Starting phenix.real_space_refine on Tue Apr 16 07:56:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/04_2024/6d00_7782_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/04_2024/6d00_7782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/04_2024/6d00_7782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/04_2024/6d00_7782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/04_2024/6d00_7782_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d00_7782/04_2024/6d00_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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38328 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "2" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "3" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "4" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "5" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "6" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6334 Classifications: {'peptide': 804} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 778} Chain breaks: 6 Chain: "1" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.11, per 1000 atoms: 0.50 Number of scatterers: 38328 At special positions: 0 Unit cell: (187.62, 179.14, 154.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 24 15.00 O 7284 8.00 N 6960 7.00 C 23910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.14 Conformation dependent library (CDL) restraints added in 6.9 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: 8.58 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: 13.39 Time building geometry restraints manager: 15.32 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: 0.830 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: 5.890 Check model and map are aligned: 0.570 Set scattering table: 0.360 Process input model: 96.800 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.280 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.430 ------------------------------------------------------------------------------- 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 % Allowed : 1.89 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.09), residues: 4740 helix: -4.55 (0.04), residues: 2245 sheet: -1.97 (0.30), residues: 309 loop : -1.83 (0.11), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP 3 544 HIS 0.002 0.000 HIS 6 684 PHE 0.002 0.000 PHE 6 329 TYR 0.003 0.000 TYR 4 813 ARG 0.001 0.000 ARG 4 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9480 Ramachandran restraints generated. 4740 Oldfield, 0 Emsley, 4740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1383 time to evaluate : 4.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 199 ASN cc_start: 0.5581 (p0) cc_final: 0.5012 (p0) REVERT: 1 461 GLU cc_start: 0.0058 (tt0) cc_final: -0.0398 (tt0) REVERT: 2 630 ILE cc_start: 0.5910 (mt) cc_final: 0.5705 (tt) REVERT: 2 718 THR cc_start: 0.5417 (m) cc_final: 0.5189 (p) REVERT: 2 835 LEU cc_start: 0.5435 (mt) cc_final: 0.5217 (mm) REVERT: 3 278 THR cc_start: 0.6838 (p) cc_final: 0.6404 (p) REVERT: 3 389 LEU cc_start: 0.5447 (mt) cc_final: 0.4943 (mt) REVERT: 3 614 LEU cc_start: 0.5446 (tp) cc_final: 0.5153 (tp) REVERT: 4 383 PRO cc_start: 0.8314 (Cg_endo) cc_final: 0.8091 (Cg_exo) REVERT: 5 330 GLN cc_start: 0.7562 (tp40) cc_final: 0.7236 (tm-30) REVERT: 6 798 ASP cc_start: 0.4465 (m-30) cc_final: 0.4108 (m-30) outliers start: 2 outliers final: 0 residues processed: 1384 average time/residue: 0.6530 time to fit residues: 1373.4443 Evaluate side-chains 742 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 742 time to evaluate : 4.481 ------------------------------------------------------------------------------- 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 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** ** 2 784 GLN ** 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 4 625 ASN 4 756 ASN 4 771 ASN 4 784 GLN 4 791 GLN 4 806 GLN 5 28 GLN 5 71 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 6 749 HIS ** 6 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 860 ASN 6 861 HIS Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5264 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 38814 Z= 0.297 Angle : 0.788 11.313 52326 Z= 0.382 Chirality : 0.045 0.182 6042 Planarity : 0.006 0.130 6756 Dihedral : 7.752 136.648 5400 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 3.56 % Allowed : 12.37 % Favored : 84.07 % 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: -3.13 (0.11), residues: 4740 helix: -2.62 (0.08), residues: 2431 sheet: -1.50 (0.27), residues: 355 loop : -1.15 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP 6 544 HIS 0.011 0.002 HIS 5 415 PHE 0.023 0.003 PHE 2 677 TYR 0.019 0.002 TYR 3 499 ARG 0.013 0.001 ARG 3 328 *********************** 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 958 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 813 time to evaluate : 5.083 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 revert: symmetry clash revert: symmetry clash REVERT: 1 68 MET cc_start: 0.3114 (ttp) cc_final: 0.2871 (ttm) REVERT: 1 226 ASP cc_start: 0.6119 (m-30) cc_final: 0.5841 (m-30) REVERT: 1 366 ILE cc_start: 0.5681 (mp) cc_final: 0.5440 (mm) REVERT: 1 824 HIS cc_start: 0.5189 (m-70) cc_final: 0.3864 (m-70) REVERT: 2 160 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6483 (mt) REVERT: 2 260 VAL cc_start: 0.6506 (t) cc_final: 0.6240 (p) REVERT: 2 372 LEU cc_start: 0.5330 (tp) cc_final: 0.5106 (tp) REVERT: 2 821 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7458 (tp) REVERT: 3 38 MET cc_start: 0.1259 (ppp) cc_final: -0.0510 (ptt) REVERT: 3 165 ILE cc_start: 0.5935 (mm) cc_final: 0.5642 (mm) REVERT: 3 596 ASN cc_start: 0.5092 (OUTLIER) cc_final: 0.4795 (p0) REVERT: 4 828 THR cc_start: 0.6891 (m) cc_final: 0.6661 (t) REVERT: 5 223 VAL cc_start: 0.7287 (t) cc_final: 0.7027 (t) REVERT: 5 563 MET cc_start: 0.4006 (ptm) cc_final: 0.3668 (ptt) REVERT: 5 639 MET cc_start: 0.6597 (mtm) cc_final: 0.5698 (mtm) REVERT: 6 353 TYR cc_start: 0.6057 (m-80) cc_final: 0.5767 (m-80) REVERT: 6 536 GLN cc_start: 0.5382 (mp-120) cc_final: 0.5154 (mp10) outliers start: 145 outliers final: 72 residues processed: 896 average time/residue: 0.5993 time to fit residues: 823.3062 Evaluate side-chains 699 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 624 time to evaluate : 4.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 253 PHE Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 388 ASP Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 763 VAL Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 2 residue 160 LEU Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 280 LEU Chi-restraints excluded: chain 2 residue 338 SER Chi-restraints excluded: chain 2 residue 340 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 821 LEU Chi-restraints excluded: chain 3 residue 180 ILE Chi-restraints excluded: chain 3 residue 235 VAL Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 562 HIS Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 616 VAL Chi-restraints excluded: chain 3 residue 622 PHE Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 716 VAL Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 3 residue 860 ASN Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 345 ILE Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 697 ASP Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 531 VAL Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 714 ILE Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 186 ILE Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 537 ILE Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 687 VAL Chi-restraints excluded: chain 6 residue 694 ILE Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 776 VAL Chi-restraints excluded: chain 6 residue 785 GLU Chi-restraints excluded: chain 6 residue 787 LEU Chi-restraints excluded: chain 6 residue 828 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 362 optimal weight: 0.6980 chunk 296 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 436 optimal weight: 0.9990 chunk 471 optimal weight: 1.9990 chunk 388 optimal weight: 9.9990 chunk 433 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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** 1 771 ASN ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 95 HIS ** 2 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 108 GLN ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 141 HIS 4 371 GLN 4 400 GLN 4 473 GLN 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 24 ASN ** 5 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 470 ASN ** 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 6 513 GLN ** 6 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5320 moved from start: 0.6206 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= 0.180 Angle : 0.617 10.990 52326 Z= 0.287 Chirality : 0.042 0.226 6042 Planarity : 0.004 0.040 6756 Dihedral : 6.876 136.313 5400 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 3.26 % Allowed : 15.17 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.12), residues: 4740 helix: -1.59 (0.09), residues: 2508 sheet: -1.36 (0.27), residues: 367 loop : -0.85 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 544 HIS 0.005 0.001 HIS 1 684 PHE 0.017 0.001 PHE 2 381 TYR 0.024 0.001 TYR 3 20 ARG 0.010 0.001 ARG 5 586 *********************** 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 849 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 716 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 68 MET cc_start: 0.4341 (ttp) cc_final: 0.4053 (ttm) REVERT: 1 366 ILE cc_start: 0.5617 (mp) cc_final: 0.5386 (mm) REVERT: 1 568 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5821 (mtpp) REVERT: 1 824 HIS cc_start: 0.4492 (m-70) cc_final: 0.4147 (m-70) REVERT: 2 160 LEU cc_start: 0.6768 (mt) cc_final: 0.6563 (mt) REVERT: 2 260 VAL cc_start: 0.6779 (t) cc_final: 0.6439 (p) REVERT: 3 38 MET cc_start: 0.1035 (ppp) cc_final: -0.0444 (ptt) REVERT: 3 384 ASP cc_start: 0.4787 (t0) cc_final: 0.4552 (t0) REVERT: 4 476 ASP cc_start: 0.4635 (OUTLIER) cc_final: 0.4331 (p0) REVERT: 5 483 GLU cc_start: 0.6584 (tp30) cc_final: 0.6326 (tp30) REVERT: 5 487 ARG cc_start: 0.6580 (mtt90) cc_final: 0.5357 (mtt90) REVERT: 6 236 TYR cc_start: 0.6300 (m-10) cc_final: 0.6076 (m-10) REVERT: 6 755 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5578 (pp) outliers start: 133 outliers final: 80 residues processed: 799 average time/residue: 0.6065 time to fit residues: 751.7435 Evaluate side-chains 703 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 620 time to evaluate : 4.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 274 ASP Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 568 LYS Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 647 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 763 VAL Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 1 residue 812 VAL Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 280 LEU Chi-restraints excluded: chain 2 residue 338 SER Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 505 LEU Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 582 CYS Chi-restraints excluded: chain 2 residue 716 VAL Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 776 VAL Chi-restraints excluded: chain 2 residue 792 ILE Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 270 ILE Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 788 ASP Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 3 residue 860 ASN Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 270 ILE Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 476 ASP Chi-restraints excluded: chain 4 residue 515 GLU Chi-restraints excluded: chain 4 residue 560 LEU Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 796 VAL Chi-restraints excluded: chain 4 residue 835 LEU Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 531 VAL Chi-restraints excluded: chain 5 residue 541 VAL Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 713 THR Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 428 GLU Chi-restraints excluded: chain 6 residue 687 VAL Chi-restraints excluded: chain 6 residue 694 ILE Chi-restraints excluded: chain 6 residue 711 LYS Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 755 ILE Chi-restraints excluded: chain 6 residue 803 LEU Chi-restraints excluded: chain 6 residue 818 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 8.9990 chunk 328 optimal weight: 7.9990 chunk 226 optimal weight: 0.0030 chunk 48 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 293 optimal weight: 4.9990 chunk 438 optimal weight: 0.9990 chunk 463 optimal weight: 3.9990 chunk 228 optimal weight: 0.5980 chunk 415 optimal weight: 0.4980 chunk 125 optimal weight: 5.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 83 HIS ** 1 415 HIS ** 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** 3 860 ASN ** 4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 400 GLN 4 596 ASN 4 806 GLN ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 435 GLN 6 473 GLN ** 6 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 756 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5292 moved from start: 0.6453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 38814 Z= 0.139 Angle : 0.588 9.039 52326 Z= 0.269 Chirality : 0.041 0.187 6042 Planarity : 0.004 0.063 6756 Dihedral : 6.191 148.543 5400 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 2.68 % Allowed : 16.08 % Favored : 81.25 % 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: -1.44 (0.12), residues: 4740 helix: -0.98 (0.10), residues: 2507 sheet: -1.16 (0.29), residues: 330 loop : -0.60 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 6 544 HIS 0.016 0.001 HIS 4 562 PHE 0.015 0.001 PHE 2 381 TYR 0.018 0.001 TYR 3 20 ARG 0.008 0.000 ARG 4 328 *********************** 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 789 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 680 time to evaluate : 4.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 4 MET cc_start: 0.6931 (mmm) cc_final: 0.6623 (mmp) REVERT: 1 98 MET cc_start: 0.3626 (ttp) cc_final: 0.3143 (ttp) REVERT: 3 38 MET cc_start: 0.0573 (ppp) cc_final: -0.0284 (ptt) REVERT: 3 278 THR cc_start: 0.6782 (p) cc_final: 0.6507 (t) REVERT: 5 366 ILE cc_start: 0.5629 (OUTLIER) cc_final: 0.5392 (mt) REVERT: 5 483 GLU cc_start: 0.6792 (tp30) cc_final: 0.6496 (tp30) REVERT: 5 487 ARG cc_start: 0.6617 (mtt90) cc_final: 0.5403 (mtt90) REVERT: 6 68 MET cc_start: 0.1236 (mtt) cc_final: 0.0618 (mtt) REVERT: 6 236 TYR cc_start: 0.6389 (m-10) cc_final: 0.6112 (m-10) REVERT: 6 360 ARG cc_start: 0.3281 (mtt90) cc_final: 0.3010 (mtt90) outliers start: 109 outliers final: 79 residues processed: 748 average time/residue: 0.5887 time to fit residues: 684.1968 Evaluate side-chains 684 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 604 time to evaluate : 4.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 83 HIS Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 274 ASP Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 568 LYS Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 2 residue 183 ASP Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 293 ASN Chi-restraints excluded: chain 2 residue 338 SER Chi-restraints excluded: chain 2 residue 384 ASP Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 505 LEU Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 623 LEU Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 776 VAL Chi-restraints excluded: chain 2 residue 783 VAL Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 162 LYS Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 788 ASP Chi-restraints excluded: chain 3 residue 799 LYS Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 95 HIS Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 400 GLN Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 560 LEU Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 828 THR Chi-restraints excluded: chain 4 residue 835 LEU Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 186 ILE Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 231 LEU Chi-restraints excluded: chain 5 residue 366 ILE Chi-restraints excluded: chain 5 residue 541 VAL Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 200 ASN Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 231 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 428 GLU Chi-restraints excluded: chain 6 residue 551 ASN Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 687 VAL Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 839 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 345 optimal weight: 0.0170 chunk 191 optimal weight: 1.9990 chunk 395 optimal weight: 2.9990 chunk 320 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 416 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- 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** 1 293 ASN ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 95 HIS ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 791 GLN 4 396 ASN 4 473 GLN 4 536 GLN 4 562 HIS 4 596 ASN 4 625 ASN 4 756 ASN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 829 GLN ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 593 GLN 5 784 GLN ** 5 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 473 GLN 6 593 GLN 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: 0.5425 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38814 Z= 0.175 Angle : 0.615 9.170 52326 Z= 0.284 Chirality : 0.041 0.156 6042 Planarity : 0.004 0.052 6756 Dihedral : 6.109 153.065 5400 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 3.31 % Allowed : 16.40 % Favored : 80.29 % 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: -1.03 (0.12), residues: 4740 helix: -0.63 (0.10), residues: 2543 sheet: -1.04 (0.29), residues: 346 loop : -0.41 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 544 HIS 0.017 0.001 HIS 1 83 PHE 0.019 0.001 PHE 2 325 TYR 0.017 0.001 TYR 3 20 ARG 0.007 0.001 ARG 3 182 *********************** 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 792 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 657 time to evaluate : 4.761 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: 2 563 MET cc_start: 0.5824 (OUTLIER) cc_final: 0.5586 (ttm) REVERT: 3 38 MET cc_start: 0.0810 (ppp) cc_final: -0.0333 (ptm) REVERT: 3 68 MET cc_start: 0.3102 (mtp) cc_final: 0.2639 (mtm) REVERT: 3 98 MET cc_start: 0.2464 (tpp) cc_final: 0.2253 (tpp) REVERT: 3 682 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7707 (ptmm) REVERT: 4 329 PHE cc_start: 0.7713 (m-80) cc_final: 0.7307 (m-10) REVERT: 4 414 ARG cc_start: 0.5773 (mmm160) cc_final: 0.5515 (mmm160) REVERT: 5 231 LEU cc_start: 0.4829 (OUTLIER) cc_final: 0.4537 (mm) REVERT: 5 483 GLU cc_start: 0.6913 (tp30) cc_final: 0.6336 (tp30) REVERT: 5 487 ARG cc_start: 0.6659 (mtt90) cc_final: 0.5485 (mtt90) REVERT: 5 676 LEU cc_start: 0.5761 (tp) cc_final: 0.5455 (tp) REVERT: 6 236 TYR cc_start: 0.6409 (m-10) cc_final: 0.6201 (m-10) outliers start: 135 outliers final: 97 residues processed: 735 average time/residue: 0.5843 time to fit residues: 670.7045 Evaluate side-chains 709 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 610 time to evaluate : 4.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 142 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 274 ASP Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 550 SER Chi-restraints excluded: chain 1 residue 568 LYS Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 633 ILE Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 293 ASN Chi-restraints excluded: chain 2 residue 322 ASP Chi-restraints excluded: chain 2 residue 338 SER Chi-restraints excluded: chain 2 residue 384 ASP Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 505 LEU Chi-restraints excluded: chain 2 residue 563 MET Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 623 LEU Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 792 ILE Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 162 LYS Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 753 GLU Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 788 ASP Chi-restraints excluded: chain 3 residue 794 LEU Chi-restraints excluded: chain 3 residue 799 LYS Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 515 GLU Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 742 VAL Chi-restraints excluded: chain 4 residue 835 LEU Chi-restraints excluded: chain 5 residue 164 CYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 186 ILE Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 227 ILE Chi-restraints excluded: chain 5 residue 231 LEU Chi-restraints excluded: chain 5 residue 541 VAL Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 186 ILE Chi-restraints excluded: chain 6 residue 200 ASN Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 428 GLU Chi-restraints excluded: chain 6 residue 551 ASN Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 694 ILE Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 798 ASP Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 826 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 2.9990 chunk 417 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 272 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 464 optimal weight: 2.9990 chunk 385 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 243 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** 2 625 ASN ** 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** 4 396 ASN 4 536 GLN 4 569 GLN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 268 GLN ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 473 GLN 6 829 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5443 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 38814 Z= 0.158 Angle : 0.608 15.549 52326 Z= 0.277 Chirality : 0.041 0.183 6042 Planarity : 0.004 0.066 6756 Dihedral : 5.993 150.546 5400 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 3.31 % Allowed : 17.30 % Favored : 79.38 % 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: -0.78 (0.12), residues: 4740 helix: -0.38 (0.10), residues: 2570 sheet: -0.94 (0.29), residues: 340 loop : -0.36 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 2 544 HIS 0.016 0.001 HIS 4 562 PHE 0.015 0.001 PHE 2 325 TYR 0.017 0.001 TYR 3 20 ARG 0.006 0.000 ARG 3 328 *********************** 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 772 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 637 time to evaluate : 4.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 366 ILE cc_start: 0.5310 (mp) cc_final: 0.4990 (mm) REVERT: 1 568 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6295 (mtpp) REVERT: 2 280 LEU cc_start: 0.5151 (mt) cc_final: 0.4779 (mt) REVERT: 3 38 MET cc_start: 0.0791 (ppp) cc_final: -0.0215 (ptm) REVERT: 4 329 PHE cc_start: 0.7579 (m-80) cc_final: 0.7244 (m-10) REVERT: 4 414 ARG cc_start: 0.5665 (mmm160) cc_final: 0.5443 (mmm160) REVERT: 5 483 GLU cc_start: 0.7028 (tp30) cc_final: 0.6004 (tp30) REVERT: 5 487 ARG cc_start: 0.6595 (mtt90) cc_final: 0.5405 (mtt90) REVERT: 6 236 TYR cc_start: 0.6415 (m-10) cc_final: 0.6128 (m-10) outliers start: 135 outliers final: 101 residues processed: 720 average time/residue: 0.5821 time to fit residues: 660.8987 Evaluate side-chains 705 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 603 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 142 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 339 VAL Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 550 SER Chi-restraints excluded: chain 1 residue 568 LYS Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 739 LYS Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 293 ASN Chi-restraints excluded: chain 2 residue 338 SER Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 505 LEU Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 623 LEU Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 792 ILE Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 788 ASP Chi-restraints excluded: chain 3 residue 799 LYS Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 587 LEU Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 704 LYS Chi-restraints excluded: chain 5 residue 120 SER Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 190 ILE Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 227 ILE Chi-restraints excluded: chain 5 residue 531 VAL Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 200 ASN Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 378 THR Chi-restraints excluded: chain 6 residue 379 GLN Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 428 GLU Chi-restraints excluded: chain 6 residue 544 TRP Chi-restraints excluded: chain 6 residue 551 ASN Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 694 ILE Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 785 GLU Chi-restraints excluded: chain 6 residue 798 ASP Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 829 GLN Chi-restraints excluded: chain 6 residue 839 VAL Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 339 optimal weight: 1.9990 chunk 262 optimal weight: 9.9990 chunk 390 optimal weight: 6.9990 chunk 259 optimal weight: 0.9990 chunk 462 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 282 optimal weight: 0.5980 chunk 213 optimal weight: 9.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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** 1 101 GLN ** 1 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 356 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 33 HIS ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 396 ASN 4 536 GLN 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 108 GLN ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 551 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5443 moved from start: 0.7516 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= 0.150 Angle : 0.624 25.409 52326 Z= 0.280 Chirality : 0.041 0.161 6042 Planarity : 0.003 0.045 6756 Dihedral : 5.849 147.993 5400 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 3.14 % Allowed : 17.70 % Favored : 79.16 % 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: -0.58 (0.13), residues: 4740 helix: -0.20 (0.11), residues: 2566 sheet: -0.97 (0.29), residues: 328 loop : -0.27 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 544 HIS 0.006 0.001 HIS 4 562 PHE 0.016 0.001 PHE 3 622 TYR 0.020 0.001 TYR 3 163 ARG 0.007 0.000 ARG 2 586 *********************** 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 757 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 629 time to evaluate : 4.395 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: 1 366 ILE cc_start: 0.5254 (mp) cc_final: 0.5043 (mm) REVERT: 1 568 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6308 (mtpp) REVERT: 2 382 MET cc_start: 0.4417 (tpp) cc_final: 0.3764 (tmm) REVERT: 2 665 GLU cc_start: 0.4024 (tp30) cc_final: 0.3670 (tp30) REVERT: 3 38 MET cc_start: 0.0668 (ppp) cc_final: -0.0166 (ptm) REVERT: 3 121 MET cc_start: 0.5255 (tpp) cc_final: 0.4472 (tpt) REVERT: 3 274 ASP cc_start: 0.5654 (t0) cc_final: 0.4874 (p0) REVERT: 4 98 MET cc_start: 0.0757 (tmm) cc_final: 0.0279 (tmm) REVERT: 4 329 PHE cc_start: 0.7568 (m-80) cc_final: 0.7236 (m-10) REVERT: 5 404 GLN cc_start: 0.2993 (tt0) cc_final: 0.2521 (tt0) REVERT: 5 563 MET cc_start: 0.5342 (ppp) cc_final: 0.4852 (tmm) REVERT: 6 68 MET cc_start: 0.1358 (mtt) cc_final: 0.0642 (mtt) REVERT: 6 236 TYR cc_start: 0.6320 (m-10) cc_final: 0.6089 (m-10) outliers start: 128 outliers final: 108 residues processed: 705 average time/residue: 0.5826 time to fit residues: 639.3286 Evaluate side-chains 719 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 610 time to evaluate : 4.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 142 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 339 VAL Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 550 SER Chi-restraints excluded: chain 1 residue 568 LYS Chi-restraints excluded: chain 1 residue 588 SER Chi-restraints excluded: chain 1 residue 634 ASP Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 739 LYS Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 293 ASN Chi-restraints excluded: chain 2 residue 448 GLN Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 505 LEU Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 623 LEU Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 792 ILE Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 276 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 377 ILE Chi-restraints excluded: chain 3 residue 532 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 622 PHE Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 774 LYS Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 788 ASP Chi-restraints excluded: chain 3 residue 794 LEU Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 819 ASN Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 95 HIS Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 384 ASP Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 678 ASP Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 5 residue 120 SER Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 227 ILE Chi-restraints excluded: chain 5 residue 531 VAL Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 186 ILE Chi-restraints excluded: chain 6 residue 200 ASN Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 344 SER Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 378 THR Chi-restraints excluded: chain 6 residue 379 GLN Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 428 GLU Chi-restraints excluded: chain 6 residue 544 TRP Chi-restraints excluded: chain 6 residue 551 ASN Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 694 ILE Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 798 ASP Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 829 GLN Chi-restraints excluded: chain 6 residue 839 VAL Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 139 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 chunk 315 optimal weight: 3.9990 chunk 228 optimal weight: 0.0970 chunk 43 optimal weight: 0.9980 chunk 363 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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** ** 1 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 771 ASN ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 371 GLN ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 396 ASN 4 536 GLN 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 829 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.7625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 38814 Z= 0.142 Angle : 0.622 25.938 52326 Z= 0.278 Chirality : 0.041 0.178 6042 Planarity : 0.003 0.044 6756 Dihedral : 5.687 145.720 5400 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.72 % Favored : 97.26 % Rotamer: Outliers : 2.77 % Allowed : 18.31 % Favored : 78.92 % 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: -0.35 (0.13), residues: 4740 helix: -0.01 (0.11), residues: 2533 sheet: -0.80 (0.29), residues: 346 loop : -0.18 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 2 544 HIS 0.010 0.001 HIS 4 562 PHE 0.017 0.001 PHE 1 6 TYR 0.022 0.001 TYR 3 20 ARG 0.014 0.000 ARG 2 669 *********************** 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 755 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 642 time to evaluate : 4.145 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: 1 38 MET cc_start: 0.5014 (ptt) cc_final: 0.4418 (mtt) REVERT: 1 366 ILE cc_start: 0.5282 (mp) cc_final: 0.5058 (mm) REVERT: 1 478 LEU cc_start: 0.0488 (OUTLIER) cc_final: 0.0153 (mm) REVERT: 1 565 GLU cc_start: 0.4517 (pp20) cc_final: 0.4247 (pp20) REVERT: 1 568 LYS cc_start: 0.6507 (OUTLIER) cc_final: 0.6162 (mtpp) REVERT: 2 260 VAL cc_start: 0.6950 (t) cc_final: 0.6621 (p) REVERT: 2 382 MET cc_start: 0.4449 (OUTLIER) cc_final: 0.4084 (tmm) REVERT: 2 685 LYS cc_start: 0.6574 (ttmt) cc_final: 0.6247 (ttpt) REVERT: 3 38 MET cc_start: 0.0621 (ppp) cc_final: -0.0095 (ptm) REVERT: 3 274 ASP cc_start: 0.5898 (t0) cc_final: 0.5139 (p0) REVERT: 3 275 GLU cc_start: 0.4924 (mt-10) cc_final: 0.4596 (mt-10) REVERT: 3 757 ARG cc_start: 0.6441 (mmm-85) cc_final: 0.6147 (mmm-85) REVERT: 4 98 MET cc_start: 0.0822 (tmm) cc_final: 0.0342 (tmm) REVERT: 4 329 PHE cc_start: 0.7571 (m-80) cc_final: 0.7130 (m-10) REVERT: 4 547 ILE cc_start: 0.6809 (pt) cc_final: 0.6475 (pt) REVERT: 4 556 GLU cc_start: 0.5005 (mp0) cc_final: 0.4777 (mp0) REVERT: 5 404 GLN cc_start: 0.3029 (tt0) cc_final: 0.2517 (tt0) REVERT: 5 563 MET cc_start: 0.5400 (ppp) cc_final: 0.4889 (tmm) REVERT: 6 68 MET cc_start: 0.1279 (mtt) cc_final: 0.0563 (mtt) REVERT: 6 236 TYR cc_start: 0.6294 (m-10) cc_final: 0.6022 (m-10) outliers start: 113 outliers final: 85 residues processed: 708 average time/residue: 0.5623 time to fit residues: 623.7654 Evaluate side-chains 691 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 603 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 164 CYS Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 339 VAL Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 550 SER Chi-restraints excluded: chain 1 residue 568 LYS Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 739 LYS Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 382 MET Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 505 LEU Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 623 LEU Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 792 ILE Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 276 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 774 LYS Chi-restraints excluded: chain 3 residue 778 VAL Chi-restraints excluded: chain 3 residue 788 ASP Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 819 ASN Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 95 HIS Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 165 ILE Chi-restraints excluded: chain 4 residue 184 GLU Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 384 ASP Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 704 LYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 190 ILE Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 227 ILE Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 200 ASN Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 379 GLN Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 428 GLU Chi-restraints excluded: chain 6 residue 544 TRP Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 839 VAL Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 2.9990 chunk 443 optimal weight: 6.9990 chunk 404 optimal weight: 10.0000 chunk 431 optimal weight: 6.9990 chunk 259 optimal weight: 0.9980 chunk 187 optimal weight: 20.0000 chunk 338 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 389 optimal weight: 9.9990 chunk 407 optimal weight: 0.0070 chunk 429 optimal weight: 6.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- 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 83 HIS 1 95 HIS ** 1 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 357 HIS ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 861 HIS ** 3 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 137 ASN 4 396 ASN 4 536 GLN 4 562 HIS 4 596 ASN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 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** 5 806 GLN ** 5 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5673 moved from start: 0.8489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 38814 Z= 0.270 Angle : 0.774 37.137 52326 Z= 0.361 Chirality : 0.045 0.234 6042 Planarity : 0.005 0.066 6756 Dihedral : 6.490 150.260 5400 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.93 % Rotamer: Outliers : 2.87 % Allowed : 18.53 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.12), residues: 4740 helix: -0.42 (0.10), residues: 2589 sheet: -1.04 (0.27), residues: 383 loop : -0.34 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 3 544 HIS 0.009 0.002 HIS 2 33 PHE 0.023 0.002 PHE 6 329 TYR 0.037 0.002 TYR 3 20 ARG 0.013 0.001 ARG 2 757 *********************** 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 721 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 604 time to evaluate : 4.539 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: 1 38 MET cc_start: 0.5796 (ptt) cc_final: 0.5122 (mtt) REVERT: 1 366 ILE cc_start: 0.5532 (mp) cc_final: 0.5270 (mm) REVERT: 1 823 GLN cc_start: 0.5812 (mm110) cc_final: 0.5611 (mm-40) REVERT: 2 680 MET cc_start: 0.7431 (ptp) cc_final: 0.6709 (ptm) REVERT: 2 685 LYS cc_start: 0.6817 (ttmt) cc_final: 0.6469 (ttpt) REVERT: 3 38 MET cc_start: 0.1337 (ppp) cc_final: -0.0133 (ptm) REVERT: 3 121 MET cc_start: 0.5622 (tpp) cc_final: 0.4859 (tpt) REVERT: 3 274 ASP cc_start: 0.5598 (t0) cc_final: 0.5045 (p0) REVERT: 3 444 MET cc_start: 0.1418 (ptp) cc_final: 0.0789 (ptt) REVERT: 4 198 LYS cc_start: 0.7100 (ptpt) cc_final: 0.6896 (mtmt) REVERT: 4 329 PHE cc_start: 0.7505 (m-80) cc_final: 0.7087 (m-10) REVERT: 4 701 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8019 (p) REVERT: 5 563 MET cc_start: 0.5626 (ppp) cc_final: 0.5286 (tmm) REVERT: 6 68 MET cc_start: 0.1734 (mtt) cc_final: 0.0955 (mtt) REVERT: 6 236 TYR cc_start: 0.6251 (m-10) cc_final: 0.6007 (m-10) REVERT: 6 328 ARG cc_start: 0.6260 (ptp-110) cc_final: 0.5986 (ptp-110) outliers start: 117 outliers final: 93 residues processed: 676 average time/residue: 0.5822 time to fit residues: 612.8067 Evaluate side-chains 668 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 574 time to evaluate : 4.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 27 VAL Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 311 THR Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 550 SER Chi-restraints excluded: chain 1 residue 647 LEU Chi-restraints excluded: chain 1 residue 692 LEU Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 739 LYS Chi-restraints excluded: chain 1 residue 742 VAL Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 505 LEU Chi-restraints excluded: chain 2 residue 572 VAL Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 619 LEU Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 714 ILE Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 792 ILE Chi-restraints excluded: chain 2 residue 802 ASP Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 270 ILE Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 276 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 389 LEU Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 567 MET Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 742 VAL Chi-restraints excluded: chain 3 residue 759 ASP Chi-restraints excluded: chain 3 residue 774 LYS Chi-restraints excluded: chain 3 residue 794 LEU Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 384 ASP Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 414 ARG Chi-restraints excluded: chain 4 residue 427 LYS Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 601 SER Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 4 residue 704 LYS Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 227 ILE Chi-restraints excluded: chain 5 residue 645 SER Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 177 ASP Chi-restraints excluded: chain 6 residue 186 ILE Chi-restraints excluded: chain 6 residue 200 ASN Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 378 THR Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 428 GLU Chi-restraints excluded: chain 6 residue 544 TRP Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 694 ILE Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 785 GLU Chi-restraints excluded: chain 6 residue 818 LEU Chi-restraints excluded: chain 6 residue 855 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 7.9990 chunk 455 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 chunk 316 optimal weight: 9.9990 chunk 478 optimal weight: 0.4980 chunk 440 optimal weight: 0.5980 chunk 380 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 294 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 83 HIS 1 97 HIS ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 108 GLN ** 2 574 GLN ** 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 28 GLN ** 4 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 HIS ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 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** 5 806 GLN ** 5 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 806 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.8466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38814 Z= 0.172 Angle : 0.704 31.170 52326 Z= 0.318 Chirality : 0.043 0.164 6042 Planarity : 0.004 0.069 6756 Dihedral : 6.090 147.516 5400 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 2.04 % Allowed : 20.20 % Favored : 77.76 % 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: -0.09 (0.11), residues: 2556 sheet: -1.01 (0.27), residues: 372 loop : -0.23 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP 4 544 HIS 0.014 0.001 HIS 4 562 PHE 0.021 0.001 PHE 6 329 TYR 0.024 0.001 TYR 3 20 ARG 0.014 0.001 ARG 3 707 ********************** 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 704 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 621 time to evaluate : 4.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 38 MET cc_start: 0.5632 (ptt) cc_final: 0.5331 (mtt) REVERT: 1 823 GLN cc_start: 0.5852 (mm110) cc_final: 0.5532 (mm110) REVERT: 2 105 TYR cc_start: 0.4777 (m-10) cc_final: 0.4554 (m-10) REVERT: 2 685 LYS cc_start: 0.6886 (ttmt) cc_final: 0.6520 (ttpt) REVERT: 3 38 MET cc_start: 0.0910 (ppp) cc_final: -0.0233 (ptm) REVERT: 3 121 MET cc_start: 0.5675 (tpp) cc_final: 0.4927 (tpt) REVERT: 3 274 ASP cc_start: 0.5818 (t0) cc_final: 0.5385 (p0) REVERT: 3 428 GLU cc_start: 0.4660 (mt-10) cc_final: 0.4354 (mt-10) REVERT: 3 444 MET cc_start: 0.1370 (ptp) cc_final: 0.0698 (ptp) REVERT: 4 98 MET cc_start: 0.1278 (tmm) cc_final: 0.0784 (tmm) REVERT: 4 329 PHE cc_start: 0.7367 (m-80) cc_final: 0.6947 (m-10) REVERT: 4 701 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.7946 (p) REVERT: 5 257 LEU cc_start: 0.6776 (mm) cc_final: 0.6532 (mm) REVERT: 5 277 HIS cc_start: 0.6031 (p90) cc_final: 0.5737 (p90) REVERT: 5 332 VAL cc_start: 0.7240 (t) cc_final: 0.7003 (t) REVERT: 5 333 MET cc_start: 0.7228 (tpp) cc_final: 0.6831 (tpp) REVERT: 5 563 MET cc_start: 0.5542 (ppp) cc_final: 0.5180 (tmm) REVERT: 6 68 MET cc_start: 0.1240 (mtt) cc_final: 0.0130 (mtt) REVERT: 6 99 LYS cc_start: 0.5864 (mmmm) cc_final: 0.5063 (mmtm) REVERT: 6 236 TYR cc_start: 0.6206 (m-10) cc_final: 0.5991 (m-10) outliers start: 83 outliers final: 69 residues processed: 676 average time/residue: 0.5884 time to fit residues: 621.5020 Evaluate side-chains 657 residues out of total 4074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 587 time to evaluate : 4.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 83 HIS Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 346 LEU Chi-restraints excluded: chain 1 residue 361 ILE Chi-restraints excluded: chain 1 residue 478 LEU Chi-restraints excluded: chain 1 residue 531 VAL Chi-restraints excluded: chain 1 residue 537 ILE Chi-restraints excluded: chain 1 residue 708 VAL Chi-restraints excluded: chain 1 residue 795 ASP Chi-restraints excluded: chain 2 residue 103 ASP Chi-restraints excluded: chain 2 residue 177 ASP Chi-restraints excluded: chain 2 residue 239 ASP Chi-restraints excluded: chain 2 residue 243 LEU Chi-restraints excluded: chain 2 residue 504 ASP Chi-restraints excluded: chain 2 residue 505 LEU Chi-restraints excluded: chain 2 residue 608 THR Chi-restraints excluded: chain 2 residue 663 LEU Chi-restraints excluded: chain 2 residue 761 LEU Chi-restraints excluded: chain 2 residue 792 ILE Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 3 residue 183 ASP Chi-restraints excluded: chain 3 residue 273 ILE Chi-restraints excluded: chain 3 residue 276 ILE Chi-restraints excluded: chain 3 residue 278 THR Chi-restraints excluded: chain 3 residue 295 LEU Chi-restraints excluded: chain 3 residue 359 VAL Chi-restraints excluded: chain 3 residue 367 VAL Chi-restraints excluded: chain 3 residue 541 VAL Chi-restraints excluded: chain 3 residue 687 VAL Chi-restraints excluded: chain 3 residue 712 ASN Chi-restraints excluded: chain 3 residue 742 VAL Chi-restraints excluded: chain 3 residue 774 LYS Chi-restraints excluded: chain 3 residue 803 LEU Chi-restraints excluded: chain 3 residue 822 ILE Chi-restraints excluded: chain 3 residue 847 VAL Chi-restraints excluded: chain 3 residue 855 ILE Chi-restraints excluded: chain 4 residue 105 TYR Chi-restraints excluded: chain 4 residue 193 LEU Chi-restraints excluded: chain 4 residue 209 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 4 residue 346 LEU Chi-restraints excluded: chain 4 residue 381 PHE Chi-restraints excluded: chain 4 residue 384 ASP Chi-restraints excluded: chain 4 residue 401 LEU Chi-restraints excluded: chain 4 residue 562 HIS Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 4 residue 619 LEU Chi-restraints excluded: chain 4 residue 663 LEU Chi-restraints excluded: chain 4 residue 678 ASP Chi-restraints excluded: chain 4 residue 701 THR Chi-restraints excluded: chain 5 residue 176 LEU Chi-restraints excluded: chain 5 residue 209 VAL Chi-restraints excluded: chain 5 residue 227 ILE Chi-restraints excluded: chain 5 residue 537 ILE Chi-restraints excluded: chain 5 residue 700 CYS Chi-restraints excluded: chain 5 residue 763 VAL Chi-restraints excluded: chain 5 residue 812 VAL Chi-restraints excluded: chain 6 residue 69 VAL Chi-restraints excluded: chain 6 residue 200 ASN Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 355 THR Chi-restraints excluded: chain 6 residue 367 VAL Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 428 GLU Chi-restraints excluded: chain 6 residue 603 LEU Chi-restraints excluded: chain 6 residue 740 ASN Chi-restraints excluded: chain 6 residue 743 LEU Chi-restraints excluded: chain 6 residue 818 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 5.9990 chunk 405 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 351 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 381 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 391 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 83 HIS ** 2 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 574 GLN ** 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** ** 3 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 861 HIS 4 356 HIS 4 562 HIS 4 596 ASN ** 4 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 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** ** 5 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 806 GLN ** 5 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.121702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.109308 restraints weight = 187509.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.111004 restraints weight = 137356.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.113086 restraints weight = 97002.993| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.8983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 38814 Z= 0.270 Angle : 0.792 37.535 52326 Z= 0.368 Chirality : 0.045 0.197 6042 Planarity : 0.005 0.080 6756 Dihedral : 6.592 147.779 5400 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 2.38 % Allowed : 20.69 % Favored : 76.93 % 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: -0.92 (0.12), residues: 4740 helix: -0.43 (0.10), residues: 2595 sheet: -1.08 (0.27), residues: 385 loop : -0.48 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP 6 544 HIS 0.028 0.002 HIS 1 83 PHE 0.023 0.002 PHE 2 622 TYR 0.033 0.002 TYR 3 20 ARG 0.017 0.001 ARG 3 707 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11228.13 seconds wall clock time: 202 minutes 53.04 seconds (12173.04 seconds total)