Starting phenix.real_space_refine on Sat Jul 27 09:07:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/07_2024/6d00_7782.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/07_2024/6d00_7782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/07_2024/6d00_7782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/07_2024/6d00_7782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/07_2024/6d00_7782.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/07_2024/6d00_7782.cif" } resolution = 4.0 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= 0.001 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 150 5.16 5 C 23910 2.51 5 N 6960 2.21 5 O 7284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 70": "NH1" <-> "NH2" Residue "1 ARG 256": "NH1" <-> "NH2" Residue "1 ARG 375": "NH1" <-> "NH2" Residue "1 ARG 413": "NH1" <-> "NH2" Residue "1 ARG 414": "NH1" <-> "NH2" Residue "1 ARG 543": "NH1" <-> "NH2" Residue "1 ARG 597": "NH1" <-> "NH2" Residue "1 ARG 632": "NH1" <-> "NH2" Residue "1 ARG 669": "NH1" <-> "NH2" Residue "1 ARG 706": "NH1" <-> "NH2" Residue "1 ARG 779": "NH1" <-> "NH2" Residue "1 ARG 820": "NH1" <-> "NH2" Residue "2 ARG 70": "NH1" <-> "NH2" Residue "2 ARG 256": "NH1" <-> "NH2" Residue "2 ARG 375": "NH1" <-> "NH2" Residue "2 ARG 413": "NH1" <-> "NH2" Residue "2 ARG 414": "NH1" <-> "NH2" Residue "2 ARG 543": "NH1" <-> "NH2" Residue "2 ARG 597": "NH1" <-> "NH2" Residue "2 ARG 632": "NH1" <-> "NH2" Residue "2 ARG 669": "NH1" <-> "NH2" Residue "2 ARG 706": "NH1" <-> "NH2" Residue "2 ARG 779": "NH1" <-> "NH2" Residue "2 ARG 820": "NH1" <-> "NH2" Residue "3 ARG 70": "NH1" <-> "NH2" Residue "3 ARG 256": "NH1" <-> "NH2" Residue "3 ARG 375": "NH1" <-> "NH2" Residue "3 ARG 413": "NH1" <-> "NH2" Residue "3 ARG 414": "NH1" <-> "NH2" Residue "3 ARG 543": "NH1" <-> "NH2" Residue "3 ARG 597": "NH1" <-> "NH2" Residue "3 ARG 632": "NH1" <-> "NH2" Residue "3 ARG 669": "NH1" <-> "NH2" Residue "3 ARG 706": "NH1" <-> "NH2" Residue "3 ARG 779": "NH1" <-> "NH2" Residue "3 ARG 820": "NH1" <-> "NH2" Residue "4 ARG 70": "NH1" <-> "NH2" Residue "4 ARG 256": "NH1" <-> "NH2" Residue "4 ARG 375": "NH1" <-> "NH2" Residue "4 ARG 413": "NH1" <-> "NH2" Residue "4 ARG 414": "NH1" <-> "NH2" Residue "4 ARG 543": "NH1" <-> "NH2" Residue "4 ARG 597": "NH1" <-> "NH2" Residue "4 ARG 632": "NH1" <-> "NH2" Residue "4 ARG 669": "NH1" <-> "NH2" Residue "4 ARG 706": "NH1" <-> "NH2" Residue "4 ARG 779": "NH1" <-> "NH2" Residue "4 ARG 820": "NH1" <-> "NH2" Residue "5 ARG 70": "NH1" <-> "NH2" Residue "5 ARG 256": "NH1" <-> "NH2" Residue "5 ARG 375": "NH1" <-> "NH2" Residue "5 ARG 413": "NH1" <-> "NH2" Residue "5 ARG 414": "NH1" <-> "NH2" Residue "5 ARG 543": "NH1" <-> "NH2" Residue "5 ARG 597": "NH1" <-> "NH2" Residue "5 ARG 632": "NH1" <-> "NH2" Residue "5 ARG 669": "NH1" <-> "NH2" Residue "5 ARG 706": "NH1" <-> "NH2" Residue "5 ARG 779": "NH1" <-> "NH2" Residue "5 ARG 820": "NH1" <-> "NH2" Residue "6 ARG 70": "NH1" <-> "NH2" Residue "6 ARG 256": "NH1" <-> "NH2" Residue "6 ARG 375": "NH1" <-> "NH2" Residue "6 ARG 413": "NH1" <-> "NH2" Residue "6 ARG 414": "NH1" <-> "NH2" Residue "6 ARG 543": "NH1" <-> "NH2" Residue "6 ARG 597": "NH1" <-> "NH2" Residue "6 ARG 632": "NH1" <-> "NH2" Residue "6 ARG 669": "NH1" <-> "NH2" Residue "6 ARG 706": "NH1" <-> "NH2" Residue "6 ARG 779": "NH1" <-> "NH2" Residue "6 ARG 820": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 38328 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "2" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "3" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "4" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "5" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "6" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "1" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.07, per 1000 atoms: 0.50 Number of scatterers: 38328 At special positions: 0 Unit cell: (187.62, 179.14, 154.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 24 15.00 O 7284 8.00 N 6960 7.00 C 23910 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.73 Conformation dependent library (CDL) restraints added in 7.5 seconds 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9156 Finding SS restraints... Secondary structure from input PDB file: 261 helices and 34 sheets defined 61.1% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain '1' and resid 7 through 23 removed outlier: 3.506A pdb=" N THR 1 11 " --> pdb=" O THR 1 7 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA 1 17 " --> pdb=" O THR 1 13 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS 1 19 " --> pdb=" O ASN 1 15 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR 1 20 " --> pdb=" O ALA 1 16 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA 1 21 " --> pdb=" O ALA 1 17 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA 1 22 " --> pdb=" O ALA 1 18 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU 1 23 " --> pdb=" O LYS 1 19 " (cutoff:3.500A) Processing helix chain '1' and resid 31 through 39 removed outlier: 4.166A pdb=" N ALA 1 35 " --> pdb=" O PRO 1 31 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL 1 36 " --> pdb=" O SER 1 32 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 53 removed outlier: 3.573A pdb=" N ILE 1 49 " --> pdb=" O LEU 1 45 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU 1 50 " --> pdb=" O PHE 1 46 " (cutoff:3.500A) Processing helix chain '1' and resid 56 through 70 removed outlier: 3.633A pdb=" N ILE 1 60 " --> pdb=" O ASP 1 56 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS 1 65 " --> pdb=" O GLU 1 61 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS 1 66 " --> pdb=" O ARG 1 62 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE 1 67 " --> pdb=" O GLY 1 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET 1 68 " --> pdb=" O PHE 1 64 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG 1 70 " --> pdb=" O LYS 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 84 through 97 removed outlier: 4.112A pdb=" N LYS 1 89 " --> pdb=" O PRO 1 85 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA 1 94 " --> pdb=" O LEU 1 90 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU 1 96 " --> pdb=" O HIS 1 92 " (cutoff:3.500A) Processing helix chain '1' and resid 114 through 118 removed outlier: 3.621A pdb=" N ASP 1 117 " --> pdb=" O ALA 1 114 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU 1 118 " --> pdb=" O LEU 1 115 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 114 through 118' Processing helix chain '1' and resid 121 through 129 removed outlier: 4.334A pdb=" N LEU 1 125 " --> pdb=" O MET 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 131 through 142 removed outlier: 4.211A pdb=" N GLU 1 136 " --> pdb=" O LYS 1 132 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN 1 137 " --> pdb=" O LYS 1 133 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL 1 139 " --> pdb=" O LEU 1 135 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS 1 141 " --> pdb=" O ASN 1 137 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL 1 142 " --> pdb=" O ALA 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 158 through 163 Processing helix chain '1' and resid 167 through 173 removed outlier: 3.682A pdb=" N ALA 1 172 " --> pdb=" O THR 1 168 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER 1 173 " --> pdb=" O GLU 1 169 " (cutoff:3.500A) Processing helix chain '1' and resid 182 through 194 removed outlier: 3.693A pdb=" N ARG 1 191 " --> pdb=" O SER 1 187 " (cutoff:3.500A) Processing helix chain '1' and resid 211 through 225 removed outlier: 3.912A pdb=" N ALA 1 215 " --> pdb=" O LYS 1 211 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA 1 219 " --> pdb=" O ALA 1 215 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN 1 220 " --> pdb=" O GLU 1 216 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG 1 221 " --> pdb=" O GLY 1 217 " (cutoff:3.500A) Processing helix chain '1' and resid 239 through 244 removed outlier: 4.014A pdb=" N LEU 1 243 " --> pdb=" O ASP 1 239 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU 1 244 " --> pdb=" O ILE 1 240 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 239 through 244' Processing helix chain '1' and resid 252 through 266 removed outlier: 3.720A pdb=" N LYS 1 258 " --> pdb=" O GLU 1 254 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU 1 266 " --> pdb=" O LYS 1 262 " (cutoff:3.500A) Processing helix chain '1' and resid 275 through 280 removed outlier: 4.272A pdb=" N VAL 1 279 " --> pdb=" O GLU 1 275 " (cutoff:3.500A) Processing helix chain '1' and resid 294 through 301 removed outlier: 3.755A pdb=" N MET 1 298 " --> pdb=" O LEU 1 294 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG 1 301 " --> pdb=" O PRO 1 297 " (cutoff:3.500A) Processing helix chain '1' and resid 314 through 319 Processing helix chain '1' and resid 322 through 327 removed outlier: 3.699A pdb=" N GLU 1 326 " --> pdb=" O ASP 1 322 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG 1 327 " --> pdb=" O PRO 1 323 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 322 through 327' Processing helix chain '1' and resid 338 through 349 removed outlier: 3.562A pdb=" N SER 1 344 " --> pdb=" O THR 1 340 " (cutoff:3.500A) Processing helix chain '1' and resid 363 through 372 removed outlier: 4.278A pdb=" N VAL 1 367 " --> pdb=" O ASP 1 363 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA 1 370 " --> pdb=" O ILE 1 366 " (cutoff:3.500A) Processing helix chain '1' and resid 383 through 403 removed outlier: 4.192A pdb=" N ASP 1 388 " --> pdb=" O ASP 1 384 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU 1 389 " --> pdb=" O LYS 1 385 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE 1 390 " --> pdb=" O ALA 1 386 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA 1 393 " --> pdb=" O LEU 1 389 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN 1 396 " --> pdb=" O GLU 1 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR 1 397 " --> pdb=" O ALA 1 393 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG 1 398 " --> pdb=" O CYS 1 394 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL 1 399 " --> pdb=" O ALA 1 395 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN 1 400 " --> pdb=" O ASN 1 396 " (cutoff:3.500A) Processing helix chain '1' and resid 405 through 428 removed outlier: 3.685A pdb=" N LYS 1 410 " --> pdb=" O GLU 1 406 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU 1 411 " --> pdb=" O ALA 1 407 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG 1 414 " --> pdb=" O LYS 1 410 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS 1 415 " --> pdb=" O LEU 1 411 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL 1 420 " --> pdb=" O LEU 1 416 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU 1 421 " --> pdb=" O GLN 1 417 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR 1 423 " --> pdb=" O GLU 1 419 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA 1 424 " --> pdb=" O VAL 1 420 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU 1 428 " --> pdb=" O ALA 1 424 " (cutoff:3.500A) Processing helix chain '1' and resid 433 through 486 removed outlier: 3.605A pdb=" N GLN 1 438 " --> pdb=" O LYS 1 434 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU 1 439 " --> pdb=" O GLN 1 435 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG 1 446 " --> pdb=" O ALA 1 442 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU 1 450 " --> pdb=" O ARG 1 446 " (cutoff:3.500A) Proline residue: 1 453 - end of helix removed outlier: 4.375A pdb=" N LYS 1 457 " --> pdb=" O PRO 1 453 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR 1 458 " --> pdb=" O LEU 1 454 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER 1 460 " --> pdb=" O MET 1 456 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG 1 464 " --> pdb=" O SER 1 460 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP 1 466 " --> pdb=" O LYS 1 462 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG 1 469 " --> pdb=" O LEU 1 465 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG 1 474 " --> pdb=" O ASN 1 470 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU 1 483 " --> pdb=" O LYS 1 479 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP 1 484 " --> pdb=" O ALA 1 480 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA 1 485 " --> pdb=" O LYS 1 481 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU 1 486 " --> pdb=" O ALA 1 482 " (cutoff:3.500A) Processing helix chain '1' and resid 490 through 498 removed outlier: 3.799A pdb=" N ASP 1 496 " --> pdb=" O ALA 1 492 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE 1 497 " --> pdb=" O ARG 1 493 " (cutoff:3.500A) Processing helix chain '1' and resid 500 through 518 removed outlier: 3.655A pdb=" N ARG 1 508 " --> pdb=" O ASP 1 504 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU 1 509 " --> pdb=" O LEU 1 505 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN 1 518 " --> pdb=" O ALA 1 514 " (cutoff:3.500A) Processing helix chain '1' and resid 533 through 545 removed outlier: 4.250A pdb=" N GLU 1 539 " --> pdb=" O ASP 1 535 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL 1 540 " --> pdb=" O GLN 1 536 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL 1 541 " --> pdb=" O ILE 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 548 through 552 Processing helix chain '1' and resid 555 through 560 removed outlier: 3.868A pdb=" N LEU 1 560 " --> pdb=" O GLU 1 556 " (cutoff:3.500A) Processing helix chain '1' and resid 562 through 567 removed outlier: 3.586A pdb=" N MET 1 567 " --> pdb=" O MET 1 563 " (cutoff:3.500A) Processing helix chain '1' and resid 574 through 579 removed outlier: 4.166A pdb=" N LYS 1 579 " --> pdb=" O ASP 1 575 " (cutoff:3.500A) Processing helix chain '1' and resid 580 through 586 removed outlier: 4.113A pdb=" N ALA 1 584 " --> pdb=" O ALA 1 580 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE 1 585 " --> pdb=" O ILE 1 581 " (cutoff:3.500A) Processing helix chain '1' and resid 613 through 623 removed outlier: 3.738A pdb=" N ALA 1 620 " --> pdb=" O VAL 1 616 " (cutoff:3.500A) Processing helix chain '1' and resid 662 through 669 removed outlier: 3.756A pdb=" N ARG 1 669 " --> pdb=" O GLU 1 665 " (cutoff:3.500A) Processing helix chain '1' and resid 685 through 691 removed outlier: 3.593A pdb=" N ASN 1 689 " --> pdb=" O LYS 1 685 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU 1 690 " --> pdb=" O ASP 1 686 " (cutoff:3.500A) Processing helix chain '1' and resid 739 through 750 removed outlier: 3.664A pdb=" N LEU 1 743 " --> pdb=" O LYS 1 739 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA 1 744 " --> pdb=" O ASN 1 740 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR 1 745 " --> pdb=" O ALA 1 741 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA 1 746 " --> pdb=" O VAL 1 742 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG 1 747 " --> pdb=" O LEU 1 743 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG 1 748 " --> pdb=" O ALA 1 744 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS 1 749 " --> pdb=" O THR 1 745 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE 1 750 " --> pdb=" O ALA 1 746 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 739 through 750' Processing helix chain '1' and resid 751 through 756 removed outlier: 3.665A pdb=" N ILE 1 755 " --> pdb=" O ALA 1 751 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN 1 756 " --> pdb=" O ASN 1 752 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 751 through 756' Processing helix chain '1' and resid 768 through 786 removed outlier: 4.390A pdb=" N ARG 1 773 " --> pdb=" O PRO 1 769 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS 1 774 " --> pdb=" O SER 1 770 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE 1 775 " --> pdb=" O ASN 1 771 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP 1 777 " --> pdb=" O ARG 1 773 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL 1 778 " --> pdb=" O LYS 1 774 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU 1 780 " --> pdb=" O VAL 1 776 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS 1 781 " --> pdb=" O ASP 1 777 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU 1 782 " --> pdb=" O VAL 1 778 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL 1 783 " --> pdb=" O ARG 1 779 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG 1 786 " --> pdb=" O GLU 1 782 " (cutoff:3.500A) Processing helix chain '1' and resid 787 through 791 Processing helix chain '1' and resid 799 through 807 removed outlier: 3.754A pdb=" N LEU 1 803 " --> pdb=" O LYS 1 799 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA 1 805 " --> pdb=" O LYS 1 801 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN 1 807 " --> pdb=" O LEU 1 803 " (cutoff:3.500A) Processing helix chain '1' and resid 816 through 826 removed outlier: 3.808A pdb=" N ARG 1 820 " --> pdb=" O ARG 1 816 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS 1 824 " --> pdb=" O ARG 1 820 " (cutoff:3.500A) Processing helix chain '1' and resid 826 through 834 removed outlier: 3.790A pdb=" N LEU 1 830 " --> pdb=" O LEU 1 826 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU 1 834 " --> pdb=" O LEU 1 830 " (cutoff:3.500A) Processing helix chain '2' and resid 7 through 23 removed outlier: 3.915A pdb=" N LEU 2 14 " --> pdb=" O ALA 2 10 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN 2 15 " --> pdb=" O THR 2 11 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU 2 23 " --> pdb=" O LYS 2 19 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 39 removed outlier: 4.246A pdb=" N ALA 2 35 " --> pdb=" O PRO 2 31 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL 2 36 " --> pdb=" O SER 2 32 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 54 removed outlier: 4.440A pdb=" N SER 2 48 " --> pdb=" O SER 2 44 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU 2 50 " --> pdb=" O PHE 2 46 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS 2 52 " --> pdb=" O SER 2 48 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA 2 53 " --> pdb=" O ILE 2 49 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 70 removed outlier: 3.659A pdb=" N ILE 2 67 " --> pdb=" O GLY 2 63 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET 2 68 " --> pdb=" O PHE 2 64 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL 2 69 " --> pdb=" O LYS 2 65 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG 2 70 " --> pdb=" O LYS 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 84 through 97 removed outlier: 3.913A pdb=" N LYS 2 89 " --> pdb=" O PRO 2 85 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU 2 90 " --> pdb=" O GLU 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 98 through 100 No H-bonds generated for 'chain '2' and resid 98 through 100' Processing helix chain '2' and resid 110 through 117 removed outlier: 3.954A pdb=" N ALA 2 114 " --> pdb=" O HIS 2 110 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 2 115 " --> pdb=" O LEU 2 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP 2 117 " --> pdb=" O LEU 2 113 " (cutoff:3.500A) Processing helix chain '2' and resid 118 through 129 removed outlier: 3.640A pdb=" N GLN 2 123 " --> pdb=" O PRO 2 119 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL 2 124 " --> pdb=" O SER 2 120 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 2 125 " --> pdb=" O MET 2 121 " (cutoff:3.500A) Processing helix chain '2' and resid 131 through 142 removed outlier: 3.745A pdb=" N LEU 2 135 " --> pdb=" O THR 2 131 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU 2 136 " --> pdb=" O LYS 2 132 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN 2 137 " --> pdb=" O LYS 2 133 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL 2 139 " --> pdb=" O LEU 2 135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR 2 140 " --> pdb=" O GLU 2 136 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS 2 141 " --> pdb=" O ASN 2 137 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL 2 142 " --> pdb=" O ALA 2 138 " (cutoff:3.500A) Processing helix chain '2' and resid 158 through 163 removed outlier: 3.953A pdb=" N LYS 2 162 " --> pdb=" O GLU 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 167 through 173 Processing helix chain '2' and resid 182 through 194 removed outlier: 3.786A pdb=" N SER 2 187 " --> pdb=" O ASP 2 183 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG 2 188 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG 2 191 " --> pdb=" O SER 2 187 " (cutoff:3.500A) Processing helix chain '2' and resid 211 through 224 removed outlier: 4.130A pdb=" N ALA 2 215 " --> pdb=" O LYS 2 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU 2 216 " --> pdb=" O THR 2 212 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY 2 217 " --> pdb=" O ALA 2 213 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU 2 218 " --> pdb=" O ILE 2 214 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA 2 219 " --> pdb=" O ALA 2 215 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN 2 220 " --> pdb=" O GLU 2 216 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG 2 221 " --> pdb=" O GLY 2 217 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE 2 222 " --> pdb=" O LEU 2 218 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL 2 223 " --> pdb=" O ALA 2 219 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS 2 224 " --> pdb=" O ASN 2 220 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 211 through 224' Processing helix chain '2' and resid 239 through 244 removed outlier: 3.643A pdb=" N LEU 2 243 " --> pdb=" O ASP 2 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU 2 244 " --> pdb=" O ILE 2 240 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 239 through 244' Processing helix chain '2' and resid 252 through 268 removed outlier: 3.866A pdb=" N ARG 2 256 " --> pdb=" O GLU 2 252 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA 2 259 " --> pdb=" O GLU 2 255 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL 2 260 " --> pdb=" O ARG 2 256 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU 2 266 " --> pdb=" O LYS 2 262 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA 2 267 " --> pdb=" O GLU 2 263 " (cutoff:3.500A) Processing helix chain '2' and resid 275 through 280 removed outlier: 4.120A pdb=" N VAL 2 279 " --> pdb=" O GLU 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 291 through 294 removed outlier: 3.670A pdb=" N LEU 2 294 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 291 through 294' Processing helix chain '2' and resid 295 through 301 Processing helix chain '2' and resid 311 through 316 removed outlier: 3.783A pdb=" N ARG 2 316 " --> pdb=" O LEU 2 312 " (cutoff:3.500A) Processing helix chain '2' and resid 322 through 327 removed outlier: 3.540A pdb=" N GLU 2 326 " --> pdb=" O ASP 2 322 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG 2 327 " --> pdb=" O PRO 2 323 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 322 through 327' Processing helix chain '2' and resid 338 through 349 removed outlier: 3.915A pdb=" N ILE 2 343 " --> pdb=" O VAL 2 339 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER 2 344 " --> pdb=" O THR 2 340 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY 2 348 " --> pdb=" O SER 2 344 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU 2 349 " --> pdb=" O ILE 2 345 " (cutoff:3.500A) Processing helix chain '2' and resid 349 through 357 removed outlier: 3.524A pdb=" N TYR 2 353 " --> pdb=" O LEU 2 349 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS 2 356 " --> pdb=" O ARG 2 352 " (cutoff:3.500A) Processing helix chain '2' and resid 363 through 373 removed outlier: 4.052A pdb=" N VAL 2 367 " --> pdb=" O ASP 2 363 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA 2 368 " --> pdb=" O ALA 2 364 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA 2 370 " --> pdb=" O ILE 2 366 " (cutoff:3.500A) Processing helix chain '2' and resid 383 through 403 removed outlier: 4.051A pdb=" N ASP 2 388 " --> pdb=" O ASP 2 384 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU 2 389 " --> pdb=" O LYS 2 385 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE 2 390 " --> pdb=" O ALA 2 386 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR 2 397 " --> pdb=" O ALA 2 393 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG 2 398 " --> pdb=" O CYS 2 394 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL 2 399 " --> pdb=" O ALA 2 395 " (cutoff:3.500A) Processing helix chain '2' and resid 405 through 427 removed outlier: 4.394A pdb=" N LEU 2 411 " --> pdb=" O ALA 2 407 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU 2 418 " --> pdb=" O ARG 2 414 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU 2 421 " --> pdb=" O GLN 2 417 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA 2 424 " --> pdb=" O VAL 2 420 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU 2 425 " --> pdb=" O GLU 2 421 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS 2 427 " --> pdb=" O THR 2 423 " (cutoff:3.500A) Processing helix chain '2' and resid 430 through 488 removed outlier: 3.952A pdb=" N GLN 2 435 " --> pdb=" O ALA 2 431 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG 2 436 " --> pdb=" O ALA 2 432 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU 2 439 " --> pdb=" O GLN 2 435 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU 2 443 " --> pdb=" O GLU 2 439 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG 2 446 " --> pdb=" O ALA 2 442 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE 2 447 " --> pdb=" O GLU 2 443 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU 2 450 " --> pdb=" O ARG 2 446 " (cutoff:3.500A) Proline residue: 2 453 - end of helix removed outlier: 3.650A pdb=" N LYS 2 457 " --> pdb=" O PRO 2 453 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY 2 463 " --> pdb=" O GLU 2 459 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG 2 464 " --> pdb=" O SER 2 460 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG 2 469 " --> pdb=" O LEU 2 465 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG 2 474 " --> pdb=" O ASN 2 470 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU 2 475 " --> pdb=" O LEU 2 471 " (cutoff:3.500A) Processing helix chain '2' and resid 493 through 497 Processing helix chain '2' and resid 505 through 523 removed outlier: 3.811A pdb=" N ALA 2 521 " --> pdb=" O SER 2 517 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU 2 522 " --> pdb=" O GLN 2 518 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG 2 523 " --> pdb=" O ALA 2 519 " (cutoff:3.500A) Processing helix chain '2' and resid 533 through 544 removed outlier: 3.520A pdb=" N GLU 2 539 " --> pdb=" O ASP 2 535 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL 2 540 " --> pdb=" O GLN 2 536 " (cutoff:3.500A) Processing helix chain '2' and resid 548 through 552 Processing helix chain '2' and resid 555 through 562 removed outlier: 3.728A pdb=" N LEU 2 560 " --> pdb=" O GLU 2 556 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU 2 561 " --> pdb=" O LYS 2 557 " (cutoff:3.500A) Processing helix chain '2' and resid 563 through 568 removed outlier: 3.717A pdb=" N LYS 2 568 " --> pdb=" O GLU 2 564 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 590 removed outlier: 3.923A pdb=" N LYS 2 579 " --> pdb=" O ASP 2 575 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA 2 580 " --> pdb=" O GLU 2 576 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS 2 582 " --> pdb=" O ILE 2 578 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA 2 584 " --> pdb=" O ALA 2 580 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU 2 587 " --> pdb=" O ASP 2 583 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER 2 588 " --> pdb=" O ALA 2 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG 2 589 " --> pdb=" O ILE 2 585 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR 2 590 " --> pdb=" O ARG 2 586 " (cutoff:3.500A) Processing helix chain '2' and resid 613 through 621 removed outlier: 3.671A pdb=" N ALA 2 620 " --> pdb=" O VAL 2 616 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA 2 621 " --> pdb=" O LYS 2 617 " (cutoff:3.500A) Processing helix chain '2' and resid 640 through 644 Processing helix chain '2' and resid 662 through 670 removed outlier: 3.514A pdb=" N ARG 2 668 " --> pdb=" O THR 2 664 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG 2 669 " --> pdb=" O GLU 2 665 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG 2 670 " --> pdb=" O ALA 2 666 " (cutoff:3.500A) Processing helix chain '2' and resid 679 through 683 Processing helix chain '2' and resid 684 through 691 removed outlier: 4.088A pdb=" N SER 2 688 " --> pdb=" O HIS 2 684 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU 2 690 " --> pdb=" O ASP 2 686 " (cutoff:3.500A) Processing helix chain '2' and resid 691 through 698 removed outlier: 3.591A pdb=" N LEU 2 695 " --> pdb=" O LEU 2 691 " (cutoff:3.500A) Processing helix chain '2' and resid 739 through 750 removed outlier: 3.693A pdb=" N ALA 2 746 " --> pdb=" O VAL 2 742 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG 2 747 " --> pdb=" O LEU 2 743 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG 2 748 " --> pdb=" O ALA 2 744 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS 2 749 " --> pdb=" O THR 2 745 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE 2 750 " --> pdb=" O ALA 2 746 " (cutoff:3.500A) Processing helix chain '2' and resid 753 through 758 removed outlier: 3.734A pdb=" N ILE 2 758 " --> pdb=" O PHE 2 754 " (cutoff:3.500A) Processing helix chain '2' and resid 768 through 770 No H-bonds generated for 'chain '2' and resid 768 through 770' Processing helix chain '2' and resid 771 through 786 removed outlier: 3.559A pdb=" N VAL 2 776 " --> pdb=" O ILE 2 772 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP 2 777 " --> pdb=" O ARG 2 773 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU 2 780 " --> pdb=" O VAL 2 776 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS 2 781 " --> pdb=" O ASP 2 777 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU 2 782 " --> pdb=" O VAL 2 778 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL 2 783 " --> pdb=" O ARG 2 779 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN 2 784 " --> pdb=" O LEU 2 780 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 791 Processing helix chain '2' and resid 797 through 808 removed outlier: 3.596A pdb=" N LYS 2 801 " --> pdb=" O ASP 2 797 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP 2 802 " --> pdb=" O ASP 2 798 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU 2 803 " --> pdb=" O LYS 2 799 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU 2 804 " --> pdb=" O ALA 2 800 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA 2 805 " --> pdb=" O LYS 2 801 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN 2 806 " --> pdb=" O ASP 2 802 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN 2 807 " --> pdb=" O LEU 2 803 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY 2 808 " --> pdb=" O LEU 2 804 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 797 through 808' Processing helix chain '2' and resid 815 through 824 removed outlier: 4.193A pdb=" N ASN 2 819 " --> pdb=" O ALA 2 815 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG 2 820 " --> pdb=" O ARG 2 816 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE 2 822 " --> pdb=" O LEU 2 818 " (cutoff:3.500A) Processing helix chain '2' and resid 825 through 831 removed outlier: 3.508A pdb=" N GLN 2 829 " --> pdb=" O ALA 2 825 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER 2 831 " --> pdb=" O LEU 2 827 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 24 removed outlier: 3.505A pdb=" N THR 3 13 " --> pdb=" O LYS 3 9 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA 3 18 " --> pdb=" O LEU 3 14 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS 3 19 " --> pdb=" O ASN 3 15 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN 3 24 " --> pdb=" O TYR 3 20 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 40 removed outlier: 4.192A pdb=" N ALA 3 35 " --> pdb=" O PRO 3 31 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL 3 36 " --> pdb=" O SER 3 32 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL 3 37 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP 3 40 " --> pdb=" O VAL 3 36 " (cutoff:3.500A) Processing helix chain '3' and resid 46 through 53 removed outlier: 3.640A pdb=" N LEU 3 50 " --> pdb=" O PHE 3 46 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU 3 51 " --> pdb=" O ARG 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 56 through 61 removed outlier: 3.748A pdb=" N ILE 3 60 " --> pdb=" O ASP 3 56 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU 3 61 " --> pdb=" O VAL 3 57 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 56 through 61' Processing helix chain '3' and resid 64 through 71 removed outlier: 3.732A pdb=" N MET 3 68 " --> pdb=" O PHE 3 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL 3 69 " --> pdb=" O LYS 3 65 " (cutoff:3.500A) Processing helix chain '3' and resid 87 through 99 removed outlier: 3.696A pdb=" N LEU 3 91 " --> pdb=" O LEU 3 87 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU 3 96 " --> pdb=" O HIS 3 92 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS 3 97 " --> pdb=" O TYR 3 93 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS 3 99 " --> pdb=" O HIS 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 111 removed outlier: 3.698A pdb=" N HIS 3 110 " --> pdb=" O ALA 3 107 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU 3 111 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 107 through 111' Processing helix chain '3' and resid 112 through 117 removed outlier: 3.704A pdb=" N ALA 3 116 " --> pdb=" O LEU 3 113 " (cutoff:3.500A) Processing helix chain '3' and resid 121 through 129 removed outlier: 3.586A pdb=" N LEU 3 125 " --> pdb=" O MET 3 121 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY 3 128 " --> pdb=" O VAL 3 124 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 137 removed outlier: 3.874A pdb=" N GLU 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN 3 137 " --> pdb=" O LYS 3 133 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 142 removed outlier: 3.950A pdb=" N HIS 3 141 " --> pdb=" O ASN 3 137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL 3 142 " --> pdb=" O ALA 3 138 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 137 through 142' Processing helix chain '3' and resid 158 through 163 removed outlier: 3.523A pdb=" N TYR 3 163 " --> pdb=" O ALA 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 167 through 173 Processing helix chain '3' and resid 182 through 194 removed outlier: 4.092A pdb=" N SER 3 187 " --> pdb=" O ASP 3 183 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG 3 188 " --> pdb=" O GLU 3 184 " (cutoff:3.500A) Processing helix chain '3' and resid 211 through 223 removed outlier: 3.857A pdb=" N ALA 3 215 " --> pdb=" O LYS 3 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY 3 217 " --> pdb=" O ALA 3 213 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU 3 218 " --> pdb=" O ILE 3 214 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA 3 219 " --> pdb=" O ALA 3 215 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN 3 220 " --> pdb=" O GLU 3 216 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG 3 221 " --> pdb=" O GLY 3 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL 3 223 " --> pdb=" O ALA 3 219 " (cutoff:3.500A) Processing helix chain '3' and resid 239 through 245 removed outlier: 4.034A pdb=" N LEU 3 243 " --> pdb=" O ASP 3 239 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU 3 244 " --> pdb=" O ILE 3 240 " (cutoff:3.500A) Processing helix chain '3' and resid 252 through 267 removed outlier: 3.537A pdb=" N LEU 3 257 " --> pdb=" O PHE 3 253 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA 3 259 " --> pdb=" O GLU 3 255 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL 3 260 " --> pdb=" O ARG 3 256 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS 3 265 " --> pdb=" O LEU 3 261 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU 3 266 " --> pdb=" O LYS 3 262 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA 3 267 " --> pdb=" O GLU 3 263 " (cutoff:3.500A) Processing helix chain '3' and resid 275 through 281 removed outlier: 3.836A pdb=" N VAL 3 279 " --> pdb=" O GLU 3 275 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY 3 281 " --> pdb=" O HIS 3 277 " (cutoff:3.500A) Processing helix chain '3' and resid 291 through 294 removed outlier: 3.715A pdb=" N LEU 3 294 " --> pdb=" O ALA 3 291 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 291 through 294' Processing helix chain '3' and resid 295 through 301 Processing helix chain '3' and resid 314 through 319 removed outlier: 3.678A pdb=" N TYR 3 318 " --> pdb=" O GLU 3 314 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL 3 319 " --> pdb=" O TYR 3 315 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 314 through 319' Processing helix chain '3' and resid 339 through 349 removed outlier: 3.614A pdb=" N ILE 3 343 " --> pdb=" O VAL 3 339 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER 3 344 " --> pdb=" O THR 3 340 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY 3 348 " --> pdb=" O SER 3 344 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU 3 349 " --> pdb=" O ILE 3 345 " (cutoff:3.500A) Processing helix chain '3' and resid 349 through 358 Processing helix chain '3' and resid 363 through 373 removed outlier: 3.770A pdb=" N VAL 3 367 " --> pdb=" O ASP 3 363 " (cutoff:3.500A) Processing helix chain '3' and resid 383 through 403 removed outlier: 3.909A pdb=" N ASP 3 388 " --> pdb=" O ASP 3 384 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU 3 389 " --> pdb=" O LYS 3 385 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE 3 390 " --> pdb=" O ALA 3 386 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA 3 393 " --> pdb=" O LEU 3 389 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR 3 397 " --> pdb=" O ALA 3 393 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG 3 398 " --> pdb=" O CYS 3 394 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL 3 399 " --> pdb=" O ALA 3 395 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN 3 400 " --> pdb=" O ASN 3 396 " (cutoff:3.500A) Processing helix chain '3' and resid 405 through 428 removed outlier: 4.294A pdb=" N LEU 3 411 " --> pdb=" O ALA 3 407 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN 3 417 " --> pdb=" O ARG 3 413 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL 3 420 " --> pdb=" O LEU 3 416 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS 3 427 " --> pdb=" O THR 3 423 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU 3 428 " --> pdb=" O ALA 3 424 " (cutoff:3.500A) Processing helix chain '3' and resid 430 through 488 removed outlier: 3.599A pdb=" N LYS 3 434 " --> pdb=" O ASP 3 430 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN 3 435 " --> pdb=" O ALA 3 431 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG 3 436 " --> pdb=" O ALA 3 432 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN 3 438 " --> pdb=" O LYS 3 434 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU 3 439 " --> pdb=" O GLN 3 435 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA 3 442 " --> pdb=" O GLN 3 438 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA 3 445 " --> pdb=" O ARG 3 441 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG 3 446 " --> pdb=" O ALA 3 442 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU 3 449 " --> pdb=" O ALA 3 445 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU 3 450 " --> pdb=" O ARG 3 446 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG 3 452 " --> pdb=" O GLN 3 448 " (cutoff:3.500A) Proline residue: 3 453 - end of helix removed outlier: 4.715A pdb=" N LYS 3 457 " --> pdb=" O PRO 3 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR 3 458 " --> pdb=" O LEU 3 454 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG 3 464 " --> pdb=" O SER 3 460 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU 3 467 " --> pdb=" O GLY 3 463 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG 3 469 " --> pdb=" O LEU 3 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU 3 477 " --> pdb=" O GLN 3 473 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA 3 480 " --> pdb=" O ASP 3 476 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU 3 483 " --> pdb=" O LYS 3 479 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP 3 484 " --> pdb=" O ALA 3 480 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA 3 485 " --> pdb=" O LYS 3 481 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU 3 486 " --> pdb=" O ALA 3 482 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG 3 487 " --> pdb=" O GLU 3 483 " (cutoff:3.500A) Processing helix chain '3' and resid 490 through 495 removed outlier: 3.773A pdb=" N ALA 3 494 " --> pdb=" O ASP 3 490 " (cutoff:3.500A) Processing helix chain '3' and resid 501 through 522 removed outlier: 3.988A pdb=" N LYS 3 507 " --> pdb=" O PRO 3 503 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG 3 508 " --> pdb=" O ASP 3 504 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU 3 509 " --> pdb=" O LEU 3 505 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA 3 510 " --> pdb=" O GLU 3 506 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA 3 514 " --> pdb=" O ALA 3 510 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU 3 515 " --> pdb=" O GLN 3 511 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER 3 517 " --> pdb=" O GLN 3 513 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN 3 518 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA 3 519 " --> pdb=" O GLU 3 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA 3 521 " --> pdb=" O SER 3 517 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU 3 522 " --> pdb=" O GLN 3 518 " (cutoff:3.500A) Processing helix chain '3' and resid 533 through 542 removed outlier: 3.522A pdb=" N ILE 3 537 " --> pdb=" O GLY 3 533 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU 3 539 " --> pdb=" O ASP 3 535 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL 3 540 " --> pdb=" O GLN 3 536 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 3 541 " --> pdb=" O ILE 3 537 " (cutoff:3.500A) Processing helix chain '3' and resid 555 through 562 removed outlier: 3.636A pdb=" N LYS 3 559 " --> pdb=" O SER 3 555 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU 3 561 " --> pdb=" O LYS 3 557 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS 3 562 " --> pdb=" O GLU 3 558 " (cutoff:3.500A) Processing helix chain '3' and resid 563 through 568 removed outlier: 3.972A pdb=" N LYS 3 568 " --> pdb=" O GLU 3 564 " (cutoff:3.500A) Processing helix chain '3' and resid 577 through 584 removed outlier: 3.528A pdb=" N ILE 3 581 " --> pdb=" O ALA 3 577 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS 3 582 " --> pdb=" O ILE 3 578 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP 3 583 " --> pdb=" O LYS 3 579 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA 3 584 " --> pdb=" O ALA 3 580 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 577 through 584' Processing helix chain '3' and resid 585 through 590 Processing helix chain '3' and resid 613 through 619 removed outlier: 3.731A pdb=" N LEU 3 619 " --> pdb=" O CYS 3 615 " (cutoff:3.500A) Processing helix chain '3' and resid 662 through 667 removed outlier: 3.623A pdb=" N VAL 3 667 " --> pdb=" O LEU 3 663 " (cutoff:3.500A) Processing helix chain '3' and resid 684 through 691 removed outlier: 3.596A pdb=" N SER 3 688 " --> pdb=" O HIS 3 684 " (cutoff:3.500A) Processing helix chain '3' and resid 691 through 697 removed outlier: 3.705A pdb=" N LEU 3 695 " --> pdb=" O LEU 3 691 " (cutoff:3.500A) Processing helix chain '3' and resid 742 through 750 removed outlier: 4.328A pdb=" N ALA 3 746 " --> pdb=" O VAL 3 742 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG 3 747 " --> pdb=" O LEU 3 743 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG 3 748 " --> pdb=" O ALA 3 744 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE 3 750 " --> pdb=" O ALA 3 746 " (cutoff:3.500A) Processing helix chain '3' and resid 768 through 771 Processing helix chain '3' and resid 772 through 785 removed outlier: 3.686A pdb=" N VAL 3 776 " --> pdb=" O ILE 3 772 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP 3 777 " --> pdb=" O ARG 3 773 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL 3 778 " --> pdb=" O LYS 3 774 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG 3 779 " --> pdb=" O ILE 3 775 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS 3 781 " --> pdb=" O ASP 3 777 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU 3 782 " --> pdb=" O VAL 3 778 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL 3 783 " --> pdb=" O ARG 3 779 " (cutoff:3.500A) Processing helix chain '3' and resid 799 through 808 removed outlier: 3.506A pdb=" N LEU 3 803 " --> pdb=" O LYS 3 799 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN 3 806 " --> pdb=" O ASP 3 802 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN 3 807 " --> pdb=" O LEU 3 803 " (cutoff:3.500A) Processing helix chain '3' and resid 815 through 822 removed outlier: 3.585A pdb=" N ARG 3 820 " --> pdb=" O ARG 3 816 " (cutoff:3.500A) Processing helix chain '3' and resid 825 through 834 removed outlier: 4.183A pdb=" N GLN 3 829 " --> pdb=" O ALA 3 825 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU 3 830 " --> pdb=" O LEU 3 826 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG 3 832 " --> pdb=" O THR 3 828 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU 3 833 " --> pdb=" O GLN 3 829 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU 3 834 " --> pdb=" O LEU 3 830 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 24 removed outlier: 3.582A pdb=" N LYS 4 19 " --> pdb=" O ASN 4 15 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN 4 24 " --> pdb=" O TYR 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 31 through 39 removed outlier: 4.391A pdb=" N ALA 4 35 " --> pdb=" O PRO 4 31 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL 4 36 " --> pdb=" O SER 4 32 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 4 39 " --> pdb=" O ALA 4 35 " (cutoff:3.500A) Processing helix chain '4' and resid 46 through 54 removed outlier: 3.846A pdb=" N LEU 4 50 " --> pdb=" O PHE 4 46 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU 4 51 " --> pdb=" O ARG 4 47 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS 4 52 " --> pdb=" O SER 4 48 " (cutoff:3.500A) Processing helix chain '4' and resid 56 through 62 Processing helix chain '4' and resid 63 through 71 removed outlier: 4.217A pdb=" N ILE 4 67 " --> pdb=" O GLY 4 63 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 99 removed outlier: 3.954A pdb=" N LYS 4 89 " --> pdb=" O PRO 4 85 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS 4 95 " --> pdb=" O LEU 4 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU 4 96 " --> pdb=" O HIS 4 92 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS 4 99 " --> pdb=" O HIS 4 95 " (cutoff:3.500A) Processing helix chain '4' and resid 107 through 113 removed outlier: 4.016A pdb=" N LEU 4 111 " --> pdb=" O ALA 4 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE 4 112 " --> pdb=" O GLN 4 108 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU 4 113 " --> pdb=" O ASP 4 109 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 107 through 113' Processing helix chain '4' and resid 121 through 129 removed outlier: 4.020A pdb=" N LEU 4 125 " --> pdb=" O MET 4 121 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY 4 128 " --> pdb=" O VAL 4 124 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY 4 129 " --> pdb=" O LEU 4 125 " (cutoff:3.500A) Processing helix chain '4' and resid 131 through 137 removed outlier: 3.542A pdb=" N ASN 4 137 " --> pdb=" O LYS 4 133 " (cutoff:3.500A) Processing helix chain '4' and resid 138 through 144 removed outlier: 3.800A pdb=" N VAL 4 142 " --> pdb=" O ALA 4 138 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG 4 143 " --> pdb=" O VAL 4 139 " (cutoff:3.500A) Processing helix chain '4' and resid 158 through 163 removed outlier: 3.650A pdb=" N TYR 4 163 " --> pdb=" O ALA 4 159 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 173 Processing helix chain '4' and resid 185 through 194 removed outlier: 3.861A pdb=" N ILE 4 190 " --> pdb=" O ILE 4 186 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG 4 191 " --> pdb=" O SER 4 187 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL 4 192 " --> pdb=" O ARG 4 188 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER 4 194 " --> pdb=" O ILE 4 190 " (cutoff:3.500A) Processing helix chain '4' and resid 211 through 225 removed outlier: 4.058A pdb=" N ALA 4 215 " --> pdb=" O LYS 4 211 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU 4 218 " --> pdb=" O ILE 4 214 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 4 219 " --> pdb=" O ALA 4 215 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN 4 220 " --> pdb=" O GLU 4 216 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG 4 221 " --> pdb=" O GLY 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 228 through 232 removed outlier: 4.080A pdb=" N GLN 4 232 " --> pdb=" O SER 4 229 " (cutoff:3.500A) Processing helix chain '4' and resid 252 through 267 removed outlier: 4.030A pdb=" N LYS 4 258 " --> pdb=" O GLU 4 254 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU 4 263 " --> pdb=" O ALA 4 259 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU 4 264 " --> pdb=" O VAL 4 260 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS 4 265 " --> pdb=" O LEU 4 261 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU 4 266 " --> pdb=" O LYS 4 262 " (cutoff:3.500A) Processing helix chain '4' and resid 275 through 280 removed outlier: 4.347A pdb=" N VAL 4 279 " --> pdb=" O GLU 4 275 " (cutoff:3.500A) Processing helix chain '4' and resid 291 through 301 removed outlier: 3.857A pdb=" N LEU 4 295 " --> pdb=" O ALA 4 291 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS 4 296 " --> pdb=" O ALA 4 292 " (cutoff:3.500A) Proline residue: 4 297 - end of helix Processing helix chain '4' and resid 312 through 319 removed outlier: 3.652A pdb=" N ARG 4 316 " --> pdb=" O LEU 4 312 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN 4 317 " --> pdb=" O THR 4 313 " (cutoff:3.500A) Processing helix chain '4' and resid 322 through 327 Processing helix chain '4' and resid 338 through 349 removed outlier: 3.635A pdb=" N ILE 4 343 " --> pdb=" O VAL 4 339 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER 4 344 " --> pdb=" O THR 4 340 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU 4 349 " --> pdb=" O ILE 4 345 " (cutoff:3.500A) Processing helix chain '4' and resid 349 through 357 removed outlier: 4.004A pdb=" N THR 4 355 " --> pdb=" O GLU 4 351 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS 4 356 " --> pdb=" O ARG 4 352 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS 4 357 " --> pdb=" O TYR 4 353 " (cutoff:3.500A) Processing helix chain '4' and resid 363 through 374 removed outlier: 4.423A pdb=" N VAL 4 367 " --> pdb=" O ASP 4 363 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA 4 368 " --> pdb=" O ALA 4 364 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA 4 369 " --> pdb=" O ALA 4 365 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA 4 370 " --> pdb=" O ILE 4 366 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN 4 371 " --> pdb=" O VAL 4 367 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA 4 374 " --> pdb=" O ALA 4 370 " (cutoff:3.500A) Processing helix chain '4' and resid 383 through 403 removed outlier: 3.611A pdb=" N ASP 4 388 " --> pdb=" O ASP 4 384 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU 4 389 " --> pdb=" O LYS 4 385 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE 4 390 " --> pdb=" O ALA 4 386 " (cutoff:3.500A) Processing helix chain '4' and resid 405 through 425 removed outlier: 3.618A pdb=" N LYS 4 410 " --> pdb=" O GLU 4 406 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU 4 411 " --> pdb=" O ALA 4 407 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG 4 414 " --> pdb=" O LYS 4 410 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN 4 417 " --> pdb=" O ARG 4 413 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL 4 420 " --> pdb=" O LEU 4 416 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU 4 421 " --> pdb=" O GLN 4 417 " (cutoff:3.500A) Processing helix chain '4' and resid 430 through 488 removed outlier: 4.150A pdb=" N GLN 4 435 " --> pdb=" O ALA 4 431 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG 4 436 " --> pdb=" O ALA 4 432 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN 4 438 " --> pdb=" O LYS 4 434 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU 4 439 " --> pdb=" O GLN 4 435 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 4 442 " --> pdb=" O GLN 4 438 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG 4 446 " --> pdb=" O ALA 4 442 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU 4 450 " --> pdb=" O ARG 4 446 " (cutoff:3.500A) Proline residue: 4 453 - end of helix removed outlier: 3.760A pdb=" N LYS 4 457 " --> pdb=" O PRO 4 453 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER 4 460 " --> pdb=" O MET 4 456 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG 4 464 " --> pdb=" O SER 4 460 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP 4 476 " --> pdb=" O SER 4 472 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU 4 477 " --> pdb=" O GLN 4 473 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA 4 480 " --> pdb=" O ASP 4 476 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU 4 483 " --> pdb=" O LYS 4 479 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP 4 484 " --> pdb=" O ALA 4 480 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA 4 485 " --> pdb=" O LYS 4 481 " (cutoff:3.500A) Processing helix chain '4' and resid 490 through 501 removed outlier: 4.313A pdb=" N ASP 4 496 " --> pdb=" O ALA 4 492 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 4 497 " --> pdb=" O ARG 4 493 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA 4 501 " --> pdb=" O ILE 4 497 " (cutoff:3.500A) Processing helix chain '4' and resid 501 through 522 removed outlier: 3.632A pdb=" N LYS 4 507 " --> pdb=" O PRO 4 503 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG 4 508 " --> pdb=" O ASP 4 504 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU 4 509 " --> pdb=" O LEU 4 505 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU 4 515 " --> pdb=" O GLN 4 511 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER 4 517 " --> pdb=" O GLN 4 513 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN 4 518 " --> pdb=" O ALA 4 514 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU 4 522 " --> pdb=" O GLN 4 518 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 545 removed outlier: 3.526A pdb=" N ILE 4 537 " --> pdb=" O GLY 4 533 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL 4 540 " --> pdb=" O GLN 4 536 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL 4 541 " --> pdb=" O ILE 4 537 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG 4 543 " --> pdb=" O GLU 4 539 " (cutoff:3.500A) Processing helix chain '4' and resid 548 through 553 removed outlier: 3.862A pdb=" N LEU 4 552 " --> pdb=" O PRO 4 548 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN 4 553 " --> pdb=" O VAL 4 549 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 548 through 553' Processing helix chain '4' and resid 555 through 562 removed outlier: 3.821A pdb=" N LEU 4 561 " --> pdb=" O LYS 4 557 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS 4 562 " --> pdb=" O GLU 4 558 " (cutoff:3.500A) Processing helix chain '4' and resid 562 through 571 removed outlier: 3.757A pdb=" N TYR 4 566 " --> pdb=" O HIS 4 562 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET 4 567 " --> pdb=" O MET 4 563 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS 4 568 " --> pdb=" O GLU 4 564 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN 4 569 " --> pdb=" O GLU 4 565 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS 4 570 " --> pdb=" O TYR 4 566 " (cutoff:3.500A) Processing helix chain '4' and resid 574 through 587 removed outlier: 4.359A pdb=" N LYS 4 579 " --> pdb=" O ASP 4 575 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA 4 580 " --> pdb=" O GLU 4 576 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA 4 584 " --> pdb=" O ALA 4 580 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE 4 585 " --> pdb=" O ILE 4 581 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG 4 586 " --> pdb=" O CYS 4 582 " (cutoff:3.500A) Processing helix chain '4' and resid 613 through 623 Processing helix chain '4' and resid 646 through 647 No H-bonds generated for 'chain '4' and resid 646 through 647' Processing helix chain '4' and resid 661 through 661 No H-bonds generated for 'chain '4' and resid 661 through 661' Processing helix chain '4' and resid 662 through 667 removed outlier: 3.820A pdb=" N VAL 4 667 " --> pdb=" O LEU 4 663 " (cutoff:3.500A) Processing helix chain '4' and resid 680 through 683 Processing helix chain '4' and resid 686 through 691 removed outlier: 3.798A pdb=" N LEU 4 690 " --> pdb=" O ASP 4 686 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU 4 691 " --> pdb=" O VAL 4 687 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 686 through 691' Processing helix chain '4' and resid 691 through 698 removed outlier: 3.516A pdb=" N LEU 4 695 " --> pdb=" O LEU 4 691 " (cutoff:3.500A) Processing helix chain '4' and resid 739 through 750 removed outlier: 3.789A pdb=" N LEU 4 743 " --> pdb=" O LYS 4 739 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA 4 746 " --> pdb=" O VAL 4 742 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG 4 747 " --> pdb=" O LEU 4 743 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG 4 748 " --> pdb=" O ALA 4 744 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS 4 749 " --> pdb=" O THR 4 745 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE 4 750 " --> pdb=" O ALA 4 746 " (cutoff:3.500A) Processing helix chain '4' and resid 768 through 772 removed outlier: 3.518A pdb=" N ILE 4 772 " --> pdb=" O PRO 4 769 " (cutoff:3.500A) Processing helix chain '4' and resid 774 through 786 removed outlier: 3.849A pdb=" N VAL 4 778 " --> pdb=" O LYS 4 774 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU 4 780 " --> pdb=" O VAL 4 776 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS 4 781 " --> pdb=" O ASP 4 777 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU 4 782 " --> pdb=" O VAL 4 778 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL 4 783 " --> pdb=" O ARG 4 779 " (cutoff:3.500A) Processing helix chain '4' and resid 787 through 791 removed outlier: 3.503A pdb=" N LYS 4 790 " --> pdb=" O LEU 4 787 " (cutoff:3.500A) Processing helix chain '4' and resid 797 through 808 removed outlier: 3.797A pdb=" N LYS 4 801 " --> pdb=" O ASP 4 797 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP 4 802 " --> pdb=" O ASP 4 798 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU 4 803 " --> pdb=" O LYS 4 799 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU 4 804 " --> pdb=" O ALA 4 800 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA 4 805 " --> pdb=" O LYS 4 801 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY 4 808 " --> pdb=" O LEU 4 804 " (cutoff:3.500A) Processing helix chain '4' and resid 815 through 824 removed outlier: 3.963A pdb=" N ASN 4 819 " --> pdb=" O ALA 4 815 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG 4 820 " --> pdb=" O ARG 4 816 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE 4 822 " --> pdb=" O LEU 4 818 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN 4 823 " --> pdb=" O ASN 4 819 " (cutoff:3.500A) Processing helix chain '4' and resid 825 through 834 removed outlier: 3.606A pdb=" N GLN 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG 4 832 " --> pdb=" O THR 4 828 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 4 834 " --> pdb=" O LEU 4 830 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 24 removed outlier: 3.632A pdb=" N GLU 5 12 " --> pdb=" O ASP 5 8 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR 5 13 " --> pdb=" O LYS 5 9 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA 5 16 " --> pdb=" O GLU 5 12 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS 5 19 " --> pdb=" O ASN 5 15 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA 5 21 " --> pdb=" O ALA 5 17 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA 5 22 " --> pdb=" O ALA 5 18 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU 5 23 " --> pdb=" O LYS 5 19 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN 5 24 " --> pdb=" O TYR 5 20 " (cutoff:3.500A) Processing helix chain '5' and resid 31 through 40 removed outlier: 4.400A pdb=" N ALA 5 35 " --> pdb=" O PRO 5 31 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL 5 36 " --> pdb=" O SER 5 32 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 54 removed outlier: 3.649A pdb=" N LEU 5 50 " --> pdb=" O PHE 5 46 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS 5 52 " --> pdb=" O SER 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 56 through 71 removed outlier: 3.645A pdb=" N ILE 5 67 " --> pdb=" O GLY 5 63 " (cutoff:3.500A) Processing helix chain '5' and resid 84 through 101 removed outlier: 4.155A pdb=" N ALA 5 88 " --> pdb=" O SER 5 84 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS 5 89 " --> pdb=" O PRO 5 85 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS 5 92 " --> pdb=" O ALA 5 88 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR 5 93 " --> pdb=" O LYS 5 89 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU 5 96 " --> pdb=" O HIS 5 92 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS 5 97 " --> pdb=" O TYR 5 93 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET 5 98 " --> pdb=" O ALA 5 94 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS 5 99 " --> pdb=" O HIS 5 95 " (cutoff:3.500A) Processing helix chain '5' and resid 107 through 114 removed outlier: 3.998A pdb=" N LEU 5 111 " --> pdb=" O ALA 5 107 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA 5 114 " --> pdb=" O HIS 5 110 " (cutoff:3.500A) Processing helix chain '5' and resid 115 through 117 No H-bonds generated for 'chain '5' and resid 115 through 117' Processing helix chain '5' and resid 121 through 129 removed outlier: 4.310A pdb=" N LEU 5 125 " --> pdb=" O MET 5 121 " (cutoff:3.500A) Processing helix chain '5' and resid 131 through 144 removed outlier: 3.722A pdb=" N GLU 5 136 " --> pdb=" O LYS 5 132 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN 5 137 " --> pdb=" O LYS 5 133 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL 5 139 " --> pdb=" O LEU 5 135 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR 5 140 " --> pdb=" O GLU 5 136 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS 5 141 " --> pdb=" O ASN 5 137 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL 5 142 " --> pdb=" O ALA 5 138 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG 5 143 " --> pdb=" O VAL 5 139 " (cutoff:3.500A) Processing helix chain '5' and resid 157 through 163 removed outlier: 3.531A pdb=" N TYR 5 163 " --> pdb=" O ALA 5 159 " (cutoff:3.500A) Processing helix chain '5' and resid 167 through 173 Processing helix chain '5' and resid 182 through 194 removed outlier: 3.511A pdb=" N SER 5 187 " --> pdb=" O ASP 5 183 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG 5 188 " --> pdb=" O GLU 5 184 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL 5 189 " --> pdb=" O ILE 5 185 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE 5 190 " --> pdb=" O ILE 5 186 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG 5 191 " --> pdb=" O SER 5 187 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL 5 192 " --> pdb=" O ARG 5 188 " (cutoff:3.500A) Processing helix chain '5' and resid 211 through 224 removed outlier: 4.019A pdb=" N ALA 5 215 " --> pdb=" O LYS 5 211 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA 5 219 " --> pdb=" O ALA 5 215 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN 5 220 " --> pdb=" O GLU 5 216 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG 5 221 " --> pdb=" O GLY 5 217 " (cutoff:3.500A) Processing helix chain '5' and resid 228 through 232 removed outlier: 3.637A pdb=" N GLN 5 232 " --> pdb=" O SER 5 229 " (cutoff:3.500A) Processing helix chain '5' and resid 239 through 245 removed outlier: 3.844A pdb=" N LEU 5 243 " --> pdb=" O ASP 5 239 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA 5 245 " --> pdb=" O GLY 5 241 " (cutoff:3.500A) Processing helix chain '5' and resid 252 through 268 removed outlier: 3.537A pdb=" N LYS 5 258 " --> pdb=" O GLU 5 254 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS 5 265 " --> pdb=" O LEU 5 261 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU 5 266 " --> pdb=" O LYS 5 262 " (cutoff:3.500A) Processing helix chain '5' and resid 339 through 347 removed outlier: 3.640A pdb=" N ILE 5 343 " --> pdb=" O VAL 5 339 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER 5 344 " --> pdb=" O THR 5 340 " (cutoff:3.500A) Processing helix chain '5' and resid 349 through 357 removed outlier: 3.515A pdb=" N THR 5 355 " --> pdb=" O GLU 5 351 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS 5 357 " --> pdb=" O TYR 5 353 " (cutoff:3.500A) Processing helix chain '5' and resid 363 through 374 removed outlier: 3.960A pdb=" N VAL 5 367 " --> pdb=" O ASP 5 363 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA 5 369 " --> pdb=" O ALA 5 365 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA 5 370 " --> pdb=" O ILE 5 366 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA 5 374 " --> pdb=" O ALA 5 370 " (cutoff:3.500A) Processing helix chain '5' and resid 383 through 403 removed outlier: 3.783A pdb=" N ASP 5 388 " --> pdb=" O ASP 5 384 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE 5 390 " --> pdb=" O ALA 5 386 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA 5 393 " --> pdb=" O LEU 5 389 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA 5 395 " --> pdb=" O ASP 5 391 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR 5 397 " --> pdb=" O ALA 5 393 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG 5 398 " --> pdb=" O CYS 5 394 " (cutoff:3.500A) Processing helix chain '5' and resid 405 through 428 removed outlier: 4.693A pdb=" N LEU 5 411 " --> pdb=" O ALA 5 407 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN 5 417 " --> pdb=" O ARG 5 413 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU 5 425 " --> pdb=" O GLU 5 421 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU 5 426 " --> pdb=" O ALA 5 422 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS 5 427 " --> pdb=" O THR 5 423 " (cutoff:3.500A) Processing helix chain '5' and resid 430 through 488 removed outlier: 3.801A pdb=" N LYS 5 434 " --> pdb=" O ASP 5 430 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN 5 435 " --> pdb=" O ALA 5 431 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN 5 438 " --> pdb=" O LYS 5 434 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU 5 439 " --> pdb=" O GLN 5 435 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA 5 442 " --> pdb=" O GLN 5 438 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA 5 445 " --> pdb=" O ARG 5 441 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG 5 446 " --> pdb=" O ALA 5 442 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU 5 450 " --> pdb=" O ARG 5 446 " (cutoff:3.500A) Proline residue: 5 453 - end of helix removed outlier: 3.859A pdb=" N LYS 5 457 " --> pdb=" O PRO 5 453 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG 5 474 " --> pdb=" O ASN 5 470 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP 5 476 " --> pdb=" O SER 5 472 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU 5 477 " --> pdb=" O GLN 5 473 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU 5 483 " --> pdb=" O LYS 5 479 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP 5 484 " --> pdb=" O ALA 5 480 " (cutoff:3.500A) Processing helix chain '5' and resid 490 through 499 removed outlier: 3.636A pdb=" N ALA 5 494 " --> pdb=" O ASP 5 490 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA 5 495 " --> pdb=" O LEU 5 491 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASP 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE 5 497 " --> pdb=" O ARG 5 493 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR 5 499 " --> pdb=" O ALA 5 495 " (cutoff:3.500A) Processing helix chain '5' and resid 500 through 524 removed outlier: 4.089A pdb=" N ARG 5 508 " --> pdb=" O ASP 5 504 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU 5 509 " --> pdb=" O LEU 5 505 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 5 512 " --> pdb=" O ARG 5 508 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA 5 514 " --> pdb=" O ALA 5 510 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU 5 515 " --> pdb=" O GLN 5 511 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA 5 521 " --> pdb=" O SER 5 517 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU 5 522 " --> pdb=" O GLN 5 518 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG 5 523 " --> pdb=" O ALA 5 519 " (cutoff:3.500A) Processing helix chain '5' and resid 533 through 546 removed outlier: 3.585A pdb=" N ILE 5 537 " --> pdb=" O GLY 5 533 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU 5 539 " --> pdb=" O ASP 5 535 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL 5 540 " --> pdb=" O GLN 5 536 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL 5 541 " --> pdb=" O ILE 5 537 " (cutoff:3.500A) Processing helix chain '5' and resid 548 through 553 removed outlier: 3.735A pdb=" N LEU 5 552 " --> pdb=" O PRO 5 548 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN 5 553 " --> pdb=" O VAL 5 549 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 548 through 553' Processing helix chain '5' and resid 556 through 561 removed outlier: 3.619A pdb=" N LEU 5 560 " --> pdb=" O GLU 5 556 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU 5 561 " --> pdb=" O LYS 5 557 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 556 through 561' Processing helix chain '5' and resid 562 through 567 removed outlier: 3.642A pdb=" N TYR 5 566 " --> pdb=" O HIS 5 562 " (cutoff:3.500A) Processing helix chain '5' and resid 574 through 588 removed outlier: 4.302A pdb=" N LYS 5 579 " --> pdb=" O ASP 5 575 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA 5 580 " --> pdb=" O GLU 5 576 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP 5 583 " --> pdb=" O LYS 5 579 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA 5 584 " --> pdb=" O ALA 5 580 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE 5 585 " --> pdb=" O ILE 5 581 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU 5 587 " --> pdb=" O ASP 5 583 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER 5 588 " --> pdb=" O ALA 5 584 " (cutoff:3.500A) Processing helix chain '5' and resid 612 through 620 removed outlier: 3.774A pdb=" N VAL 5 616 " --> pdb=" O LYS 5 612 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA 5 620 " --> pdb=" O VAL 5 616 " (cutoff:3.500A) Processing helix chain '5' and resid 662 through 670 removed outlier: 3.511A pdb=" N VAL 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG 5 669 " --> pdb=" O GLU 5 665 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG 5 670 " --> pdb=" O ALA 5 666 " (cutoff:3.500A) Processing helix chain '5' and resid 684 through 698 removed outlier: 3.978A pdb=" N ASN 5 689 " --> pdb=" O LYS 5 685 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU 5 690 " --> pdb=" O ASP 5 686 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU 5 691 " --> pdb=" O VAL 5 687 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN 5 693 " --> pdb=" O ASN 5 689 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE 5 694 " --> pdb=" O LEU 5 690 " (cutoff:3.500A) Processing helix chain '5' and resid 739 through 748 removed outlier: 3.715A pdb=" N ALA 5 744 " --> pdb=" O ASN 5 740 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR 5 745 " --> pdb=" O ALA 5 741 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA 5 746 " --> pdb=" O VAL 5 742 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG 5 747 " --> pdb=" O LEU 5 743 " (cutoff:3.500A) Processing helix chain '5' and resid 768 through 770 No H-bonds generated for 'chain '5' and resid 768 through 770' Processing helix chain '5' and resid 771 through 788 removed outlier: 3.547A pdb=" N ILE 5 775 " --> pdb=" O ASN 5 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL 5 776 " --> pdb=" O ILE 5 772 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP 5 777 " --> pdb=" O ARG 5 773 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL 5 778 " --> pdb=" O LYS 5 774 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG 5 779 " --> pdb=" O ILE 5 775 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU 5 780 " --> pdb=" O VAL 5 776 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU 5 782 " --> pdb=" O VAL 5 778 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL 5 783 " --> pdb=" O ARG 5 779 " (cutoff:3.500A) Processing helix chain '5' and resid 797 through 805 removed outlier: 3.969A pdb=" N LYS 5 801 " --> pdb=" O ASP 5 797 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP 5 802 " --> pdb=" O ASP 5 798 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU 5 803 " --> pdb=" O LYS 5 799 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU 5 804 " --> pdb=" O ALA 5 800 " (cutoff:3.500A) Processing helix chain '5' and resid 815 through 826 removed outlier: 3.809A pdb=" N ASN 5 819 " --> pdb=" O ALA 5 815 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG 5 820 " --> pdb=" O ARG 5 816 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE 5 822 " --> pdb=" O LEU 5 818 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN 5 823 " --> pdb=" O ASN 5 819 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS 5 824 " --> pdb=" O ARG 5 820 " (cutoff:3.500A) Processing helix chain '5' and resid 826 through 836 removed outlier: 3.714A pdb=" N LEU 5 830 " --> pdb=" O LEU 5 826 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER 5 831 " --> pdb=" O LEU 5 827 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG 5 832 " --> pdb=" O THR 5 828 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU 5 834 " --> pdb=" O LEU 5 830 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU 5 835 " --> pdb=" O SER 5 831 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP 5 836 " --> pdb=" O ARG 5 832 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 24 removed outlier: 3.540A pdb=" N GLU 6 12 " --> pdb=" O ASP 6 8 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU 6 14 " --> pdb=" O ALA 6 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA 6 18 " --> pdb=" O LEU 6 14 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS 6 19 " --> pdb=" O ASN 6 15 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR 6 20 " --> pdb=" O ALA 6 16 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU 6 23 " --> pdb=" O LYS 6 19 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN 6 24 " --> pdb=" O TYR 6 20 " (cutoff:3.500A) Processing helix chain '6' and resid 31 through 40 removed outlier: 4.200A pdb=" N ALA 6 35 " --> pdb=" O PRO 6 31 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL 6 36 " --> pdb=" O SER 6 32 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 54 removed outlier: 3.560A pdb=" N SER 6 48 " --> pdb=" O SER 6 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU 6 50 " --> pdb=" O PHE 6 46 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS 6 52 " --> pdb=" O SER 6 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA 6 53 " --> pdb=" O ILE 6 49 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY 6 54 " --> pdb=" O LEU 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 56 through 71 removed outlier: 3.693A pdb=" N ILE 6 60 " --> pdb=" O ASP 6 56 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE 6 64 " --> pdb=" O ILE 6 60 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS 6 65 " --> pdb=" O GLU 6 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS 6 66 " --> pdb=" O ARG 6 62 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE 6 67 " --> pdb=" O GLY 6 63 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET 6 68 " --> pdb=" O PHE 6 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL 6 69 " --> pdb=" O LYS 6 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG 6 70 " --> pdb=" O LYS 6 66 " (cutoff:3.500A) Processing helix chain '6' and resid 84 through 102 removed outlier: 3.633A pdb=" N ALA 6 88 " --> pdb=" O SER 6 84 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS 6 89 " --> pdb=" O PRO 6 85 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 6 90 " --> pdb=" O GLU 6 86 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU 6 91 " --> pdb=" O LEU 6 87 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU 6 96 " --> pdb=" O HIS 6 92 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS 6 97 " --> pdb=" O TYR 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 108 through 112 Processing helix chain '6' and resid 121 through 129 removed outlier: 3.919A pdb=" N LEU 6 125 " --> pdb=" O MET 6 121 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY 6 128 " --> pdb=" O VAL 6 124 " (cutoff:3.500A) Processing helix chain '6' and resid 131 through 144 removed outlier: 3.838A pdb=" N GLU 6 136 " --> pdb=" O LYS 6 132 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN 6 137 " --> pdb=" O LYS 6 133 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR 6 140 " --> pdb=" O GLU 6 136 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL 6 142 " --> pdb=" O ALA 6 138 " (cutoff:3.500A) Processing helix chain '6' and resid 158 through 163 Processing helix chain '6' and resid 167 through 173 Processing helix chain '6' and resid 182 through 194 removed outlier: 3.903A pdb=" N SER 6 187 " --> pdb=" O ASP 6 183 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG 6 188 " --> pdb=" O GLU 6 184 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE 6 190 " --> pdb=" O ILE 6 186 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG 6 191 " --> pdb=" O SER 6 187 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER 6 194 " --> pdb=" O ILE 6 190 " (cutoff:3.500A) Processing helix chain '6' and resid 211 through 225 removed outlier: 4.178A pdb=" N ALA 6 215 " --> pdb=" O LYS 6 211 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU 6 218 " --> pdb=" O ILE 6 214 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG 6 221 " --> pdb=" O GLY 6 217 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE 6 222 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL 6 223 " --> pdb=" O ALA 6 219 " (cutoff:3.500A) Processing helix chain '6' and resid 241 through 245 removed outlier: 3.561A pdb=" N ALA 6 245 " --> pdb=" O SER 6 242 " (cutoff:3.500A) Processing helix chain '6' and resid 252 through 268 removed outlier: 3.547A pdb=" N LYS 6 258 " --> pdb=" O GLU 6 254 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU 6 263 " --> pdb=" O ALA 6 259 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU 6 264 " --> pdb=" O VAL 6 260 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS 6 265 " --> pdb=" O LEU 6 261 " (cutoff:3.500A) Processing helix chain '6' and resid 295 through 301 Processing helix chain '6' and resid 312 through 317 removed outlier: 3.570A pdb=" N ARG 6 316 " --> pdb=" O LEU 6 312 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN 6 317 " --> pdb=" O THR 6 313 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 312 through 317' Processing helix chain '6' and resid 322 through 327 removed outlier: 3.551A pdb=" N ARG 6 327 " --> pdb=" O PRO 6 323 " (cutoff:3.500A) Processing helix chain '6' and resid 339 through 349 removed outlier: 3.618A pdb=" N SER 6 344 " --> pdb=" O THR 6 340 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY 6 348 " --> pdb=" O SER 6 344 " (cutoff:3.500A) Processing helix chain '6' and resid 349 through 357 removed outlier: 3.653A pdb=" N TYR 6 353 " --> pdb=" O LEU 6 349 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR 6 355 " --> pdb=" O GLU 6 351 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS 6 356 " --> pdb=" O ARG 6 352 " (cutoff:3.500A) Processing helix chain '6' and resid 363 through 377 removed outlier: 3.925A pdb=" N VAL 6 367 " --> pdb=" O ASP 6 363 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA 6 370 " --> pdb=" O ILE 6 366 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA 6 374 " --> pdb=" O ALA 6 370 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG 6 375 " --> pdb=" O GLN 6 371 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR 6 376 " --> pdb=" O LEU 6 372 " (cutoff:3.500A) Processing helix chain '6' and resid 383 through 403 removed outlier: 3.642A pdb=" N ASP 6 388 " --> pdb=" O ASP 6 384 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU 6 389 " --> pdb=" O LYS 6 385 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE 6 390 " --> pdb=" O ALA 6 386 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA 6 395 " --> pdb=" O ASP 6 391 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN 6 396 " --> pdb=" O GLU 6 392 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR 6 397 " --> pdb=" O ALA 6 393 " (cutoff:3.500A) Processing helix chain '6' and resid 405 through 426 removed outlier: 4.259A pdb=" N LEU 6 411 " --> pdb=" O ALA 6 407 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA 6 424 " --> pdb=" O VAL 6 420 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU 6 426 " --> pdb=" O ALA 6 422 " (cutoff:3.500A) Processing helix chain '6' and resid 433 through 450 removed outlier: 3.519A pdb=" N GLN 6 438 " --> pdb=" O LYS 6 434 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU 6 439 " --> pdb=" O GLN 6 435 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG 6 446 " --> pdb=" O ALA 6 442 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU 6 450 " --> pdb=" O ARG 6 446 " (cutoff:3.500A) Processing helix chain '6' and resid 451 through 488 removed outlier: 4.139A pdb=" N LYS 6 457 " --> pdb=" O PRO 6 453 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU 6 467 " --> pdb=" O GLY 6 463 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG 6 469 " --> pdb=" O LEU 6 465 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG 6 474 " --> pdb=" O ASN 6 470 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP 6 476 " --> pdb=" O SER 6 472 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU 6 477 " --> pdb=" O GLN 6 473 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU 6 483 " --> pdb=" O LYS 6 479 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG 6 487 " --> pdb=" O GLU 6 483 " (cutoff:3.500A) Processing helix chain '6' and resid 490 through 495 removed outlier: 3.642A pdb=" N ALA 6 495 " --> pdb=" O LEU 6 491 " (cutoff:3.500A) Processing helix chain '6' and resid 501 through 524 removed outlier: 3.588A pdb=" N LYS 6 507 " --> pdb=" O PRO 6 503 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN 6 511 " --> pdb=" O LYS 6 507 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU 6 512 " --> pdb=" O ARG 6 508 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER 6 517 " --> pdb=" O GLN 6 513 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN 6 518 " --> pdb=" O ALA 6 514 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP 6 520 " --> pdb=" O LYS 6 516 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA 6 521 " --> pdb=" O SER 6 517 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU 6 522 " --> pdb=" O GLN 6 518 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG 6 523 " --> pdb=" O ALA 6 519 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA 6 524 " --> pdb=" O ASP 6 520 " (cutoff:3.500A) Processing helix chain '6' and resid 533 through 545 removed outlier: 3.552A pdb=" N ILE 6 537 " --> pdb=" O GLY 6 533 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU 6 539 " --> pdb=" O ASP 6 535 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL 6 540 " --> pdb=" O GLN 6 536 " (cutoff:3.500A) Processing helix chain '6' and resid 548 through 552 removed outlier: 3.671A pdb=" N ASN 6 551 " --> pdb=" O PRO 6 548 " (cutoff:3.500A) Processing helix chain '6' and resid 555 through 562 removed outlier: 3.521A pdb=" N LYS 6 559 " --> pdb=" O SER 6 555 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU 6 560 " --> pdb=" O GLU 6 556 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS 6 562 " --> pdb=" O GLU 6 558 " (cutoff:3.500A) Processing helix chain '6' and resid 562 through 568 removed outlier: 3.795A pdb=" N TYR 6 566 " --> pdb=" O HIS 6 562 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS 6 568 " --> pdb=" O GLU 6 564 " (cutoff:3.500A) Processing helix chain '6' and resid 574 through 591 removed outlier: 3.718A pdb=" N ILE 6 578 " --> pdb=" O GLN 6 574 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS 6 579 " --> pdb=" O ASP 6 575 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA 6 580 " --> pdb=" O GLU 6 576 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE 6 581 " --> pdb=" O ALA 6 577 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS 6 582 " --> pdb=" O ILE 6 578 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA 6 584 " --> pdb=" O ALA 6 580 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU 6 587 " --> pdb=" O ASP 6 583 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER 6 588 " --> pdb=" O ALA 6 584 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR 6 590 " --> pdb=" O ARG 6 586 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY 6 591 " --> pdb=" O LEU 6 587 " (cutoff:3.500A) Processing helix chain '6' and resid 613 through 621 removed outlier: 3.580A pdb=" N LYS 6 617 " --> pdb=" O THR 6 613 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA 6 620 " --> pdb=" O VAL 6 616 " (cutoff:3.500A) Processing helix chain '6' and resid 636 through 638 No H-bonds generated for 'chain '6' and resid 636 through 638' Processing helix chain '6' and resid 662 through 667 removed outlier: 3.639A pdb=" N VAL 6 667 " --> pdb=" O LEU 6 663 " (cutoff:3.500A) Processing helix chain '6' and resid 679 through 683 Processing helix chain '6' and resid 684 through 689 removed outlier: 3.644A pdb=" N ASN 6 689 " --> pdb=" O LYS 6 685 " (cutoff:3.500A) Processing helix chain '6' and resid 689 through 698 removed outlier: 3.779A pdb=" N GLN 6 693 " --> pdb=" O ASN 6 689 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE 6 694 " --> pdb=" O LEU 6 690 " (cutoff:3.500A) Processing helix chain '6' and resid 739 through 750 removed outlier: 3.717A pdb=" N LEU 6 743 " --> pdb=" O LYS 6 739 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA 6 744 " --> pdb=" O ASN 6 740 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR 6 745 " --> pdb=" O ALA 6 741 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA 6 746 " --> pdb=" O VAL 6 742 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG 6 747 " --> pdb=" O LEU 6 743 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG 6 748 " --> pdb=" O ALA 6 744 " (cutoff:3.500A) Processing helix chain '6' and resid 751 through 756 removed outlier: 3.923A pdb=" N ASN 6 756 " --> pdb=" O ASN 6 752 " (cutoff:3.500A) Processing helix chain '6' and resid 768 through 770 No H-bonds generated for 'chain '6' and resid 768 through 770' Processing helix chain '6' and resid 771 through 785 removed outlier: 3.547A pdb=" N ILE 6 775 " --> pdb=" O ASN 6 771 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL 6 776 " --> pdb=" O ILE 6 772 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP 6 777 " --> pdb=" O ARG 6 773 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL 6 778 " --> pdb=" O LYS 6 774 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS 6 781 " --> pdb=" O ASP 6 777 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU 6 782 " --> pdb=" O VAL 6 778 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL 6 783 " --> pdb=" O ARG 6 779 " (cutoff:3.500A) Processing helix chain '6' and resid 799 through 807 removed outlier: 3.805A pdb=" N LEU 6 803 " --> pdb=" O LYS 6 799 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU 6 804 " --> pdb=" O ALA 6 800 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA 6 805 " --> pdb=" O LYS 6 801 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN 6 806 " --> pdb=" O ASP 6 802 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN 6 807 " --> pdb=" O LEU 6 803 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 799 through 807' Processing helix chain '6' and resid 817 through 824 removed outlier: 3.631A pdb=" N ILE 6 822 " --> pdb=" O LEU 6 818 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN 6 823 " --> pdb=" O ASN 6 819 " (cutoff:3.500A) Processing helix chain '6' and resid 825 through 834 removed outlier: 3.960A pdb=" N GLN 6 829 " --> pdb=" O ALA 6 825 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU 6 830 " --> pdb=" O LEU 6 826 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER 6 831 " --> pdb=" O LEU 6 827 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 164 through 166 removed outlier: 6.554A pdb=" N TYR 1 236 " --> pdb=" O PHE 1 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 308 through 310 removed outlier: 3.510A pdb=" N THR 1 310 " --> pdb=" O LEU 1 203 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN 1 330 " --> pdb=" O CYS 1 202 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL 1 204 " --> pdb=" O GLN 1 330 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL 1 332 " --> pdb=" O VAL 1 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 360 through 361 removed outlier: 7.383A pdb=" N ARG 1 360 " --> pdb=" O VAL 1 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain '1' and resid 630 through 634 removed outlier: 3.650A pdb=" N LEU 1 676 " --> pdb=" O VAL 1 631 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR 1 673 " --> pdb=" O ILE 1 714 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N VAL 1 716 " --> pdb=" O THR 1 673 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL 1 675 " --> pdb=" O VAL 1 716 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 699 through 701 removed outlier: 3.734A pdb=" N CYS 1 700 " --> pdb=" O VAL 1 708 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL 1 708 " --> pdb=" O CYS 1 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '1' and resid 793 through 796 removed outlier: 6.901A pdb=" N THR 1 793 " --> pdb=" O ALA 1 845 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL 1 847 " --> pdb=" O THR 1 793 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP 1 795 " --> pdb=" O VAL 1 847 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N VAL 1 849 " --> pdb=" O ASP 1 795 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS 1 846 " --> pdb=" O ILE 1 858 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 164 through 166 removed outlier: 6.070A pdb=" N TYR 2 236 " --> pdb=" O PHE 2 272 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 200 through 204 removed outlier: 6.572A pdb=" N GLN 2 330 " --> pdb=" O CYS 2 202 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL 2 204 " --> pdb=" O GLN 2 330 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL 2 332 " --> pdb=" O VAL 2 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '2' and resid 360 through 361 removed outlier: 7.311A pdb=" N ARG 2 360 " --> pdb=" O VAL 2 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '2' and resid 630 through 634 removed outlier: 6.920A pdb=" N VAL 2 631 " --> pdb=" O LEU 2 676 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASP 2 678 " --> pdb=" O VAL 2 631 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE 2 633 " --> pdb=" O ASP 2 678 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL 2 675 " --> pdb=" O VAL 2 716 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain '2' and resid 699 through 701 removed outlier: 4.178A pdb=" N CYS 2 700 " --> pdb=" O VAL 2 708 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL 2 708 " --> pdb=" O CYS 2 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain '2' and resid 794 through 796 removed outlier: 7.203A pdb=" N ASP 2 795 " --> pdb=" O VAL 2 847 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N VAL 2 849 " --> pdb=" O ASP 2 795 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS 2 846 " --> pdb=" O ILE 2 858 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR 2 848 " --> pdb=" O ILE 2 856 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE 2 856 " --> pdb=" O THR 2 848 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 164 through 166 removed outlier: 5.509A pdb=" N LYS 3 234 " --> pdb=" O ILE 3 270 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE 3 272 " --> pdb=" O LYS 3 234 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR 3 236 " --> pdb=" O PHE 3 272 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 308 through 310 removed outlier: 3.638A pdb=" N THR 3 310 " --> pdb=" O LEU 3 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '3' and resid 360 through 361 removed outlier: 6.808A pdb=" N ARG 3 360 " --> pdb=" O VAL 3 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '3' and resid 630 through 633 removed outlier: 6.797A pdb=" N VAL 3 675 " --> pdb=" O VAL 3 716 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '3' and resid 699 through 701 removed outlier: 3.846A pdb=" N CYS 3 700 " --> pdb=" O VAL 3 708 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL 3 708 " --> pdb=" O CYS 3 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain '3' and resid 793 through 796 removed outlier: 6.388A pdb=" N THR 3 793 " --> pdb=" O ALA 3 845 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL 3 847 " --> pdb=" O THR 3 793 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP 3 795 " --> pdb=" O VAL 3 847 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N VAL 3 849 " --> pdb=" O ASP 3 795 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS 3 846 " --> pdb=" O ILE 3 858 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR 3 848 " --> pdb=" O ILE 3 856 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE 3 856 " --> pdb=" O THR 3 848 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 164 through 166 removed outlier: 6.395A pdb=" N TYR 4 236 " --> pdb=" O PHE 4 272 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL 4 271 " --> pdb=" O ILE 4 307 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ALA 4 309 " --> pdb=" O VAL 4 271 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE 4 273 " --> pdb=" O ALA 4 309 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N THR 4 311 " --> pdb=" O ILE 4 273 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY 4 205 " --> pdb=" O THR 4 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 360 through 361 removed outlier: 7.757A pdb=" N ARG 4 360 " --> pdb=" O VAL 4 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain '4' and resid 604 through 605 removed outlier: 3.559A pdb=" N SER 4 719 " --> pdb=" O PHE 4 604 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL 4 675 " --> pdb=" O VAL 4 716 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N THR 4 718 " --> pdb=" O VAL 4 675 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE 4 677 " --> pdb=" O THR 4 718 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 699 through 701 removed outlier: 3.646A pdb=" N VAL 4 708 " --> pdb=" O CYS 4 700 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '4' and resid 793 through 796 removed outlier: 6.267A pdb=" N THR 4 793 " --> pdb=" O ALA 4 845 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL 4 847 " --> pdb=" O THR 4 793 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP 4 795 " --> pdb=" O VAL 4 847 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N VAL 4 849 " --> pdb=" O ASP 4 795 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS 4 846 " --> pdb=" O ILE 4 858 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 164 through 166 removed outlier: 5.732A pdb=" N LYS 5 234 " --> pdb=" O ILE 5 270 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE 5 272 " --> pdb=" O LYS 5 234 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR 5 236 " --> pdb=" O PHE 5 272 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ILE 5 307 " --> pdb=" O ALA 5 269 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL 5 271 " --> pdb=" O ILE 5 307 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 201 through 203 removed outlier: 6.416A pdb=" N CYS 5 202 " --> pdb=" O VAL 5 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '5' and resid 360 through 361 removed outlier: 7.045A pdb=" N ARG 5 360 " --> pdb=" O VAL 5 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '5' and resid 630 through 632 removed outlier: 6.747A pdb=" N VAL 5 675 " --> pdb=" O VAL 5 716 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR 5 718 " --> pdb=" O VAL 5 675 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE 5 677 " --> pdb=" O THR 5 718 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 793 through 796 removed outlier: 6.931A pdb=" N THR 5 793 " --> pdb=" O ALA 5 845 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL 5 847 " --> pdb=" O THR 5 793 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP 5 795 " --> pdb=" O VAL 5 847 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N VAL 5 849 " --> pdb=" O ASP 5 795 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS 5 846 " --> pdb=" O ILE 5 858 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 165 through 166 removed outlier: 3.789A pdb=" N ILE 6 165 " --> pdb=" O SER 6 237 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR 6 236 " --> pdb=" O PHE 6 272 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 308 through 311 removed outlier: 3.700A pdb=" N GLY 6 205 " --> pdb=" O THR 6 310 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS 6 202 " --> pdb=" O GLN 6 330 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 360 through 361 removed outlier: 7.041A pdb=" N ARG 6 360 " --> pdb=" O VAL 6 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain '6' and resid 602 through 605 removed outlier: 4.423A pdb=" N LEU 6 603 " --> pdb=" O GLU 6 760 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE 6 762 " --> pdb=" O LEU 6 603 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 6 605 " --> pdb=" O ILE 6 762 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '6' and resid 630 through 634 removed outlier: 3.520A pdb=" N ASP 6 678 " --> pdb=" O ILE 6 633 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL 6 675 " --> pdb=" O VAL 6 716 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 794 through 796 removed outlier: 3.552A pdb=" N VAL 6 847 " --> pdb=" O ASP 6 795 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS 6 846 " --> pdb=" O ILE 6 858 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE 6 858 " --> pdb=" O LYS 6 846 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR 6 848 " --> pdb=" O ILE 6 856 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3345 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: 13.59 Time building geometry restraints manager: 16.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13176 1.34 - 1.46: 7246 1.46 - 1.58: 18104 1.58 - 1.69: 36 1.69 - 1.81: 252 Bond restraints: 38814 Sorted by residual: bond pdb=" C ARG 2 816 " pdb=" N PRO 2 817 " ideal model delta sigma weight residual 1.337 1.351 -0.014 1.11e-02 8.12e+03 1.69e+00 bond pdb=" C4 ADP 6 901 " pdb=" C5 ADP 6 901 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.83e-01 bond pdb=" C4 ADP 4 902 " pdb=" C5 ADP 4 902 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.58e-01 bond pdb=" C4 ADP 5 901 " pdb=" C5 ADP 5 901 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.49e-01 bond pdb=" C4 ADP 3 902 " pdb=" C5 ADP 3 902 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.47e-01 ... (remaining 38809 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.86: 1206 107.86 - 114.92: 24040 114.92 - 121.99: 19423 121.99 - 129.06: 7473 129.06 - 136.12: 184 Bond angle restraints: 52326 Sorted by residual: angle pdb=" N ALA 3 386 " pdb=" CA ALA 3 386 " pdb=" C ALA 3 386 " ideal model delta sigma weight residual 114.62 110.70 3.92 1.14e+00 7.69e-01 1.18e+01 angle pdb=" N ILE 6 497 " pdb=" CA ILE 6 497 " pdb=" C ILE 6 497 " ideal model delta sigma weight residual 111.62 109.42 2.20 7.90e-01 1.60e+00 7.79e+00 angle pdb=" N VAL 4 549 " pdb=" CA VAL 4 549 " pdb=" C VAL 4 549 " ideal model delta sigma weight residual 113.07 109.66 3.41 1.36e+00 5.41e-01 6.30e+00 angle pdb=" CA ALA 3 386 " pdb=" C ALA 3 386 " pdb=" N ILE 3 387 " ideal model delta sigma weight residual 119.71 116.82 2.89 1.17e+00 7.31e-01 6.09e+00 angle pdb=" N ILE 2 497 " pdb=" CA ILE 2 497 " pdb=" C ILE 2 497 " ideal model delta sigma weight residual 111.48 109.42 2.06 9.40e-01 1.13e+00 4.80e+00 ... (remaining 52321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.51: 23743 27.51 - 55.03: 394 55.03 - 82.54: 29 82.54 - 110.06: 7 110.06 - 137.57: 13 Dihedral angle restraints: 24186 sinusoidal: 10140 harmonic: 14046 Sorted by residual: dihedral pdb=" C5' ADP 4 901 " pdb=" O5' ADP 4 901 " pdb=" PA ADP 4 901 " pdb=" O2A ADP 4 901 " ideal model delta sinusoidal sigma weight residual 300.00 162.43 137.57 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C5' ADP 4 902 " pdb=" O5' ADP 4 902 " pdb=" PA ADP 4 902 " pdb=" O2A ADP 4 902 " ideal model delta sinusoidal sigma weight residual -60.00 76.23 -136.23 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP 1 901 " pdb=" O3A ADP 1 901 " pdb=" PA ADP 1 901 " pdb=" PB ADP 1 901 " ideal model delta sinusoidal sigma weight residual 300.00 165.27 134.73 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 24183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3456 0.026 - 0.052: 1802 0.052 - 0.078: 404 0.078 - 0.104: 272 0.104 - 0.130: 108 Chirality restraints: 6042 Sorted by residual: chirality pdb=" CA ILE 2 547 " pdb=" N ILE 2 547 " pdb=" C ILE 2 547 " pdb=" CB ILE 2 547 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE 1 547 " pdb=" N ILE 1 547 " pdb=" C ILE 1 547 " pdb=" CB ILE 1 547 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE 5 547 " pdb=" N ILE 5 547 " pdb=" C ILE 5 547 " pdb=" CB ILE 5 547 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 6039 not shown) Planarity restraints: 6756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET 6 382 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.83e+00 pdb=" N PRO 6 383 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO 6 383 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO 6 383 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET 3 382 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO 3 383 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO 3 383 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO 3 383 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET 1 382 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO 1 383 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO 1 383 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO 1 383 " -0.017 5.00e-02 4.00e+02 ... (remaining 6753 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 10438 2.81 - 3.33: 31739 3.33 - 3.85: 56223 3.85 - 4.38: 68484 4.38 - 4.90: 116318 Nonbonded interactions: 283202 Sorted by model distance: nonbonded pdb=" OD2 ASP 3 166 " pdb=" OG1 THR 3 168 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR 3 608 " pdb=" O2B ADP 3 902 " model vdw 2.298 2.440 nonbonded pdb=" O ASP 1 226 " pdb=" OG SER 2 403 " model vdw 2.305 2.440 nonbonded pdb=" OG1 THR 3 768 " pdb=" OD1 ASN 3 771 " model vdw 2.309 2.440 nonbonded pdb=" O SER 4 338 " pdb=" OG1 THR 4 342 " model vdw 2.311 2.440 ... (remaining 283197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.260 Set scattering table: 0.310 Process input model: 94.880 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4341 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 : 0.001 0.020 38814 Z= 0.086 Angle : 0.453 5.782 52326 Z= 0.251 Chirality : 0.037 0.130 6042 Planarity : 0.003 0.034 6756 Dihedral : 9.421 137.570 15030 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.50 % Favored : 92.83 % Rotamer: Outliers : 0.05 % Allowed : 1.89 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.09), residues: 4740 helix: -4.55 (0.04), residues: 2245 sheet: -1.97 (0.30), residues: 309 loop : -1.83 (0.11), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP 3 544 HIS 0.002 0.000 HIS 6 684 PHE 0.002 0.000 PHE 6 329 TYR 0.003 0.000 TYR 4 813 ARG 0.001 0.000 ARG 4 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1383 time to evaluate : 4.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 199 ASN cc_start: 0.5581 (p0) cc_final: 0.5012 (p0) REVERT: 1 461 GLU cc_start: 0.0058 (tt0) cc_final: -0.0398 (tt0) REVERT: 2 630 ILE cc_start: 0.5910 (mt) cc_final: 0.5705 (tt) REVERT: 2 718 THR cc_start: 0.5417 (m) cc_final: 0.5189 (p) REVERT: 2 835 LEU cc_start: 0.5435 (mt) cc_final: 0.5217 (mm) REVERT: 3 278 THR cc_start: 0.6838 (p) cc_final: 0.6404 (p) REVERT: 3 389 LEU cc_start: 0.5447 (mt) cc_final: 0.4943 (mt) REVERT: 3 614 LEU cc_start: 0.5446 (tp) cc_final: 0.5153 (tp) REVERT: 4 383 PRO cc_start: 0.8314 (Cg_endo) cc_final: 0.8091 (Cg_exo) REVERT: 5 330 GLN cc_start: 0.7562 (tp40) cc_final: 0.7236 (tm-30) REVERT: 6 798 ASP cc_start: 0.4465 (m-30) cc_final: 0.4108 (m-30) outliers start: 2 outliers final: 0 residues processed: 1384 average time/residue: 0.5953 time to fit residues: 1237.3540 Evaluate side-chains 742 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 742 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 7.9990 chunk 363 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 245 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 376 optimal weight: 6.9990 chunk 145 optimal weight: 0.0370 chunk 228 optimal weight: 9.9990 chunk 280 optimal weight: 3.9990 chunk 435 optimal weight: 3.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 ASN ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 GLN ** 1 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 200 ASN 1 277 HIS 1 470 ASN 1 553 GLN 1 693 GLN 1 784 GLN 2 26 HIS ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 95 HIS 2 97 HIS 2 232 GLN 2 268 GLN 2 415 HIS 2 473 GLN 2 551 ASN 2 740 ASN ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 823 GLN 2 824 HIS 3 24 ASN 3 33 HIS 3 97 HIS ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 356 HIS ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 470 ASN ** 3 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 824 HIS 4 15 ASN 4 43 ASN 4 83 HIS 4 141 HIS 4 277 HIS 4 293 ASN 4 511 GLN 4 756 ASN 4 771 ASN 4 784 GLN 4 791 GLN 4 806 GLN ** 5 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 137 ASN 5 200 ASN ** 5 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 536 GLN ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 594 ASN 5 699 HIS 5 720 ASN ** 5 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 92 HIS 6 200 ASN 6 379 GLN 6 473 GLN ** 6 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 551 ASN ** 6 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 594 ASN 6 684 HIS ** 6 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 860 ASN 6 861 HIS Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5248 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 38814 Z= 0.291 Angle : 0.781 10.971 52326 Z= 0.381 Chirality : 0.045 0.176 6042 Planarity : 0.006 0.116 6756 Dihedral : 7.754 136.549 5400 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 3.44 % Allowed : 12.17 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.11), residues: 4740 helix: -2.55 (0.08), residues: 2486 sheet: -1.49 (0.27), residues: 364 loop : -1.15 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP 6 544 HIS 0.011 0.002 HIS 5 95 PHE 0.021 0.003 PHE 4 602 TYR 0.018 0.002 TYR 5 566 ARG 0.010 0.001 ARG 5 668 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 823 time to evaluate : 4.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 68 MET cc_start: 0.3200 (ttp) cc_final: 0.2983 (ttm) REVERT: 1 226 ASP cc_start: 0.6066 (m-30) cc_final: 0.5832 (m-30) REVERT: 1 298 MET cc_start: 0.3884 (mtp) cc_final: 0.3443 (mtp) REVERT: 1 366 ILE cc_start: 0.5672 (mp) cc_final: 0.5420 (mm) REVERT: 2 160 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6465 (mt) REVERT: 2 232 GLN cc_start: 0.4962 (OUTLIER) cc_final: 0.4737 (pp30) REVERT: 2 239 ASP cc_start: 0.6114 (OUTLIER) cc_final: 0.5873 (m-30) REVERT: 2 260 VAL cc_start: 0.6399 (t) cc_final: 0.6052 (p) REVERT: 2 372 LEU cc_start: 0.5265 (tp) cc_final: 0.5038 (tp) REVERT: 2 753 GLU cc_start: 0.6475 (tm-30) cc_final: 0.6163 (tm-30) REVERT: 3 596 ASN cc_start: 0.5098 (OUTLIER) cc_final: 0.4814 (p0) REVERT: 4 192 VAL cc_start: 0.7293 (OUTLIER) cc_final: 0.6953 (p) REVERT: 4 828 THR cc_start: 0.6741 (m) cc_final: 0.6504 (t) REVERT: 5 639 MET cc_start: 0.6647 (mtm) cc_final: 0.5972 (mtm) REVERT: 6 353 TYR cc_start: 0.5867 (m-80) cc_final: 0.5523 (m-80) REVERT: 6 536 GLN cc_start: 0.5442 (mp-120) cc_final: 0.5214 (mp10) outliers start: 140 outliers final: 73 residues processed: 903 average time/residue: 0.5656 time to fit residues: 786.4634 Evaluate side-chains 713 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 635 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 83 HIS Chi-restraints excluded: chain 1 residue 184 GLU Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 253 PHE Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 388 ASP Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 763 VAL Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 1 residue 812 VAL Chi-restraints excluded: chain 2 residue 160 LEU Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 2 residue 232 GLN Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 280 LEU Chi-restraints excluded: chain 2 residue 338 SER Chi-restraints excluded: chain 2 residue 388 ASP Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 3 residue 180 ILE Chi-restraints excluded: chain 3 residue 235 VAL Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 616 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 793 THR Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 830 LEU Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 3 residue 860 ASN Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 345 ILE Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 776 VAL Chi-restraints excluded: chain 4 residue 806 GLN Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 531 VAL Chi-restraints excluded: chain 5 residue 592 LEU Chi-restraints excluded: chain 5 residue 631 VAL Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 714 ILE Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 451 LEU Chi-restraints excluded: chain 6 residue 537 ILE Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 694 ILE Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 787 LEU Chi-restraints excluded: chain 6 residue 829 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 362 optimal weight: 10.0000 chunk 296 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 436 optimal weight: 0.9990 chunk 471 optimal weight: 5.9990 chunk 388 optimal weight: 8.9990 chunk 433 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 350 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 101 GLN 1 293 ASN 1 693 GLN ** 1 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 15 ASN ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 108 GLN ** 2 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 861 HIS ** 3 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 95 HIS ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 400 GLN 4 473 GLN 4 511 GLN 4 562 HIS 4 625 ASN 4 829 GLN ** 5 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 470 ASN 5 574 GLN ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 860 ASN ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 HIS ** 6 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 473 GLN 6 536 GLN ** 6 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 642 HIS 6 749 HIS ** 6 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5466 moved from start: 0.6806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 38814 Z= 0.251 Angle : 0.697 11.992 52326 Z= 0.334 Chirality : 0.043 0.199 6042 Planarity : 0.005 0.041 6756 Dihedral : 7.271 132.598 5400 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.26 % Favored : 95.72 % Rotamer: Outliers : 4.00 % Allowed : 14.73 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.12), residues: 4740 helix: -1.53 (0.09), residues: 2596 sheet: -1.51 (0.27), residues: 369 loop : -0.83 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP 6 544 HIS 0.014 0.001 HIS 5 699 PHE 0.017 0.002 PHE 2 381 TYR 0.023 0.002 TYR 3 20 ARG 0.012 0.001 ARG 3 748 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 711 time to evaluate : 3.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 333 MET cc_start: 0.4599 (tpp) cc_final: 0.4298 (tpt) REVERT: 1 366 ILE cc_start: 0.5632 (mp) cc_final: 0.5427 (mm) REVERT: 2 260 VAL cc_start: 0.6651 (t) cc_final: 0.6271 (p) REVERT: 2 377 ILE cc_start: 0.6508 (pt) cc_final: 0.6251 (pt) REVERT: 2 685 LYS cc_start: 0.6900 (tttt) cc_final: 0.6608 (tttt) REVERT: 3 596 ASN cc_start: 0.5203 (OUTLIER) cc_final: 0.4824 (p0) REVERT: 4 38 MET cc_start: 0.4531 (ptp) cc_final: 0.4329 (ptp) REVERT: 4 298 MET cc_start: 0.4951 (OUTLIER) cc_final: 0.4678 (mtm) REVERT: 4 351 GLU cc_start: 0.6412 (pm20) cc_final: 0.6156 (pm20) REVERT: 4 634 ASP cc_start: 0.7828 (t0) cc_final: 0.7584 (t0) REVERT: 5 98 MET cc_start: 0.4707 (ttp) cc_final: 0.4361 (ttp) REVERT: 5 366 ILE cc_start: 0.6220 (mt) cc_final: 0.6006 (mt) REVERT: 6 353 TYR cc_start: 0.6082 (m-80) cc_final: 0.5163 (m-80) outliers start: 163 outliers final: 96 residues processed: 805 average time/residue: 0.5624 time to fit residues: 705.5856 Evaluate side-chains 716 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 618 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 83 HIS Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 274 ASP Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 583 ASP Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 647 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 1 residue 812 VAL Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 235 VAL Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 338 SER Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 563 MET Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 673 THR Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 270 ILE Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 387 ILE Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 515 GLU Chi-restraints excluded: chain 4 residue 560 LEU Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 581 ILE Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 759 ASP Chi-restraints excluded: chain 4 residue 796 VAL Chi-restraints excluded: chain 5 residue 164 CYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 531 VAL Chi-restraints excluded: chain 5 residue 541 VAL Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 697 ASP Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 713 THR Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 378 THR Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 545 THR Chi-restraints excluded: chain 6 residue 566 TYR Chi-restraints excluded: chain 6 residue 694 ILE Chi-restraints excluded: chain 6 residue 711 LYS Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 785 GLU Chi-restraints excluded: chain 6 residue 787 LEU Chi-restraints excluded: chain 6 residue 803 LEU Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 826 LEU Chi-restraints excluded: chain 6 residue 829 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 0.9980 chunk 328 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 293 optimal weight: 9.9990 chunk 438 optimal weight: 1.9990 chunk 463 optimal weight: 0.8980 chunk 228 optimal weight: 0.3980 chunk 415 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 771 ASN 2 83 HIS 2 108 GLN 2 268 GLN 2 277 HIS ** 2 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 356 HIS ** 2 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 26 HIS ** 3 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 860 ASN 4 473 GLN 4 625 ASN 4 756 ASN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 268 GLN ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 819 ASN ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 435 GLN 6 473 GLN 6 593 GLN 6 642 HIS 6 756 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5384 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 38814 Z= 0.144 Angle : 0.613 9.870 52326 Z= 0.283 Chirality : 0.041 0.146 6042 Planarity : 0.004 0.047 6756 Dihedral : 6.425 145.659 5400 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.76 % Favored : 97.22 % Rotamer: Outliers : 2.58 % Allowed : 16.69 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.12), residues: 4740 helix: -0.82 (0.10), residues: 2613 sheet: -1.24 (0.29), residues: 337 loop : -0.51 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP 6 544 HIS 0.016 0.001 HIS 4 562 PHE 0.018 0.001 PHE 2 272 TYR 0.019 0.001 TYR 3 20 ARG 0.008 0.000 ARG 5 586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 681 time to evaluate : 4.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 366 ILE cc_start: 0.5580 (mp) cc_final: 0.5174 (mm) REVERT: 2 232 GLN cc_start: 0.5217 (pm20) cc_final: 0.4977 (pp30) REVERT: 2 260 VAL cc_start: 0.6708 (t) cc_final: 0.6357 (p) REVERT: 2 372 LEU cc_start: 0.5120 (tp) cc_final: 0.4737 (tp) REVERT: 2 686 ASP cc_start: 0.6550 (p0) cc_final: 0.6261 (p0) REVERT: 3 68 MET cc_start: 0.3119 (mtp) cc_final: 0.2911 (mtm) REVERT: 3 121 MET cc_start: 0.5284 (tpp) cc_final: 0.4804 (tpt) REVERT: 3 278 THR cc_start: 0.6822 (p) cc_final: 0.6589 (t) REVERT: 3 596 ASN cc_start: 0.5483 (OUTLIER) cc_final: 0.4907 (p0) REVERT: 4 414 ARG cc_start: 0.5363 (mmm160) cc_final: 0.5161 (mmm160) REVERT: 4 476 ASP cc_start: 0.5022 (OUTLIER) cc_final: 0.4634 (p0) REVERT: 5 404 GLN cc_start: 0.3023 (tt0) cc_final: 0.2689 (tt0) REVERT: 6 68 MET cc_start: 0.1110 (mtt) cc_final: 0.0583 (mtt) REVERT: 6 236 TYR cc_start: 0.6315 (m-10) cc_final: 0.6056 (m-10) REVERT: 6 353 TYR cc_start: 0.5896 (m-80) cc_final: 0.5653 (m-80) outliers start: 105 outliers final: 68 residues processed: 740 average time/residue: 0.5451 time to fit residues: 633.0376 Evaluate side-chains 688 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 618 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 582 CYS Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 771 ASN Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 338 SER Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 216 GLU Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 435 GLN Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 788 ASP Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 3 residue 860 ASN Chi-restraints excluded: chain 4 residue 95 HIS Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 179 VAL Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 476 ASP Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 704 LYS Chi-restraints excluded: chain 4 residue 828 THR Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 190 ILE Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 562 HIS Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 200 ASN Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 507 LYS Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 539 GLU Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 803 LEU Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 0.0050 chunk 263 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 345 optimal weight: 20.0000 chunk 191 optimal weight: 0.0040 chunk 395 optimal weight: 3.9990 chunk 320 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 416 optimal weight: 5.9990 chunk 117 optimal weight: 0.0170 overall best weight: 0.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 83 HIS 1 771 ASN ** 2 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 356 HIS ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 791 GLN ** 3 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 396 ASN 4 536 GLN 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 860 ASN ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 473 GLN 6 642 HIS 6 756 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5370 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 38814 Z= 0.138 Angle : 0.607 11.134 52326 Z= 0.277 Chirality : 0.041 0.146 6042 Planarity : 0.003 0.051 6756 Dihedral : 5.978 145.189 5400 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.85 % Favored : 97.13 % Rotamer: Outliers : 2.68 % Allowed : 16.89 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.12), residues: 4740 helix: -0.46 (0.10), residues: 2628 sheet: -1.00 (0.30), residues: 315 loop : -0.42 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP 6 544 HIS 0.008 0.001 HIS 5 699 PHE 0.018 0.001 PHE 2 272 TYR 0.016 0.001 TYR 4 315 ARG 0.006 0.000 ARG 2 595 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 660 time to evaluate : 4.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 366 ILE cc_start: 0.5688 (mp) cc_final: 0.5430 (mp) REVERT: 2 260 VAL cc_start: 0.6591 (t) cc_final: 0.6333 (p) REVERT: 2 595 ARG cc_start: 0.6977 (mmp80) cc_final: 0.6596 (mmp-170) REVERT: 3 121 MET cc_start: 0.5350 (tpp) cc_final: 0.4937 (tpt) REVERT: 3 384 ASP cc_start: 0.4689 (t0) cc_final: 0.4488 (t0) REVERT: 3 596 ASN cc_start: 0.5469 (OUTLIER) cc_final: 0.4991 (p0) REVERT: 4 4 MET cc_start: 0.4658 (mmm) cc_final: 0.3765 (mmt) REVERT: 4 476 ASP cc_start: 0.4945 (OUTLIER) cc_final: 0.4491 (p0) REVERT: 4 821 LEU cc_start: 0.7433 (pp) cc_final: 0.7114 (pp) REVERT: 5 98 MET cc_start: 0.4574 (ttp) cc_final: 0.4356 (ttp) REVERT: 5 404 GLN cc_start: 0.3201 (tt0) cc_final: 0.2735 (tt0) REVERT: 5 483 GLU cc_start: 0.6204 (tp30) cc_final: 0.5814 (tp30) REVERT: 6 68 MET cc_start: 0.1009 (mtt) cc_final: 0.0486 (mtt) REVERT: 6 236 TYR cc_start: 0.6270 (m-10) cc_final: 0.5987 (m-10) REVERT: 6 639 MET cc_start: 0.6125 (mpp) cc_final: 0.5485 (mpp) outliers start: 109 outliers final: 72 residues processed: 729 average time/residue: 0.6037 time to fit residues: 691.6806 Evaluate side-chains 679 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 605 time to evaluate : 4.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 83 HIS Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 339 VAL Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 338 SER Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 545 THR Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 216 GLU Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 354 GLU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 375 ARG Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 3 residue 860 ASN Chi-restraints excluded: chain 4 residue 95 HIS Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 476 ASP Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 582 CYS Chi-restraints excluded: chain 4 residue 601 SER Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 828 THR Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 562 HIS Chi-restraints excluded: chain 5 residue 680 MET Chi-restraints excluded: chain 5 residue 691 LEU Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 200 ASN Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 397 THR Chi-restraints excluded: chain 6 residue 539 GLU Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 5.9990 chunk 417 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 272 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 464 optimal weight: 10.0000 chunk 385 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 153 optimal weight: 0.2980 chunk 243 optimal weight: 20.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 356 HIS ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 473 GLN ** 3 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 860 ASN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 551 ASN 5 860 ASN ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 473 GLN 6 642 HIS 6 829 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.7614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 38814 Z= 0.190 Angle : 0.644 12.766 52326 Z= 0.299 Chirality : 0.042 0.201 6042 Planarity : 0.004 0.041 6756 Dihedral : 6.049 148.150 5400 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.07 % Allowed : 17.28 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4740 helix: -0.29 (0.10), residues: 2652 sheet: -1.07 (0.30), residues: 331 loop : -0.29 (0.16), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP 6 544 HIS 0.025 0.001 HIS 1 83 PHE 0.028 0.002 PHE 6 329 TYR 0.017 0.001 TYR 3 20 ARG 0.018 0.001 ARG 2 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 633 time to evaluate : 4.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 565 GLU cc_start: 0.4513 (tp30) cc_final: 0.4275 (tp30) REVERT: 2 260 VAL cc_start: 0.6793 (t) cc_final: 0.6579 (p) REVERT: 2 810 ASP cc_start: 0.3554 (t0) cc_final: 0.3193 (t0) REVERT: 3 68 MET cc_start: 0.3484 (mtp) cc_final: 0.2784 (mtm) REVERT: 3 121 MET cc_start: 0.5353 (tpp) cc_final: 0.4925 (tpt) REVERT: 3 596 ASN cc_start: 0.5627 (OUTLIER) cc_final: 0.5090 (p0) REVERT: 3 757 ARG cc_start: 0.6341 (mmm-85) cc_final: 0.6075 (mmm-85) REVERT: 4 627 PRO cc_start: 0.7804 (Cg_exo) cc_final: 0.7502 (Cg_endo) REVERT: 4 821 LEU cc_start: 0.7722 (pp) cc_final: 0.7418 (pp) REVERT: 5 404 GLN cc_start: 0.3531 (tt0) cc_final: 0.3205 (tt0) REVERT: 5 483 GLU cc_start: 0.6631 (tp30) cc_final: 0.6272 (tp30) REVERT: 6 68 MET cc_start: 0.1303 (mtt) cc_final: 0.0300 (mtt) REVERT: 6 236 TYR cc_start: 0.6312 (m-10) cc_final: 0.6005 (m-10) outliers start: 125 outliers final: 94 residues processed: 708 average time/residue: 0.5761 time to fit residues: 640.4328 Evaluate side-chains 681 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 586 time to evaluate : 4.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 339 VAL Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 545 THR Chi-restraints excluded: chain 2 residue 563 MET Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 354 GLU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 375 ARG Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 389 LEU Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 788 ASP Chi-restraints excluded: chain 3 residue 799 LYS Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 3 residue 860 ASN Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 515 GLU Chi-restraints excluded: chain 4 residue 601 SER Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 704 LYS Chi-restraints excluded: chain 4 residue 796 VAL Chi-restraints excluded: chain 4 residue 828 THR Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 531 VAL Chi-restraints excluded: chain 5 residue 562 HIS Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 680 MET Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 170 LEU Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 200 ASN Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 231 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 397 THR Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 644 VAL Chi-restraints excluded: chain 6 residue 693 GLN Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 829 GLN Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 339 optimal weight: 2.9990 chunk 262 optimal weight: 10.0000 chunk 390 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 462 optimal weight: 0.0050 chunk 289 optimal weight: 7.9990 chunk 282 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 101 GLN 1 357 HIS ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 625 ASN ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 137 ASN ** 4 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 642 HIS 6 829 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 moved from start: 0.8178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 38814 Z= 0.207 Angle : 0.674 15.687 52326 Z= 0.314 Chirality : 0.043 0.170 6042 Planarity : 0.004 0.045 6756 Dihedral : 6.204 148.160 5400 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.04 % Allowed : 17.89 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4740 helix: -0.33 (0.10), residues: 2698 sheet: -0.98 (0.28), residues: 360 loop : -0.28 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP 6 544 HIS 0.014 0.001 HIS 4 277 PHE 0.022 0.002 PHE 6 329 TYR 0.018 0.001 TYR 3 20 ARG 0.009 0.001 ARG 2 669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 635 time to evaluate : 4.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 366 ILE cc_start: 0.5875 (mp) cc_final: 0.5498 (mp) REVERT: 1 382 MET cc_start: 0.6892 (tpp) cc_final: 0.6596 (tpp) REVERT: 2 121 MET cc_start: 0.3671 (tpt) cc_final: 0.3235 (tpt) REVERT: 2 260 VAL cc_start: 0.6959 (t) cc_final: 0.6744 (p) REVERT: 2 810 ASP cc_start: 0.4215 (t0) cc_final: 0.3735 (t0) REVERT: 3 68 MET cc_start: 0.3581 (mtp) cc_final: 0.2894 (mtm) REVERT: 3 121 MET cc_start: 0.5598 (tpp) cc_final: 0.5338 (tpt) REVERT: 3 274 ASP cc_start: 0.5790 (t0) cc_final: 0.5209 (p0) REVERT: 3 596 ASN cc_start: 0.5635 (OUTLIER) cc_final: 0.5198 (p0) REVERT: 4 552 LEU cc_start: 0.5766 (mm) cc_final: 0.5482 (mm) REVERT: 4 701 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8023 (p) REVERT: 4 821 LEU cc_start: 0.7840 (pp) cc_final: 0.7507 (pp) REVERT: 5 404 GLN cc_start: 0.3594 (tt0) cc_final: 0.3180 (tt0) REVERT: 6 68 MET cc_start: 0.1325 (mtt) cc_final: 0.0681 (mtt) REVERT: 6 236 TYR cc_start: 0.6317 (m-10) cc_final: 0.6047 (m-10) REVERT: 6 855 ILE cc_start: 0.2716 (OUTLIER) cc_final: 0.2309 (tt) outliers start: 124 outliers final: 92 residues processed: 714 average time/residue: 0.5673 time to fit residues: 630.1464 Evaluate side-chains 676 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 581 time to evaluate : 4.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 189 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 290 ASP Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 647 LEU Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 739 LYS Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 545 THR Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 713 THR Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 389 LEU Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 742 VAL Chi-restraints excluded: chain 3 residue 799 LYS Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 844 ILE Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 3 residue 860 ASN Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 414 ARG Chi-restraints excluded: chain 4 residue 515 GLU Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 601 SER Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 704 LYS Chi-restraints excluded: chain 4 residue 796 VAL Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 190 ILE Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 531 VAL Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 680 MET Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 782 GLU Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 200 ASN Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 231 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 428 GLU Chi-restraints excluded: chain 6 residue 507 LYS Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 539 GLU Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 644 VAL Chi-restraints excluded: chain 6 residue 693 GLN Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 844 ILE Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 276 optimal weight: 9.9990 chunk 139 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 294 optimal weight: 0.0170 chunk 315 optimal weight: 10.0000 chunk 228 optimal weight: 0.0370 chunk 43 optimal weight: 0.8980 chunk 363 optimal weight: 0.6980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 101 GLN ** 2 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 569 GLN ** 3 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 642 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 moved from start: 0.8120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 38814 Z= 0.148 Angle : 0.664 25.220 52326 Z= 0.300 Chirality : 0.042 0.187 6042 Planarity : 0.004 0.057 6756 Dihedral : 5.848 142.684 5400 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.89 % Allowed : 19.51 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 4740 helix: 0.02 (0.11), residues: 2635 sheet: -0.74 (0.30), residues: 327 loop : -0.20 (0.16), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP 6 544 HIS 0.014 0.001 HIS 4 277 PHE 0.025 0.001 PHE 6 329 TYR 0.017 0.001 TYR 3 20 ARG 0.008 0.000 ARG 4 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 640 time to evaluate : 4.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 328 ARG cc_start: 0.3286 (mmm160) cc_final: 0.2972 (mmp80) REVERT: 1 382 MET cc_start: 0.6894 (tpp) cc_final: 0.6570 (tpp) REVERT: 3 68 MET cc_start: 0.3705 (mtp) cc_final: 0.2981 (mtm) REVERT: 3 121 MET cc_start: 0.5691 (tpp) cc_final: 0.5368 (tpt) REVERT: 3 255 GLU cc_start: 0.5106 (pm20) cc_final: 0.4566 (pm20) REVERT: 3 274 ASP cc_start: 0.5869 (t0) cc_final: 0.5177 (p0) REVERT: 3 505 LEU cc_start: 0.4633 (OUTLIER) cc_final: 0.4335 (tt) REVERT: 3 596 ASN cc_start: 0.5058 (OUTLIER) cc_final: 0.4537 (p0) REVERT: 4 552 LEU cc_start: 0.5705 (mm) cc_final: 0.5473 (mm) REVERT: 4 701 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7863 (p) REVERT: 4 821 LEU cc_start: 0.7596 (pp) cc_final: 0.7232 (pp) REVERT: 6 68 MET cc_start: 0.1076 (mtt) cc_final: 0.0487 (mtt) REVERT: 6 236 TYR cc_start: 0.6363 (m-10) cc_final: 0.6131 (m-10) REVERT: 6 382 MET cc_start: 0.6616 (mmm) cc_final: 0.6169 (mmp) outliers start: 77 outliers final: 56 residues processed: 687 average time/residue: 0.5750 time to fit residues: 611.6649 Evaluate side-chains 649 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 590 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 2 residue 177 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 545 THR Chi-restraints excluded: chain 2 residue 569 GLN Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 375 ARG Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 505 LEU Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 844 ILE Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 5 residue 190 ILE Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 562 HIS Chi-restraints excluded: chain 5 residue 680 MET Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 231 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 539 GLU Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 644 VAL Chi-restraints excluded: chain 6 residue 798 ASP Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 844 ILE Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 0.9990 chunk 443 optimal weight: 0.3980 chunk 404 optimal weight: 10.0000 chunk 431 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 338 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 389 optimal weight: 9.9990 chunk 407 optimal weight: 0.0000 chunk 429 optimal weight: 0.5980 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 101 GLN 1 699 HIS ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 371 GLN 3 860 ASN ** 4 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 396 ASN ** 4 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 536 GLN 4 562 HIS 4 596 ASN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 593 GLN ** 5 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.8259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 38814 Z= 0.156 Angle : 0.681 30.202 52326 Z= 0.306 Chirality : 0.042 0.201 6042 Planarity : 0.004 0.052 6756 Dihedral : 5.771 142.926 5400 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.01 % Allowed : 19.64 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 4740 helix: 0.10 (0.11), residues: 2639 sheet: -0.69 (0.30), residues: 330 loop : -0.19 (0.16), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP 6 544 HIS 0.015 0.001 HIS 4 277 PHE 0.031 0.001 PHE 6 329 TYR 0.016 0.001 TYR 3 20 ARG 0.014 0.000 ARG 1 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 614 time to evaluate : 4.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 382 MET cc_start: 0.6936 (tpp) cc_final: 0.6643 (tpp) REVERT: 2 690 LEU cc_start: 0.7482 (pp) cc_final: 0.7236 (pp) REVERT: 2 696 ASP cc_start: 0.6011 (m-30) cc_final: 0.5780 (m-30) REVERT: 3 68 MET cc_start: 0.3695 (mtp) cc_final: 0.3017 (mtm) REVERT: 3 121 MET cc_start: 0.5686 (tpp) cc_final: 0.5407 (tpt) REVERT: 3 253 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.6247 (m-80) REVERT: 3 255 GLU cc_start: 0.5001 (pm20) cc_final: 0.4523 (pm20) REVERT: 3 274 ASP cc_start: 0.5804 (t0) cc_final: 0.5241 (p0) REVERT: 3 275 GLU cc_start: 0.4829 (mt-10) cc_final: 0.4584 (mt-10) REVERT: 3 505 LEU cc_start: 0.4727 (OUTLIER) cc_final: 0.4480 (tt) REVERT: 4 98 MET cc_start: 0.1002 (tmm) cc_final: 0.0532 (tmm) REVERT: 4 547 ILE cc_start: 0.6771 (pt) cc_final: 0.6554 (pt) REVERT: 4 552 LEU cc_start: 0.5693 (mm) cc_final: 0.5472 (mm) REVERT: 4 701 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7835 (p) REVERT: 4 821 LEU cc_start: 0.7622 (pp) cc_final: 0.7276 (pp) REVERT: 5 469 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6609 (ptm-80) REVERT: 6 68 MET cc_start: 0.1192 (mtt) cc_final: 0.0536 (mtt) REVERT: 6 236 TYR cc_start: 0.6284 (m-10) cc_final: 0.6024 (m-10) REVERT: 6 328 ARG cc_start: 0.6120 (ptp-110) cc_final: 0.5885 (ptp-110) REVERT: 6 382 MET cc_start: 0.6659 (mmm) cc_final: 0.6245 (mmp) REVERT: 6 639 MET cc_start: 0.6552 (mpp) cc_final: 0.5696 (mpp) outliers start: 82 outliers final: 66 residues processed: 663 average time/residue: 0.5891 time to fit residues: 605.9749 Evaluate side-chains 656 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 586 time to evaluate : 4.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 406 GLU Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 582 CYS Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 647 LEU Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 2 residue 177 ASP Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 545 THR Chi-restraints excluded: chain 2 residue 636 SER Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 276 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 375 ARG Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 505 LEU Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 788 ASP Chi-restraints excluded: chain 3 residue 844 ILE Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 366 ILE Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 469 ARG Chi-restraints excluded: chain 5 residue 562 HIS Chi-restraints excluded: chain 5 residue 563 MET Chi-restraints excluded: chain 5 residue 680 MET Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 778 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 231 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 428 GLU Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 644 VAL Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 844 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 2.9990 chunk 455 optimal weight: 8.9990 chunk 278 optimal weight: 0.8980 chunk 216 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 478 optimal weight: 9.9990 chunk 440 optimal weight: 0.9990 chunk 380 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 233 optimal weight: 0.0060 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 569 GLN ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 28 GLN ** 4 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 642 HIS 6 806 GLN 6 824 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.8385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 38814 Z= 0.160 Angle : 0.697 34.942 52326 Z= 0.311 Chirality : 0.042 0.188 6042 Planarity : 0.004 0.059 6756 Dihedral : 5.760 142.168 5400 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.91 % Allowed : 20.05 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 4740 helix: 0.18 (0.11), residues: 2631 sheet: -0.64 (0.29), residues: 340 loop : -0.08 (0.16), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 6 544 HIS 0.013 0.001 HIS 4 562 PHE 0.031 0.001 PHE 6 329 TYR 0.016 0.001 TYR 3 20 ARG 0.018 0.001 ARG 2 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 604 time to evaluate : 4.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 366 ILE cc_start: 0.5721 (mp) cc_final: 0.5393 (mp) REVERT: 1 382 MET cc_start: 0.6822 (tpp) cc_final: 0.6525 (tpp) REVERT: 1 603 LEU cc_start: 0.7749 (tp) cc_final: 0.7541 (tt) REVERT: 2 564 GLU cc_start: 0.4614 (pm20) cc_final: 0.4377 (pm20) REVERT: 2 696 ASP cc_start: 0.6025 (m-30) cc_final: 0.5817 (m-30) REVERT: 3 68 MET cc_start: 0.3681 (mtp) cc_final: 0.3024 (mtm) REVERT: 3 121 MET cc_start: 0.5734 (tpp) cc_final: 0.5460 (tpt) REVERT: 3 253 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.5799 (m-80) REVERT: 3 274 ASP cc_start: 0.5735 (t0) cc_final: 0.5307 (p0) REVERT: 3 505 LEU cc_start: 0.4692 (OUTLIER) cc_final: 0.4420 (tt) REVERT: 4 98 MET cc_start: 0.1072 (tmm) cc_final: 0.0581 (tmm) REVERT: 4 552 LEU cc_start: 0.5726 (mm) cc_final: 0.5299 (mm) REVERT: 4 701 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7802 (p) REVERT: 4 821 LEU cc_start: 0.7699 (pp) cc_final: 0.7380 (pp) REVERT: 5 469 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6624 (ptm-80) REVERT: 6 4 MET cc_start: -0.0607 (tpp) cc_final: -0.0853 (tpp) REVERT: 6 68 MET cc_start: 0.1310 (mtt) cc_final: 0.0705 (mtt) REVERT: 6 236 TYR cc_start: 0.6257 (m-10) cc_final: 0.6001 (m-10) REVERT: 6 382 MET cc_start: 0.6692 (mmm) cc_final: 0.6281 (mmp) outliers start: 78 outliers final: 68 residues processed: 654 average time/residue: 0.5567 time to fit residues: 565.5582 Evaluate side-chains 656 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 584 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 406 GLU Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 582 CYS Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 647 LEU Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 177 ASP Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 569 GLN Chi-restraints excluded: chain 2 residue 636 SER Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 204 VAL Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 276 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 375 ARG Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 505 LEU Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 788 ASP Chi-restraints excluded: chain 3 residue 844 ILE Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 366 ILE Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 582 CYS Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 824 HIS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 469 ARG Chi-restraints excluded: chain 5 residue 562 HIS Chi-restraints excluded: chain 5 residue 680 MET Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 778 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 231 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 428 GLU Chi-restraints excluded: chain 6 residue 517 SER Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 644 VAL Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 844 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 4.9990 chunk 405 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 351 optimal weight: 4.9990 chunk 56 optimal weight: 0.0980 chunk 105 optimal weight: 5.9990 chunk 381 optimal weight: 20.0000 chunk 159 optimal weight: 7.9990 chunk 391 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 569 GLN ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 819 ASN ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 642 HIS 6 824 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.123779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.110220 restraints weight = 176019.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.111910 restraints weight = 122747.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.113071 restraints weight = 92506.045| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.8632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38814 Z= 0.190 Angle : 0.718 31.756 52326 Z= 0.327 Chirality : 0.043 0.206 6042 Planarity : 0.004 0.050 6756 Dihedral : 5.906 143.268 5400 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.89 % Allowed : 20.27 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4740 helix: 0.10 (0.10), residues: 2658 sheet: -0.82 (0.28), residues: 370 loop : -0.09 (0.16), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP 6 544 HIS 0.015 0.001 HIS 2 570 PHE 0.027 0.002 PHE 6 329 TYR 0.017 0.001 TYR 3 20 ARG 0.009 0.001 ARG 1 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10934.57 seconds wall clock time: 195 minutes 22.70 seconds (11722.70 seconds total)