Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 24 11:43:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/08_2023/6d00_7782_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/08_2023/6d00_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_7782/08_2023/6d00_7782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/08_2023/6d00_7782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/08_2023/6d00_7782_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/08_2023/6d00_7782_updated.pdb" } 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 17.76, per 1000 atoms: 0.46 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: 13.46 Conformation dependent library (CDL) restraints added in 5.3 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... running ksdssp... Secondary structure from input PDB file: 247 helices and 29 sheets defined 52.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.44 Creating SS restraints... Processing helix chain '1' and resid 8 through 24 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) removed outlier: 3.777A pdb=" N ASN 1 24 " --> pdb=" O TYR 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 31 through 40 removed outlier: 3.585A pdb=" N ALA 1 35 " --> pdb=" O SER 1 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL 1 36 " --> pdb=" O HIS 1 33 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET 1 38 " --> pdb=" O ALA 1 35 " (cutoff:3.500A) Processing helix chain '1' and resid 46 through 52 removed outlier: 3.555A pdb=" N LEU 1 50 " --> pdb=" O PHE 1 46 " (cutoff:3.500A) Processing helix chain '1' and resid 57 through 69 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) Processing helix chain '1' and resid 85 through 96 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 115 through 117 No H-bonds generated for 'chain '1' and resid 115 through 117' Processing helix chain '1' and resid 122 through 128 Processing helix chain '1' and resid 132 through 141 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) Processing helix chain '1' and resid 159 through 162 No H-bonds generated for 'chain '1' and resid 159 through 162' Processing helix chain '1' and resid 167 through 172 removed outlier: 3.682A pdb=" N ALA 1 172 " --> pdb=" O THR 1 168 " (cutoff:3.500A) Processing helix chain '1' and resid 183 through 193 removed outlier: 3.693A pdb=" N ARG 1 191 " --> pdb=" O SER 1 187 " (cutoff:3.500A) Processing helix chain '1' and resid 212 through 224 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 240 through 243 No H-bonds generated for 'chain '1' and resid 240 through 243' Processing helix chain '1' and resid 252 through 265 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) Processing helix chain '1' and resid 276 through 279 No H-bonds generated for 'chain '1' and resid 276 through 279' Processing helix chain '1' and resid 295 through 299 Processing helix chain '1' and resid 314 through 318 removed outlier: 3.954A pdb=" N TYR 1 318 " --> pdb=" O TYR 1 315 " (cutoff:3.500A) Processing helix chain '1' and resid 323 through 326 No H-bonds generated for 'chain '1' and resid 323 through 326' Processing helix chain '1' and resid 339 through 348 removed outlier: 3.562A pdb=" N SER 1 344 " --> pdb=" O THR 1 340 " (cutoff:3.500A) Processing helix chain '1' and resid 364 through 371 removed outlier: 3.749A pdb=" N ALA 1 370 " --> pdb=" O ILE 1 366 " (cutoff:3.500A) Processing helix chain '1' and resid 384 through 402 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 406 through 427 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) Processing helix chain '1' and resid 434 through 485 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) Processing helix chain '1' and resid 491 through 497 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 501 through 519 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) removed outlier: 3.980A pdb=" N ALA 1 519 " --> pdb=" O GLU 1 515 " (cutoff:3.500A) Processing helix chain '1' and resid 534 through 544 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 549 through 551 No H-bonds generated for 'chain '1' and resid 549 through 551' Processing helix chain '1' and resid 556 through 559 No H-bonds generated for 'chain '1' and resid 556 through 559' Processing helix chain '1' and resid 563 through 566 No H-bonds generated for 'chain '1' and resid 563 through 566' Processing helix chain '1' and resid 575 through 578 No H-bonds generated for 'chain '1' and resid 575 through 578' Processing helix chain '1' and resid 581 through 585 removed outlier: 3.697A pdb=" N ILE 1 585 " --> pdb=" O ILE 1 581 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 581 through 585' Processing helix chain '1' and resid 614 through 622 removed outlier: 3.738A pdb=" N ALA 1 620 " --> pdb=" O VAL 1 616 " (cutoff:3.500A) Processing helix chain '1' and resid 663 through 668 Processing helix chain '1' and resid 686 through 690 removed outlier: 3.583A pdb=" N LEU 1 690 " --> pdb=" O ASP 1 686 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 686 through 690' Processing helix chain '1' and resid 740 through 749 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) No H-bonds generated for 'chain '1' and resid 740 through 749' Processing helix chain '1' and resid 752 through 755 No H-bonds generated for 'chain '1' and resid 752 through 755' Processing helix chain '1' and resid 769 through 785 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) Processing helix chain '1' and resid 800 through 806 removed outlier: 3.658A pdb=" N ALA 1 805 " --> pdb=" O LYS 1 801 " (cutoff:3.500A) Processing helix chain '1' and resid 817 through 825 removed outlier: 3.897A pdb=" N HIS 1 824 " --> pdb=" O ARG 1 820 " (cutoff:3.500A) Processing helix chain '1' and resid 828 through 836 removed outlier: 3.558A pdb=" N LEU 1 834 " --> pdb=" O LEU 1 830 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU 1 835 " --> pdb=" O SER 1 831 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP 1 836 " --> pdb=" O ARG 1 832 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 22 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) Processing helix chain '2' and resid 31 through 40 removed outlier: 3.578A pdb=" N ALA 2 35 " --> pdb=" O SER 2 32 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL 2 36 " --> pdb=" O HIS 2 33 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET 2 38 " --> pdb=" O ALA 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 45 through 53 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 57 through 69 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) Processing helix chain '2' and resid 85 through 99 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) removed outlier: 3.774A pdb=" N MET 2 98 " --> pdb=" O ALA 2 94 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS 2 99 " --> pdb=" O HIS 2 95 " (cutoff:3.500A) Processing helix chain '2' and resid 111 through 116 removed outlier: 3.529A pdb=" N LEU 2 115 " --> pdb=" O LEU 2 111 " (cutoff:3.500A) Processing helix chain '2' and resid 119 through 128 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 132 through 141 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) Processing helix chain '2' and resid 159 through 162 No H-bonds generated for 'chain '2' and resid 159 through 162' Processing helix chain '2' and resid 167 through 172 Processing helix chain '2' and resid 183 through 193 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 212 through 224 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 212 through 224' Processing helix chain '2' and resid 240 through 243 No H-bonds generated for 'chain '2' and resid 240 through 243' Processing helix chain '2' and resid 253 through 267 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 276 through 279 No H-bonds generated for 'chain '2' and resid 276 through 279' Processing helix chain '2' and resid 292 through 300 removed outlier: 3.905A pdb=" N LYS 2 296 " --> pdb=" O ASN 2 293 " (cutoff:3.500A) Proline residue: 2 297 - end of helix removed outlier: 3.670A pdb=" N ALA 2 300 " --> pdb=" O PRO 2 297 " (cutoff:3.500A) Processing helix chain '2' and resid 312 through 315 No H-bonds generated for 'chain '2' and resid 312 through 315' Processing helix chain '2' and resid 323 through 326 No H-bonds generated for 'chain '2' and resid 323 through 326' Processing helix chain '2' and resid 339 through 348 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) Processing helix chain '2' and resid 350 through 356 removed outlier: 3.640A pdb=" N HIS 2 356 " --> pdb=" O ARG 2 352 " (cutoff:3.500A) Processing helix chain '2' and resid 364 through 372 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 384 through 402 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 406 through 426 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) Processing helix chain '2' and resid 431 through 487 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 494 through 496 No H-bonds generated for 'chain '2' and resid 494 through 496' Processing helix chain '2' and resid 506 through 522 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) Processing helix chain '2' and resid 534 through 543 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 549 through 551 No H-bonds generated for 'chain '2' and resid 549 through 551' Processing helix chain '2' and resid 556 through 561 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) No H-bonds generated for 'chain '2' and resid 556 through 561' Processing helix chain '2' and resid 564 through 570 removed outlier: 3.717A pdb=" N LYS 2 568 " --> pdb=" O GLU 2 564 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN 2 569 " --> pdb=" O GLU 2 565 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS 2 570 " --> pdb=" O TYR 2 566 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 564 through 570' Processing helix chain '2' and resid 575 through 589 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) Processing helix chain '2' and resid 614 through 620 removed outlier: 3.671A pdb=" N ALA 2 620 " --> pdb=" O VAL 2 616 " (cutoff:3.500A) Processing helix chain '2' and resid 641 through 643 No H-bonds generated for 'chain '2' and resid 641 through 643' Processing helix chain '2' and resid 662 through 669 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) Processing helix chain '2' and resid 680 through 682 No H-bonds generated for 'chain '2' and resid 680 through 682' Processing helix chain '2' and resid 685 through 690 removed outlier: 3.518A pdb=" N LEU 2 690 " --> pdb=" O ASP 2 686 " (cutoff:3.500A) Processing helix chain '2' and resid 692 through 697 Processing helix chain '2' and resid 739 through 749 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) Processing helix chain '2' and resid 754 through 757 No H-bonds generated for 'chain '2' and resid 754 through 757' Processing helix chain '2' and resid 772 through 790 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) removed outlier: 5.165A pdb=" N GLU 2 789 " --> pdb=" O GLU 2 785 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS 2 790 " --> pdb=" O ARG 2 786 " (cutoff:3.500A) Processing helix chain '2' and resid 798 through 807 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) No H-bonds generated for 'chain '2' and resid 798 through 807' Processing helix chain '2' and resid 816 through 823 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 826 through 830 Processing helix chain '2' and resid 833 through 836 No H-bonds generated for 'chain '2' and resid 833 through 836' Processing helix chain '3' and resid 9 through 23 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) Processing helix chain '3' and resid 31 through 39 removed outlier: 4.114A pdb=" N ALA 3 35 " --> pdb=" O SER 3 32 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL 3 36 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET 3 38 " --> pdb=" O ALA 3 35 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU 3 39 " --> pdb=" O VAL 3 36 " (cutoff:3.500A) Processing helix chain '3' and resid 47 through 52 removed outlier: 3.514A pdb=" N GLU 3 51 " --> pdb=" O ARG 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 57 through 70 removed outlier: 4.238A pdb=" N GLU 3 61 " --> pdb=" O VAL 3 57 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG 3 62 " --> pdb=" O VAL 3 58 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY 3 63 " --> pdb=" O SER 3 59 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE 3 64 " --> pdb=" O ILE 3 60 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS 3 65 " --> pdb=" O GLU 3 61 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS 3 66 " --> pdb=" O ARG 3 62 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE 3 67 " --> pdb=" O GLY 3 63 " (cutoff:3.500A) 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 88 through 98 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) Processing helix chain '3' and resid 108 through 110 No H-bonds generated for 'chain '3' and resid 108 through 110' Processing helix chain '3' and resid 113 through 116 removed outlier: 3.704A pdb=" N ALA 3 116 " --> pdb=" O LEU 3 113 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 113 through 116' Processing helix chain '3' and resid 122 through 128 removed outlier: 3.928A pdb=" N GLY 3 128 " --> pdb=" O VAL 3 124 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 136 removed outlier: 3.874A pdb=" N GLU 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 132 through 136' Processing helix chain '3' and resid 138 through 141 No H-bonds generated for 'chain '3' and resid 138 through 141' Processing helix chain '3' and resid 159 through 162 No H-bonds generated for 'chain '3' and resid 159 through 162' Processing helix chain '3' and resid 167 through 172 Processing helix chain '3' and resid 183 through 193 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 212 through 222 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) Processing helix chain '3' and resid 240 through 244 removed outlier: 3.878A pdb=" N LEU 3 244 " --> pdb=" O ILE 3 240 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 240 through 244' Processing helix chain '3' and resid 253 through 266 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) Processing helix chain '3' and resid 276 through 280 Processing helix chain '3' and resid 292 through 294 No H-bonds generated for 'chain '3' and resid 292 through 294' Processing helix chain '3' and resid 296 through 300 Processing helix chain '3' and resid 315 through 318 No H-bonds generated for 'chain '3' and resid 315 through 318' Processing helix chain '3' and resid 340 through 348 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) Processing helix chain '3' and resid 350 through 357 Processing helix chain '3' and resid 364 through 374 removed outlier: 3.891A pdb=" N ALA 3 374 " --> pdb=" O ALA 3 370 " (cutoff:3.500A) Processing helix chain '3' and resid 384 through 402 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 406 through 427 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) Processing helix chain '3' and resid 431 through 487 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 491 through 496 removed outlier: 4.735A pdb=" N ASP 3 496 " --> pdb=" O ALA 3 492 " (cutoff:3.500A) Processing helix chain '3' and resid 502 through 521 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) Processing helix chain '3' and resid 534 through 543 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 556 through 562 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 564 through 567 No H-bonds generated for 'chain '3' and resid 564 through 567' Processing helix chain '3' and resid 578 through 584 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 578 through 584' Processing helix chain '3' and resid 586 through 589 No H-bonds generated for 'chain '3' and resid 586 through 589' Processing helix chain '3' and resid 614 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 663 through 666 No H-bonds generated for 'chain '3' and resid 663 through 666' Processing helix chain '3' and resid 685 through 690 Processing helix chain '3' and resid 692 through 696 Processing helix chain '3' and resid 743 through 749 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) Processing helix chain '3' and resid 769 through 784 removed outlier: 4.096A pdb=" N ARG 3 773 " --> pdb=" O SER 3 770 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL 3 776 " --> pdb=" O ARG 3 773 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP 3 777 " --> pdb=" O LYS 3 774 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG 3 779 " --> pdb=" O VAL 3 776 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU 3 780 " --> pdb=" O ASP 3 777 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 3 783 " --> pdb=" O LEU 3 780 " (cutoff:3.500A) Processing helix chain '3' and resid 800 through 807 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 816 through 821 removed outlier: 3.585A pdb=" N ARG 3 820 " --> pdb=" O ARG 3 816 " (cutoff:3.500A) Processing helix chain '3' and resid 826 through 836 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) removed outlier: 3.807A pdb=" N LEU 3 835 " --> pdb=" O SER 3 831 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP 3 836 " --> pdb=" O ARG 3 832 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 23 removed outlier: 3.582A pdb=" N LYS 4 19 " --> pdb=" O ASN 4 15 " (cutoff:3.500A) Processing helix chain '4' and resid 31 through 40 removed outlier: 3.718A pdb=" N ALA 4 35 " --> pdb=" O SER 4 32 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL 4 36 " --> pdb=" O HIS 4 33 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL 4 37 " --> pdb=" O VAL 4 34 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET 4 38 " --> pdb=" O ALA 4 35 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 53 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 57 through 61 Processing helix chain '4' and resid 64 through 70 Processing helix chain '4' and resid 85 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 108 through 112 removed outlier: 3.546A pdb=" N ILE 4 112 " --> pdb=" O GLN 4 108 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 108 through 112' Processing helix chain '4' and resid 122 through 128 removed outlier: 3.896A pdb=" N GLY 4 128 " --> pdb=" O VAL 4 124 " (cutoff:3.500A) Processing helix chain '4' and resid 132 through 136 Processing helix chain '4' and resid 139 through 143 removed outlier: 3.605A pdb=" N ARG 4 143 " --> pdb=" O VAL 4 139 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 139 through 143' Processing helix chain '4' and resid 159 through 162 No H-bonds generated for 'chain '4' and resid 159 through 162' Processing helix chain '4' and resid 167 through 172 Processing helix chain '4' and resid 186 through 193 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) Processing helix chain '4' and resid 212 through 224 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 229 through 231 No H-bonds generated for 'chain '4' and resid 229 through 231' Processing helix chain '4' and resid 252 through 266 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 276 through 279 No H-bonds generated for 'chain '4' and resid 276 through 279' Processing helix chain '4' and resid 292 through 300 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 318 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 323 through 326 No H-bonds generated for 'chain '4' and resid 323 through 326' Processing helix chain '4' and resid 339 through 348 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) Processing helix chain '4' and resid 350 through 356 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) Processing helix chain '4' and resid 364 through 373 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) Processing helix chain '4' and resid 384 through 402 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 406 through 424 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 431 through 487 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 491 through 500 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) Processing helix chain '4' and resid 502 through 523 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) removed outlier: 4.065A pdb=" N ARG 4 523 " --> pdb=" O ALA 4 519 " (cutoff:3.500A) Processing helix chain '4' and resid 534 through 544 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 549 through 552 No H-bonds generated for 'chain '4' and resid 549 through 552' Processing helix chain '4' and resid 556 through 570 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) removed outlier: 5.071A pdb=" N GLU 4 564 " --> pdb=" O LEU 4 560 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU 4 565 " --> pdb=" O LEU 4 561 " (cutoff:3.500A) 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 575 through 588 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) removed outlier: 3.896A pdb=" N SER 4 588 " --> pdb=" O ALA 4 584 " (cutoff:3.500A) Processing helix chain '4' and resid 614 through 622 Processing helix chain '4' and resid 647 through 666 removed outlier: 4.589A pdb=" N THR 4 664 " --> pdb=" O GLY 4 661 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU 4 665 " --> pdb=" O GLN 4 662 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA 4 666 " --> pdb=" O LEU 4 663 " (cutoff:3.500A) Processing helix chain '4' and resid 680 through 682 No H-bonds generated for 'chain '4' and resid 680 through 682' Processing helix chain '4' and resid 687 through 690 No H-bonds generated for 'chain '4' and resid 687 through 690' Processing helix chain '4' and resid 692 through 697 Processing helix chain '4' and resid 740 through 749 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) Processing helix chain '4' and resid 769 through 771 No H-bonds generated for 'chain '4' and resid 769 through 771' Processing helix chain '4' and resid 773 through 790 removed outlier: 3.665A pdb=" N ASP 4 777 " --> pdb=" O ARG 4 773 " (cutoff:3.500A) 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) removed outlier: 5.010A pdb=" N GLU 4 789 " --> pdb=" O GLU 4 785 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS 4 790 " --> pdb=" O ARG 4 786 " (cutoff:3.500A) Processing helix chain '4' and resid 798 through 807 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) Processing helix chain '4' and resid 816 through 823 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 826 through 836 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) removed outlier: 3.678A pdb=" N LEU 4 835 " --> pdb=" O SER 4 831 " (cutoff:3.500A) Processing helix chain '5' and resid 8 through 23 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) Processing helix chain '5' and resid 31 through 40 removed outlier: 3.744A pdb=" N ALA 5 35 " --> pdb=" O SER 5 32 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL 5 36 " --> pdb=" O HIS 5 33 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET 5 38 " --> pdb=" O ALA 5 35 " (cutoff:3.500A) Processing helix chain '5' and resid 45 through 53 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 57 through 70 removed outlier: 3.645A pdb=" N ILE 5 67 " --> pdb=" O GLY 5 63 " (cutoff:3.500A) Processing helix chain '5' and resid 85 through 100 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 108 through 116 removed outlier: 3.838A pdb=" N ALA 5 114 " --> pdb=" O HIS 5 110 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU 5 115 " --> pdb=" O LEU 5 111 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA 5 116 " --> pdb=" O ILE 5 112 " (cutoff:3.500A) Processing helix chain '5' and resid 122 through 128 Processing helix chain '5' and resid 132 through 143 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 158 through 162 Processing helix chain '5' and resid 167 through 172 Processing helix chain '5' and resid 183 through 193 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 212 through 224 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 229 through 231 No H-bonds generated for 'chain '5' and resid 229 through 231' Processing helix chain '5' and resid 240 through 244 Processing helix chain '5' and resid 252 through 267 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 340 through 348 removed outlier: 3.809A pdb=" N SER 5 344 " --> pdb=" O THR 5 340 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY 5 348 " --> pdb=" O SER 5 344 " (cutoff:3.500A) Processing helix chain '5' and resid 350 through 356 removed outlier: 3.515A pdb=" N THR 5 355 " --> pdb=" O GLU 5 351 " (cutoff:3.500A) Processing helix chain '5' and resid 364 through 373 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) Processing helix chain '5' and resid 384 through 402 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 406 through 427 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 431 through 487 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 491 through 498 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) Processing helix chain '5' and resid 501 through 523 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 534 through 545 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 549 through 552 No H-bonds generated for 'chain '5' and resid 549 through 552' Processing helix chain '5' and resid 557 through 566 removed outlier: 3.899A pdb=" N LEU 5 561 " --> pdb=" O LYS 5 557 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS 5 562 " --> pdb=" O GLU 5 558 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU 5 564 " --> pdb=" O LEU 5 560 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU 5 565 " --> pdb=" O LEU 5 561 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR 5 566 " --> pdb=" O HIS 5 562 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 587 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) Processing helix chain '5' and resid 613 through 620 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 669 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) Processing helix chain '5' and resid 685 through 697 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 747 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 769 through 787 removed outlier: 3.595A pdb=" N ILE 5 772 " --> pdb=" O PRO 5 769 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG 5 773 " --> pdb=" O SER 5 770 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL 5 776 " --> pdb=" O ARG 5 773 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP 5 777 " --> pdb=" O LYS 5 774 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL 5 778 " --> pdb=" O ILE 5 775 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG 5 779 " --> pdb=" O VAL 5 776 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU 5 780 " --> pdb=" O ASP 5 777 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS 5 781 " --> pdb=" O VAL 5 778 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU 5 782 " --> pdb=" O ARG 5 779 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL 5 783 " --> pdb=" O LEU 5 780 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU 5 785 " --> pdb=" O GLU 5 782 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG 5 786 " --> pdb=" O VAL 5 783 " (cutoff:3.500A) Processing helix chain '5' and resid 798 through 804 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) No H-bonds generated for 'chain '5' and resid 798 through 804' Processing helix chain '5' and resid 816 through 825 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 827 through 835 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) Processing helix chain '6' and resid 9 through 23 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) Processing helix chain '6' and resid 31 through 40 removed outlier: 3.602A pdb=" N ALA 6 35 " --> pdb=" O SER 6 32 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET 6 38 " --> pdb=" O ALA 6 35 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 53 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) Processing helix chain '6' and resid 57 through 70 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 85 through 101 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 109 through 111 No H-bonds generated for 'chain '6' and resid 109 through 111' Processing helix chain '6' and resid 122 through 128 removed outlier: 3.964A pdb=" N GLY 6 128 " --> pdb=" O VAL 6 124 " (cutoff:3.500A) Processing helix chain '6' and resid 132 through 143 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 159 through 162 No H-bonds generated for 'chain '6' and resid 159 through 162' Processing helix chain '6' and resid 167 through 172 Processing helix chain '6' and resid 183 through 193 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) Processing helix chain '6' and resid 211 through 224 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 242 through 244 No H-bonds generated for 'chain '6' and resid 242 through 244' Processing helix chain '6' and resid 252 through 267 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 293 through 301 Proline residue: 6 297 - end of helix Processing helix chain '6' and resid 312 through 316 removed outlier: 3.570A pdb=" N ARG 6 316 " --> pdb=" O LEU 6 312 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 312 through 316' Processing helix chain '6' and resid 323 through 326 No H-bonds generated for 'chain '6' and resid 323 through 326' Processing helix chain '6' and resid 340 through 348 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 350 through 356 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 364 through 376 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 384 through 402 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 406 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 434 through 449 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) Processing helix chain '6' and resid 452 through 487 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 491 through 494 No H-bonds generated for 'chain '6' and resid 491 through 494' Processing helix chain '6' and resid 502 through 523 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) Processing helix chain '6' and resid 534 through 544 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 549 through 551 No H-bonds generated for 'chain '6' and resid 549 through 551' Processing helix chain '6' and resid 556 through 561 removed outlier: 3.617A pdb=" N LEU 6 560 " --> pdb=" O GLU 6 556 " (cutoff:3.500A) Processing helix chain '6' and resid 563 through 567 Processing helix chain '6' and resid 575 through 590 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) Processing helix chain '6' and resid 614 through 620 removed outlier: 3.659A pdb=" N ALA 6 620 " --> pdb=" O VAL 6 616 " (cutoff:3.500A) Processing helix chain '6' and resid 635 through 637 No H-bonds generated for 'chain '6' and resid 635 through 637' Processing helix chain '6' and resid 663 through 666 No H-bonds generated for 'chain '6' and resid 663 through 666' Processing helix chain '6' and resid 680 through 682 No H-bonds generated for 'chain '6' and resid 680 through 682' Processing helix chain '6' and resid 685 through 688 No H-bonds generated for 'chain '6' and resid 685 through 688' Processing helix chain '6' and resid 690 through 697 removed outlier: 3.685A pdb=" N ILE 6 694 " --> pdb=" O LEU 6 690 " (cutoff:3.500A) Processing helix chain '6' and resid 740 through 749 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 752 through 757 removed outlier: 3.923A pdb=" N ASN 6 756 " --> pdb=" O ASN 6 752 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ARG 6 757 " --> pdb=" O GLU 6 753 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 752 through 757' Processing helix chain '6' and resid 769 through 786 removed outlier: 3.578A pdb=" N ILE 6 772 " --> pdb=" O PRO 6 769 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG 6 773 " --> pdb=" O SER 6 770 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL 6 776 " --> pdb=" O ARG 6 773 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG 6 779 " --> pdb=" O VAL 6 776 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU 6 780 " --> pdb=" O ASP 6 777 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN 6 784 " --> pdb=" O LYS 6 781 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU 6 785 " --> pdb=" O GLU 6 782 " (cutoff:3.500A) Processing helix chain '6' and resid 800 through 806 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) No H-bonds generated for 'chain '6' and resid 800 through 806' Processing helix chain '6' and resid 818 through 823 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) No H-bonds generated for 'chain '6' and resid 818 through 823' Processing helix chain '6' and resid 826 through 836 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) removed outlier: 4.322A pdb=" N LEU 6 835 " --> pdb=" O SER 6 831 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP 6 836 " --> pdb=" O ARG 6 832 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '1' and resid 164 through 166 Processing sheet with id= B, first strand: chain '1' and resid 329 through 333 removed outlier: 7.231A pdb=" N ASN 1 200 " --> pdb=" O GLN 1 330 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL 1 332 " --> pdb=" O ASN 1 200 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS 1 202 " --> pdb=" O VAL 1 332 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY 1 308 " --> pdb=" O LEU 1 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain '1' and resid 630 through 634 removed outlier: 6.663A pdb=" N VAL 1 674 " --> pdb=" O VAL 1 631 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE 1 633 " --> pdb=" O VAL 1 674 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU 1 676 " --> pdb=" O ILE 1 633 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE 1 714 " --> pdb=" O THR 1 673 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL 1 675 " --> pdb=" O ILE 1 714 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL 1 716 " --> pdb=" O VAL 1 675 " (cutoff:3.500A) Processing sheet with id= D, 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= D Processing sheet with id= E, first strand: chain '1' and resid 793 through 796 removed outlier: 4.379A pdb=" N LYS 1 846 " --> pdb=" O ILE 1 858 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 164 through 166 removed outlier: 7.021A pdb=" N ILE 2 270 " --> pdb=" O TYR 2 236 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU 2 238 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE 2 272 " --> pdb=" O LEU 2 238 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG 2 305 " --> pdb=" O VAL 2 271 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE 2 273 " --> pdb=" O ARG 2 305 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE 2 307 " --> pdb=" O ILE 2 273 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '2' and resid 200 through 204 removed outlier: 3.562A pdb=" N GLN 2 330 " --> pdb=" O ASN 2 200 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS 2 202 " --> pdb=" O GLN 2 330 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL 2 332 " --> pdb=" O CYS 2 202 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '2' and resid 630 through 634 removed outlier: 6.167A pdb=" N VAL 2 674 " --> pdb=" O VAL 2 631 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE 2 633 " --> pdb=" O VAL 2 674 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU 2 676 " --> pdb=" O ILE 2 633 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE 2 714 " --> pdb=" O VAL 2 675 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE 2 677 " --> pdb=" O ILE 2 714 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL 2 716 " --> pdb=" O PHE 2 677 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, 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= I Processing sheet with id= J, first strand: chain '2' and resid 794 through 796 removed outlier: 6.410A pdb=" N ALA 2 845 " --> 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= K, first strand: chain '3' and resid 164 through 166 removed outlier: 3.538A pdb=" N TYR 3 236 " --> pdb=" O ILE 3 270 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '3' and resid 329 through 333 removed outlier: 6.772A pdb=" N ASN 3 200 " --> pdb=" O GLN 3 330 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL 3 332 " --> pdb=" O ASN 3 200 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N CYS 3 202 " --> pdb=" O VAL 3 332 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY 3 308 " --> pdb=" O LEU 3 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain '3' and resid 630 through 633 removed outlier: 6.424A pdb=" N VAL 3 674 " --> pdb=" O VAL 3 631 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE 3 633 " --> pdb=" O VAL 3 674 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU 3 676 " --> pdb=" O ILE 3 633 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE 3 714 " --> pdb=" O VAL 3 675 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE 3 677 " --> pdb=" O ILE 3 714 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL 3 716 " --> pdb=" O PHE 3 677 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, 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= N Processing sheet with id= O, first strand: chain '3' and resid 793 through 796 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= P, first strand: chain '4' and resid 164 through 166 removed outlier: 7.166A pdb=" N ILE 4 270 " --> pdb=" O TYR 4 236 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU 4 238 " --> pdb=" O ILE 4 270 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE 4 272 " --> pdb=" O LEU 4 238 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 330 through 333 removed outlier: 6.430A pdb=" N GLY 4 308 " --> pdb=" O LEU 4 203 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLY 4 205 " --> pdb=" O GLY 4 308 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N THR 4 310 " --> pdb=" O GLY 4 205 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 630 through 634 removed outlier: 6.473A pdb=" N VAL 4 674 " --> pdb=" O VAL 4 631 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE 4 633 " --> pdb=" O VAL 4 674 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU 4 676 " --> pdb=" O ILE 4 633 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL 4 716 " --> pdb=" O VAL 4 675 " (cutoff:3.500A) Processing sheet with id= S, 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= T, first strand: chain '4' and resid 793 through 796 removed outlier: 4.074A pdb=" N LYS 4 846 " --> pdb=" O ILE 4 858 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '5' and resid 164 through 166 Processing sheet with id= V, first strand: chain '5' and resid 201 through 203 removed outlier: 5.707A pdb=" N GLN 5 330 " --> pdb=" O CYS 5 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain '5' and resid 630 through 632 removed outlier: 6.187A pdb=" N VAL 5 674 " --> pdb=" O VAL 5 631 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE 5 714 " --> pdb=" O VAL 5 675 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE 5 677 " --> pdb=" O ILE 5 714 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL 5 716 " --> pdb=" O PHE 5 677 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain '5' and resid 699 through 701 removed outlier: 3.646A pdb=" N CYS 5 700 " --> pdb=" O VAL 5 708 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL 5 708 " --> pdb=" O CYS 5 700 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain '5' and resid 793 through 796 removed outlier: 4.352A pdb=" N LYS 5 846 " --> pdb=" O ILE 5 858 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '6' and resid 329 through 333 removed outlier: 6.816A pdb=" N ASN 6 200 " --> pdb=" O GLN 6 330 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL 6 332 " --> pdb=" O ASN 6 200 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N CYS 6 202 " --> pdb=" O VAL 6 332 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY 6 308 " --> pdb=" O LEU 6 203 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLY 6 205 " --> pdb=" O GLY 6 308 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR 6 310 " --> pdb=" O GLY 6 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain '6' and resid 602 through 605 removed outlier: 7.971A pdb=" N GLU 6 760 " --> pdb=" O LEU 6 603 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N LEU 6 605 " --> pdb=" O GLU 6 760 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE 6 762 " --> pdb=" O LEU 6 605 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain '6' and resid 630 through 634 removed outlier: 6.266A pdb=" N VAL 6 674 " --> pdb=" O VAL 6 631 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE 6 633 " --> pdb=" O VAL 6 674 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU 6 676 " --> pdb=" O ILE 6 633 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE 6 714 " --> pdb=" O VAL 6 675 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N PHE 6 677 " --> pdb=" O ILE 6 714 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL 6 716 " --> pdb=" O PHE 6 677 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain '6' and resid 794 through 796 removed outlier: 6.309A pdb=" N ALA 6 845 " --> 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) 920 hydrogen bonds defined for protein. 2628 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: 12.19 Time building geometry restraints manager: 14.49 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: 10449 2.81 - 3.33: 31888 3.33 - 3.85: 56373 3.85 - 4.38: 68953 4.38 - 4.90: 116447 Nonbonded interactions: 284110 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 284105 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: 0.780 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: 7.240 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 86.050 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.410 ------------------------------------------------------------------------------- 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= 0.087 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 % 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 *********************** 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 : 4.354 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 outliers start: 2 outliers final: 0 residues processed: 1384 average time/residue: 0.6102 time to fit residues: 1268.9766 Evaluate side-chains 739 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 739 time to evaluate : 4.264 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1143 ------------------------------------------------------------------------------- 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: 1.9990 chunk 363 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 245 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 376 optimal weight: 6.9990 chunk 145 optimal weight: 0.0670 chunk 228 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 chunk 435 optimal weight: 5.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- 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 ** 1 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 277 HIS 1 470 ASN 1 553 GLN 1 693 GLN ** 1 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 784 GLN 2 26 HIS ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 97 HIS 2 108 GLN 2 232 GLN 2 268 GLN 2 415 HIS 2 473 GLN 2 551 ASN 2 689 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 3 24 ASN 3 26 HIS 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 3 824 HIS 3 860 ASN 4 15 ASN 4 43 ASN 4 83 HIS 4 277 HIS 4 293 ASN ** 4 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 511 GLN 4 756 ASN 4 771 ASN 4 784 GLN 4 791 GLN 4 806 GLN 5 28 GLN 5 137 ASN 5 200 ASN 5 536 GLN ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 594 ASN 5 699 HIS 5 720 ASN ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 92 HIS 6 95 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 6 749 HIS ** 6 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 860 ASN 6 861 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5276 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 38814 Z= 0.298 Angle : 0.787 11.329 52326 Z= 0.382 Chirality : 0.045 0.212 6042 Planarity : 0.006 0.117 6756 Dihedral : 7.803 136.570 5400 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.65 % Favored : 96.31 % Rotamer Outliers : 3.73 % 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: -3.24 (0.11), residues: 4740 helix: -2.75 (0.08), residues: 2438 sheet: -1.55 (0.27), residues: 358 loop : -1.14 (0.14), residues: 1944 *********************** 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 969 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 817 time to evaluate : 4.413 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: symmetry clash outliers start: 152 outliers final: 80 residues processed: 903 average time/residue: 0.6182 time to fit residues: 861.2509 Evaluate side-chains 706 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 626 time to evaluate : 6.496 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.3597 time to fit residues: 61.6070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 362 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 436 optimal weight: 0.9980 chunk 471 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 chunk 433 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 350 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 83 HIS 1 200 ASN 1 293 ASN 1 771 ASN ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 95 HIS 2 277 HIS ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 861 HIS 3 95 HIS ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 141 HIS 4 371 GLN 4 400 GLN 4 473 GLN 4 562 HIS 4 625 ASN 4 756 ASN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 470 ASN 5 511 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 473 GLN ** 6 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5374 moved from start: 0.6488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 38814 Z= 0.198 Angle : 0.636 10.848 52326 Z= 0.299 Chirality : 0.042 0.192 6042 Planarity : 0.004 0.058 6756 Dihedral : 6.966 136.564 5400 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.59 % Favored : 96.39 % Rotamer Outliers : 2.50 % 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: -2.18 (0.12), residues: 4740 helix: -1.67 (0.09), residues: 2549 sheet: -1.40 (0.27), residues: 375 loop : -0.77 (0.15), residues: 1816 *********************** 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 812 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 710 time to evaluate : 4.421 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 outliers start: 102 outliers final: 47 residues processed: 769 average time/residue: 0.5751 time to fit residues: 684.9970 Evaluate side-chains 651 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 604 time to evaluate : 4.826 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3864 time to fit residues: 39.3470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 208 optimal weight: 0.9980 chunk 293 optimal weight: 2.9990 chunk 438 optimal weight: 3.9990 chunk 463 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 415 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 400 GLN 4 625 ASN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 24 ASN ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 473 GLN 6 513 GLN ** 6 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 756 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 38814 Z= 0.154 Angle : 0.600 8.839 52326 Z= 0.276 Chirality : 0.041 0.176 6042 Planarity : 0.004 0.055 6756 Dihedral : 6.351 150.221 5400 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.09 % Rotamer Outliers : 1.42 % 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: -1.52 (0.12), residues: 4740 helix: -1.07 (0.10), residues: 2563 sheet: -1.20 (0.29), residues: 334 loop : -0.57 (0.15), residues: 1843 *********************** 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 735 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 677 time to evaluate : 4.793 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 outliers start: 58 outliers final: 36 residues processed: 706 average time/residue: 0.5955 time to fit residues: 652.2943 Evaluate side-chains 647 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 611 time to evaluate : 4.518 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3631 time to fit residues: 30.6172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 345 optimal weight: 0.0980 chunk 191 optimal weight: 0.9980 chunk 395 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 416 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** 1 551 ASN ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 791 GLN 4 562 HIS 4 806 GLN ** 5 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 860 ASN ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 435 GLN 6 473 GLN 6 593 GLN 6 756 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5384 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 38814 Z= 0.145 Angle : 0.596 11.021 52326 Z= 0.270 Chirality : 0.041 0.306 6042 Planarity : 0.004 0.053 6756 Dihedral : 5.963 150.512 5400 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.85 % Favored : 97.13 % Rotamer Outliers : 1.35 % 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: -1.05 (0.12), residues: 4740 helix: -0.63 (0.10), residues: 2555 sheet: -1.15 (0.29), residues: 340 loop : -0.43 (0.15), residues: 1845 *********************** 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 717 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 662 time to evaluate : 4.736 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 outliers start: 55 outliers final: 29 residues processed: 692 average time/residue: 0.5880 time to fit residues: 631.1669 Evaluate side-chains 645 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 616 time to evaluate : 4.553 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4118 time to fit residues: 27.5887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 3.9990 chunk 417 optimal weight: 0.0020 chunk 91 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 464 optimal weight: 10.0000 chunk 385 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 243 optimal weight: 0.0570 overall best weight: 2.4112 ------------------------------------------------------------------------------- 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** 1 277 HIS ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 625 ASN 2 699 HIS ** 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** ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 473 GLN ** 3 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 137 ASN 4 396 ASN 4 400 GLN 4 536 GLN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 829 GLN ** 5 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 268 GLN ** 5 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 593 GLN 5 784 GLN 5 860 ASN 6 473 GLN 6 513 GLN 6 642 HIS 6 756 ASN ** 6 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5548 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 38814 Z= 0.210 Angle : 0.651 14.183 52326 Z= 0.304 Chirality : 0.042 0.188 6042 Planarity : 0.004 0.051 6756 Dihedral : 6.177 152.193 5400 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.31 % Rotamer Outliers : 1.79 % 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: -0.97 (0.12), residues: 4740 helix: -0.53 (0.10), residues: 2582 sheet: -1.04 (0.29), residues: 349 loop : -0.45 (0.15), residues: 1809 *********************** 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 712 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 639 time to evaluate : 4.430 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 outliers start: 73 outliers final: 39 residues processed: 677 average time/residue: 0.5891 time to fit residues: 619.5048 Evaluate side-chains 627 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 588 time to evaluate : 4.413 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3530 time to fit residues: 32.1132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 339 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 390 optimal weight: 1.9990 chunk 259 optimal weight: 8.9990 chunk 462 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 101 GLN 1 357 HIS ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 791 GLN ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 33 HIS ** 3 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 371 GLN 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 108 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** ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 642 HIS 6 756 ASN 6 806 GLN 6 829 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 0.8373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 38814 Z= 0.237 Angle : 0.695 16.334 52326 Z= 0.327 Chirality : 0.043 0.169 6042 Planarity : 0.004 0.049 6756 Dihedral : 6.418 149.250 5400 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.24 % Rotamer Outliers : 1.47 % 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: -1.04 (0.12), residues: 4740 helix: -0.57 (0.10), residues: 2587 sheet: -1.15 (0.28), residues: 362 loop : -0.48 (0.15), residues: 1791 *********************** 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 684 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 624 time to evaluate : 4.427 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 outliers start: 60 outliers final: 31 residues processed: 654 average time/residue: 0.5976 time to fit residues: 603.9860 Evaluate side-chains 612 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 581 time to evaluate : 4.709 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4292 time to fit residues: 31.1979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 0.7980 chunk 184 optimal weight: 0.7980 chunk 276 optimal weight: 7.9990 chunk 139 optimal weight: 0.0270 chunk 90 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 315 optimal weight: 0.0010 chunk 228 optimal weight: 0.0870 chunk 43 optimal weight: 0.7980 chunk 363 optimal weight: 0.9990 overall best weight: 0.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 108 GLN ** 2 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 791 GLN ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 28 GLN ** 4 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 396 ASN 4 400 GLN 4 536 GLN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 642 HIS 6 806 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 0.8218 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= 0.151 Angle : 0.657 26.064 52326 Z= 0.296 Chirality : 0.042 0.154 6042 Planarity : 0.004 0.053 6756 Dihedral : 5.882 143.098 5400 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.68 % Favored : 97.30 % Rotamer Outliers : 0.42 % 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: -0.60 (0.13), residues: 4740 helix: -0.24 (0.10), residues: 2569 sheet: -0.87 (0.28), residues: 361 loop : -0.25 (0.15), residues: 1810 *********************** 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 681 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 664 time to evaluate : 4.437 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 outliers start: 17 outliers final: 6 residues processed: 672 average time/residue: 0.5906 time to fit residues: 610.6626 Evaluate side-chains 614 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 608 time to evaluate : 4.533 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4715 time to fit residues: 10.9099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 7.9990 chunk 443 optimal weight: 1.9990 chunk 404 optimal weight: 3.9990 chunk 431 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 338 optimal weight: 0.0570 chunk 132 optimal weight: 0.0980 chunk 389 optimal weight: 0.9980 chunk 407 optimal weight: 0.0980 chunk 429 optimal weight: 10.0000 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 699 HIS ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 232 GLN ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 HIS 4 596 ASN 4 625 ASN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 784 GLN 6 642 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.8273 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= 0.150 Angle : 0.675 30.461 52326 Z= 0.303 Chirality : 0.042 0.227 6042 Planarity : 0.004 0.058 6756 Dihedral : 5.714 140.873 5400 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer Outliers : 0.49 % 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: -0.41 (0.13), residues: 4740 helix: -0.09 (0.11), residues: 2552 sheet: -0.75 (0.28), residues: 363 loop : -0.17 (0.15), residues: 1825 *********************** 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 656 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 636 time to evaluate : 4.319 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 outliers start: 20 outliers final: 10 residues processed: 644 average time/residue: 0.5863 time to fit residues: 589.5256 Evaluate side-chains 603 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 593 time to evaluate : 4.216 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4020 time to fit residues: 12.9071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 6.9990 chunk 455 optimal weight: 0.4980 chunk 278 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 316 optimal weight: 4.9990 chunk 478 optimal weight: 9.9990 chunk 440 optimal weight: 2.9990 chunk 380 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 294 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 200 ASN 2 232 GLN ** 2 574 GLN ** 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** ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 30 HIS 6 642 HIS 6 806 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5599 moved from start: 0.8621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 38814 Z= 0.201 Angle : 0.715 35.521 52326 Z= 0.327 Chirality : 0.043 0.176 6042 Planarity : 0.004 0.055 6756 Dihedral : 5.969 143.985 5400 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % Rotamer Outliers : 0.44 % 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: -0.48 (0.13), residues: 4740 helix: -0.15 (0.11), residues: 2559 sheet: -0.81 (0.27), residues: 385 loop : -0.18 (0.16), residues: 1796 ********************** 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 618 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 600 time to evaluate : 4.604 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 outliers start: 18 outliers final: 9 residues processed: 605 average time/residue: 0.5901 time to fit residues: 558.1867 Evaluate side-chains 589 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 580 time to evaluate : 4.566 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3795 time to fit residues: 12.7349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.9990 chunk 405 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 351 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 381 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 391 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 232 GLN ** 2 574 GLN ** 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** ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 108 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** ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 699 HIS 6 642 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.122813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.109458 restraints weight = 179427.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.111033 restraints weight = 126249.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.112179 restraints weight = 95627.057| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.8837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 38814 Z= 0.205 Angle : 0.728 35.452 52326 Z= 0.332 Chirality : 0.043 0.196 6042 Planarity : 0.004 0.077 6756 Dihedral : 6.111 143.874 5400 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.48 % Rotamer Outliers : 0.39 % 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: -0.46 (0.13), residues: 4740 helix: -0.13 (0.10), residues: 2553 sheet: -0.79 (0.27), residues: 386 loop : -0.18 (0.16), residues: 1801 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10754.42 seconds wall clock time: 193 minutes 47.51 seconds (11627.51 seconds total)