: 0.8980 chunk 629 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 509 optimal weight: 3.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 2 427 GLN 5 59 ASN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 27 ASN 9 35 GLN F 98 GLN H 92 ASN J 92 ASN P 140 ASN R 38 ASN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 HIS T 405 GLN ** T 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 152 ASN U 196 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 152 ASN V 486 GLN X 204 HIS Y 448 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 337 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54686 Z= 0.191 Angle : 0.569 13.146 74161 Z= 0.295 Chirality : 0.042 0.159 8689 Planarity : 0.004 0.056 9510 Dihedral : 6.829 147.152 7687 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.51 % Favored : 96.38 % Rotamer: Outliers : 2.36 % Allowed : 13.78 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.37 (0.10), residues: 7038 helix: -0.68 (0.08), residues: 3863 sheet: -0.97 (0.21), residues: 632 loop : -0.98 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 9 73 HIS 0.006 0.001 HIS 4 233 PHE 0.029 0.001 PHE H 107 TYR 0.023 0.001 TYR 4 211 ARG 0.011 0.000 ARG P 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 656 time to evaluate : 4.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7055 (pm20) REVERT: 1 352 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7373 (mm-30) REVERT: 1 452 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7721 (tm-30) REVERT: 1 499 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: 1 572 ASP cc_start: 0.8193 (m-30) cc_final: 0.7859 (m-30) REVERT: 2 13 LYS cc_start: 0.7714 (mtpm) cc_final: 0.7323 (ptmm) REVERT: 2 226 LYS cc_start: 0.8215 (tptt) cc_final: 0.7846 (tptp) REVERT: 2 345 TYR cc_start: 0.7966 (m-80) cc_final: 0.7760 (m-80) REVERT: 4 13 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: 4 198 LYS cc_start: 0.8774 (mptt) cc_final: 0.8479 (mmmt) REVERT: 4 214 ASP cc_start: 0.7668 (m-30) cc_final: 0.7422 (m-30) REVERT: 5 11 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8040 (mt-10) REVERT: 7 47 GLU cc_start: 0.6971 (pm20) cc_final: 0.6651 (mp0) REVERT: 9 13 LYS cc_start: 0.7305 (pttt) cc_final: 0.7063 (pttt) REVERT: 9 80 GLN cc_start: 0.8638 (tp40) cc_final: 0.8385 (tp40) REVERT: B 92 ASN cc_start: 0.7348 (p0) cc_final: 0.6932 (p0) REVERT: C 97 LYS cc_start: 0.8277 (mptt) cc_final: 0.8063 (mmpt) REVERT: E 62 VAL cc_start: 0.8254 (p) cc_final: 0.8026 (p) REVERT: E 81 MET cc_start: 0.7719 (ttp) cc_final: 0.7440 (ttm) REVERT: E 115 LEU cc_start: 0.7212 (pp) cc_final: 0.6887 (mm) REVERT: H 85 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7724 (tp) REVERT: J 81 MET cc_start: 0.8230 (ttp) cc_final: 0.7668 (ttp) REVERT: P 99 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7880 (tp) REVERT: P 151 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7145 (tm-30) REVERT: P 175 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: Q 18 ARG cc_start: 0.8182 (ttt-90) cc_final: 0.7860 (tpp80) REVERT: Q 40 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7447 (tp-100) REVERT: Q 49 GLN cc_start: 0.8199 (pt0) cc_final: 0.7967 (pt0) REVERT: Q 52 TYR cc_start: 0.6309 (m-80) cc_final: 0.5810 (m-10) REVERT: R 127 PHE cc_start: 0.7785 (m-80) cc_final: 0.7495 (m-80) REVERT: S 48 ARG cc_start: 0.6801 (tpp-160) cc_final: 0.6360 (ttm110) REVERT: S 62 MET cc_start: 0.7305 (ptp) cc_final: 0.7033 (mtp) REVERT: S 169 ARG cc_start: 0.7742 (ptm160) cc_final: 0.7417 (ptm160) REVERT: S 229 ASP cc_start: 0.7503 (m-30) cc_final: 0.7085 (m-30) REVERT: S 234 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7664 (tm-30) REVERT: S 244 ARG cc_start: 0.7993 (tpp-160) cc_final: 0.7457 (ttp-110) REVERT: S 283 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7070 (mp0) REVERT: T 72 GLU cc_start: 0.6961 (tp30) cc_final: 0.6635 (tp30) REVERT: T 199 ARG cc_start: 0.7639 (mmm160) cc_final: 0.7224 (ptp90) REVERT: T 237 ASP cc_start: 0.7644 (m-30) cc_final: 0.7319 (m-30) REVERT: T 447 LYS cc_start: 0.7588 (mtpm) cc_final: 0.7210 (tppt) REVERT: T 471 GLN cc_start: 0.7290 (tm-30) cc_final: 0.7039 (tm-30) REVERT: T 487 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7656 (ttmt) REVERT: T 496 ARG cc_start: 0.7580 (mtt-85) cc_final: 0.7330 (mtt90) REVERT: T 522 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7132 (tp30) REVERT: T 535 ILE cc_start: 0.8384 (mt) cc_final: 0.8164 (mp) REVERT: T 551 LYS cc_start: 0.7722 (ptpp) cc_final: 0.7238 (pttp) REVERT: T 553 GLU cc_start: 0.7495 (tp30) cc_final: 0.7266 (tp30) REVERT: U 71 LYS cc_start: 0.8541 (tppt) cc_final: 0.8310 (tppt) REVERT: U 75 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7911 (mmpt) REVERT: U 84 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8850 (mp) REVERT: U 149 GLN cc_start: 0.7646 (mt0) cc_final: 0.7063 (mm110) REVERT: U 427 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8124 (m) REVERT: U 522 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: U 553 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7842 (mm-30) REVERT: V 50 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7865 (tmmt) REVERT: V 253 GLN cc_start: 0.8333 (mp10) cc_final: 0.7965 (mt0) REVERT: V 278 GLN cc_start: 0.7748 (mt0) cc_final: 0.7480 (mm-40) REVERT: V 449 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: V 535 ILE cc_start: 0.8440 (mm) cc_final: 0.8196 (mp) REVERT: V 539 ASN cc_start: 0.8595 (m-40) cc_final: 0.8301 (m-40) REVERT: X 471 GLN cc_start: 0.7707 (tt0) cc_final: 0.7427 (tt0) REVERT: X 550 LYS cc_start: 0.8046 (ptpp) cc_final: 0.7520 (pptt) REVERT: Y 140 ILE cc_start: 0.8823 (pt) cc_final: 0.8431 (pp) REVERT: Y 359 ASP cc_start: 0.7909 (m-30) cc_final: 0.7540 (m-30) REVERT: Y 385 ARG cc_start: 0.7795 (mmt90) cc_final: 0.7263 (mmm-85) REVERT: Y 414 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7245 (mt0) REVERT: Y 430 LYS cc_start: 0.6184 (mtmm) cc_final: 0.5964 (mtmm) REVERT: Y 437 ARG cc_start: 0.6857 (mtt-85) cc_final: 0.6378 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7461 (mmt-90) cc_final: 0.7186 (mmt90) REVERT: Y 497 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6307 (mt-10) REVERT: Y 533 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7142 (pm20) REVERT: Y 539 ILE cc_start: 0.7281 (pt) cc_final: 0.7028 (mm) REVERT: Z 82 ASP cc_start: 0.7498 (t0) cc_final: 0.6964 (t0) REVERT: Z 292 GLN cc_start: 0.7569 (tt0) cc_final: 0.7193 (tt0) REVERT: Z 337 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8938 (mt0) REVERT: Z 427 GLU cc_start: 0.7450 (tp30) cc_final: 0.7190 (pp20) REVERT: Z 437 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7543 (mmm160) REVERT: Z 566 LYS cc_start: 0.8251 (tttm) cc_final: 0.7978 (mppt) outliers start: 133 outliers final: 49 residues processed: 739 average time/residue: 1.4127 time to fit residues: 1322.3783 Evaluate side-chains 641 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 580 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 9 residue 35 GLN Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 175 GLU Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 427 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 533 GLU Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 568 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 2.9990 chunk 477 optimal weight: 9.9990 chunk 329 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 303 optimal weight: 0.5980 chunk 426 optimal weight: 6.9990 chunk 637 optimal weight: 8.9990 chunk 674 optimal weight: 0.9990 chunk 332 optimal weight: 3.9990 chunk 603 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 5 59 ASN 5 107 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 27 ASN 9 35 GLN A 98 GLN F 98 GLN J 92 ASN P 140 ASN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 185 HIS T 441 GLN ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN U 152 ASN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 152 ASN V 471 GLN V 529 ASN Y 322 GLN Y 448 GLN Z 286 ASN Z 337 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 54686 Z= 0.252 Angle : 0.578 15.141 74161 Z= 0.297 Chirality : 0.043 0.179 8689 Planarity : 0.004 0.062 9510 Dihedral : 6.660 134.733 7686 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.33 % Rotamer: Outliers : 2.89 % Allowed : 14.78 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.10), residues: 7038 helix: -0.16 (0.08), residues: 3890 sheet: -0.89 (0.21), residues: 636 loop : -0.83 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 37 HIS 0.009 0.001 HIS 8 78 PHE 0.030 0.001 PHE G 107 TYR 0.023 0.001 TYR 4 211 ARG 0.007 0.000 ARG Z 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 609 time to evaluate : 4.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7076 (pm20) REVERT: 1 452 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7679 (tm-30) REVERT: 1 572 ASP cc_start: 0.8185 (m-30) cc_final: 0.7855 (m-30) REVERT: 2 226 LYS cc_start: 0.8008 (tptt) cc_final: 0.7677 (tptp) REVERT: 2 345 TYR cc_start: 0.7907 (m-80) cc_final: 0.7649 (m-80) REVERT: 4 13 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: 4 198 LYS cc_start: 0.8754 (mptt) cc_final: 0.8462 (mmmt) REVERT: 4 214 ASP cc_start: 0.7666 (m-30) cc_final: 0.7397 (m-30) REVERT: 5 11 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8059 (mt-10) REVERT: 5 112 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7317 (ptm-80) REVERT: 7 47 GLU cc_start: 0.6958 (pm20) cc_final: 0.6622 (mp0) REVERT: 7 148 ASP cc_start: 0.8102 (m-30) cc_final: 0.7561 (m-30) REVERT: 9 13 LYS cc_start: 0.7441 (pttt) cc_final: 0.7158 (pttt) REVERT: B 92 ASN cc_start: 0.7328 (p0) cc_final: 0.6995 (p0) REVERT: C 95 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6837 (pp) REVERT: E 60 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7305 (tptm) REVERT: E 62 VAL cc_start: 0.8213 (p) cc_final: 0.7997 (p) REVERT: E 81 MET cc_start: 0.7702 (ttp) cc_final: 0.7414 (ttm) REVERT: E 115 LEU cc_start: 0.7333 (pp) cc_final: 0.6964 (mm) REVERT: G 95 ILE cc_start: 0.8153 (mm) cc_final: 0.7921 (mm) REVERT: H 85 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7630 (tp) REVERT: J 81 MET cc_start: 0.8296 (ttp) cc_final: 0.7693 (ttp) REVERT: M 199 LYS cc_start: 0.8412 (mptt) cc_final: 0.8150 (mmtp) REVERT: P 99 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7877 (tp) REVERT: P 151 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7454 (pp20) REVERT: P 175 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: Q 18 ARG cc_start: 0.8247 (ttt-90) cc_final: 0.7865 (tpp80) REVERT: Q 40 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7507 (tp40) REVERT: Q 49 GLN cc_start: 0.8177 (pt0) cc_final: 0.7937 (pt0) REVERT: Q 52 TYR cc_start: 0.6310 (m-80) cc_final: 0.5540 (m-10) REVERT: R 127 PHE cc_start: 0.7694 (m-80) cc_final: 0.7450 (m-80) REVERT: S 62 MET cc_start: 0.7369 (ptp) cc_final: 0.7152 (mtp) REVERT: S 96 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.5971 (p0) REVERT: S 229 ASP cc_start: 0.7494 (m-30) cc_final: 0.7055 (m-30) REVERT: S 244 ARG cc_start: 0.8006 (tpp-160) cc_final: 0.7524 (ttp-110) REVERT: T 72 GLU cc_start: 0.7058 (tp30) cc_final: 0.6692 (tp30) REVERT: T 199 ARG cc_start: 0.7601 (mmm160) cc_final: 0.7148 (ptp90) REVERT: T 237 ASP cc_start: 0.7648 (m-30) cc_final: 0.7337 (m-30) REVERT: T 447 LYS cc_start: 0.7520 (mtpm) cc_final: 0.7220 (tppt) REVERT: T 487 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7670 (ttmt) REVERT: T 496 ARG cc_start: 0.7625 (mtt-85) cc_final: 0.7324 (mtt90) REVERT: T 522 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7094 (tp30) REVERT: T 535 ILE cc_start: 0.8377 (mt) cc_final: 0.8170 (mp) REVERT: T 542 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7281 (pt) REVERT: T 551 LYS cc_start: 0.7773 (ptpp) cc_final: 0.7281 (pttp) REVERT: T 553 GLU cc_start: 0.7531 (tp30) cc_final: 0.7192 (tp30) REVERT: U 71 LYS cc_start: 0.8516 (tppt) cc_final: 0.8310 (tppt) REVERT: U 75 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7924 (mmpt) REVERT: U 149 GLN cc_start: 0.7647 (mt0) cc_final: 0.7070 (mm110) REVERT: U 283 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7700 (ttt180) REVERT: U 511 LYS cc_start: 0.7616 (mmpt) cc_final: 0.7015 (mttt) REVERT: U 522 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: U 553 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7664 (mm-30) REVERT: V 50 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7804 (tmmt) REVERT: V 253 GLN cc_start: 0.8332 (mt0) cc_final: 0.7913 (mt0) REVERT: V 278 GLN cc_start: 0.7804 (mt0) cc_final: 0.7523 (mm-40) REVERT: V 535 ILE cc_start: 0.8439 (mm) cc_final: 0.8194 (mp) REVERT: V 539 ASN cc_start: 0.8592 (m-40) cc_final: 0.8292 (m-40) REVERT: X 131 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7781 (mp0) REVERT: X 550 LYS cc_start: 0.8058 (ptpp) cc_final: 0.7555 (pptt) REVERT: Y 140 ILE cc_start: 0.8790 (pt) cc_final: 0.8393 (pp) REVERT: Y 359 ASP cc_start: 0.7765 (m-30) cc_final: 0.7440 (m-30) REVERT: Y 385 ARG cc_start: 0.7908 (mmt90) cc_final: 0.7401 (mmm-85) REVERT: Y 411 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7850 (mtpp) REVERT: Y 414 GLN cc_start: 0.7568 (tt0) cc_final: 0.7232 (mt0) REVERT: Y 431 LEU cc_start: 0.7885 (tm) cc_final: 0.7640 (tp) REVERT: Y 437 ARG cc_start: 0.6890 (mtt-85) cc_final: 0.6378 (mmm-85) REVERT: Y 441 ARG cc_start: 0.7568 (mmt-90) cc_final: 0.7252 (mmt90) REVERT: Y 497 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6278 (mt-10) REVERT: Y 501 LYS cc_start: 0.6448 (OUTLIER) cc_final: 0.6232 (tmmm) REVERT: Y 539 ILE cc_start: 0.7240 (pt) cc_final: 0.7018 (mm) REVERT: Z 82 ASP cc_start: 0.7570 (t0) cc_final: 0.7176 (t0) REVERT: Z 292 GLN cc_start: 0.7581 (tt0) cc_final: 0.7198 (tt0) REVERT: Z 337 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8883 (mt0) REVERT: Z 427 GLU cc_start: 0.7520 (tp30) cc_final: 0.7260 (pp20) REVERT: Z 437 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7425 (mtm110) REVERT: Z 566 LYS cc_start: 0.8251 (tttm) cc_final: 0.8033 (tttt) outliers start: 163 outliers final: 68 residues processed: 706 average time/residue: 1.3588 time to fit residues: 1214.4550 Evaluate side-chains 653 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 573 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 175 GLU Chi-restraints excluded: chain P residue 205 ARG Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain T residue 144 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 182 SER Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 339 LEU Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 522 GLU Chi-restraints excluded: chain U residue 550 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 409 GLU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 510 ASP Chi-restraints excluded: chain V residue 529 ASN Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 325 ILE Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 501 LYS Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 417 ILE Chi-restraints excluded: chain Z residue 532 SER Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 568 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5114 > 50: distance: 4 - 9: 27.701 distance: 9 - 10: 41.154 distance: 10 - 11: 48.194 distance: 10 - 13: 10.438 distance: 11 - 12: 30.828 distance: 11 - 16: 47.522 distance: 13 - 14: 64.413 distance: 13 - 15: 52.952 distance: 16 - 17: 37.801 distance: 17 - 18: 49.488 distance: 17 - 20: 10.600 distance: 18 - 19: 51.226 distance: 18 - 25: 25.760 distance: 20 - 21: 50.629 distance: 22 - 23: 48.726 distance: 22 - 24: 66.284 distance: 25 - 26: 40.234 distance: 26 - 27: 33.581 distance: 26 - 29: 45.369 distance: 27 - 28: 37.913 distance: 27 - 34: 55.812 distance: 29 - 30: 5.329 distance: 30 - 31: 34.711 distance: 31 - 32: 13.439 distance: 31 - 33: 18.945 distance: 34 - 35: 40.761 distance: 35 - 36: 54.238 distance: 35 - 38: 25.025 distance: 36 - 37: 54.967 distance: 36 - 42: 56.728 distance: 38 - 39: 47.451 distance: 38 - 40: 48.314 distance: 39 - 41: 20.795 distance: 42 - 43: 56.111 distance: 43 - 44: 41.471 distance: 43 - 46: 41.094 distance: 44 - 45: 58.823 distance: 44 - 49: 56.555 distance: 46 - 48: 49.467 distance: 49 - 50: 67.017 distance: 50 - 51: 55.294 distance: 50 - 53: 42.566 distance: 51 - 52: 55.329 distance: 51 - 54: 24.123 distance: 54 - 55: 34.343 distance: 54 - 60: 14.232 distance: 55 - 56: 27.962 distance: 55 - 58: 32.482 distance: 56 - 57: 22.597 distance: 56 - 61: 53.442 distance: 58 - 59: 36.119 distance: 59 - 60: 55.008 distance: 61 - 62: 6.407 distance: 62 - 63: 18.947 distance: 62 - 65: 60.187 distance: 63 - 64: 45.490 distance: 63 - 70: 49.617 distance: 65 - 66: 41.230 distance: 66 - 67: 41.628 distance: 67 - 68: 49.053 distance: 68 - 69: 26.919 distance: 70 - 71: 11.707 distance: 71 - 72: 36.803 distance: 71 - 74: 43.075 distance: 72 - 73: 10.925 distance: 72 - 77: 29.894 distance: 74 - 75: 26.017 distance: 74 - 76: 53.562 distance: 77 - 78: 39.675 distance: 78 - 79: 45.620 distance: 78 - 81: 30.516 distance: 79 - 80: 39.799 distance: 79 - 82: 34.471