Starting phenix.real_space_refine (version: dev) on Fri Feb 24 13:57:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fda_31538/02_2023/7fda_31538.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fda_31538/02_2023/7fda_31538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fda_31538/02_2023/7fda_31538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fda_31538/02_2023/7fda_31538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fda_31538/02_2023/7fda_31538.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fda_31538/02_2023/7fda_31538.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "D PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 299": "OE1" <-> "OE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 327": "OE1" <-> "OE2" Residue "Q TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 48": "OD1" <-> "OD2" Residue "X TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 64497 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 4586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4586 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 563} Chain: "B" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3706 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain breaks: 1 Chain: "C" Number of atoms: 4586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4586 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 563} Chain: "D" Number of atoms: 3681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3681 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Chain: "E" Number of atoms: 4586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4586 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 563} Chain: "F" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3699 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "G" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1802 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "H" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain: "I" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1802 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "J" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain: "K" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1802 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "L" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain: "M" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 3, 'TRANS': 214} Chain: "N" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 928 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "O" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain: "P" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3665 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 442} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6069 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 21, 'TRANS': 725} Chain breaks: 2 Chain: "S" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2793 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain: "T" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1492 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 2, 'TRANS': 197} Chain: "U" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "V" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "W" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "X" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "Y" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1146 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "Z" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "a" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "b" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1146 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "c" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "d" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 553 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "e" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 403 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "f" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 583 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 26.80, per 1000 atoms: 0.42 Number of scatterers: 64497 At special positions: 0 Unit cell: (167.4, 189, 270, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 279 16.00 O 12150 8.00 N 10738 7.00 C 41330 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: 21.64 Conformation dependent library (CDL) restraints added in 7.4 seconds 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15342 Finding SS restraints... Secondary structure from input PDB file: 326 helices and 53 sheets defined 61.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.991A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.769A pdb=" N LEU A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.655A pdb=" N SER A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.519A pdb=" N VAL A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 299 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 332 through 345 Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.692A pdb=" N TRP A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.643A pdb=" N PHE A 380 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 393 removed outlier: 4.437A pdb=" N ALA A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 389 " --> pdb=" O GLY A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 433 removed outlier: 3.543A pdb=" N THR A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.665A pdb=" N ARG A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 475 removed outlier: 3.980A pdb=" N SER A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 503 removed outlier: 3.829A pdb=" N VAL A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU A 501 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 525 removed outlier: 3.617A pdb=" N LYS A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 564 removed outlier: 3.703A pdb=" N MET A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 removed outlier: 3.709A pdb=" N ASP A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.769A pdb=" N VAL A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 587 No H-bonds generated for 'chain 'A' and resid 586 through 587' Processing helix chain 'A' and resid 588 through 591 Processing helix chain 'A' and resid 592 through 615 removed outlier: 3.524A pdb=" N VAL A 596 " --> pdb=" O GLY A 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 removed outlier: 3.680A pdb=" N VAL B 16 " --> pdb=" O ASN B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.831A pdb=" N ALA B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 254 through 271 removed outlier: 3.558A pdb=" N TYR B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.576A pdb=" N ALA B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 307 through 317 removed outlier: 3.697A pdb=" N ASP B 311 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.696A pdb=" N TYR B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 3.575A pdb=" N HIS B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 387 removed outlier: 3.959A pdb=" N ILE B 387 " --> pdb=" O LYS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 421 removed outlier: 4.622A pdb=" N ASN B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N VAL B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 420 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 443 removed outlier: 3.684A pdb=" N GLU B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 438 " --> pdb=" O GLU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 466 removed outlier: 3.846A pdb=" N GLN B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 485 removed outlier: 3.763A pdb=" N GLU B 483 " --> pdb=" O LYS B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 120 removed outlier: 3.752A pdb=" N ILE C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 244 Processing helix chain 'C' and resid 261 through 272 removed outlier: 4.603A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.848A pdb=" N GLU C 330 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 345 Processing helix chain 'C' and resid 357 through 372 removed outlier: 3.669A pdb=" N ALA C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 393 removed outlier: 3.816A pdb=" N SER C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 432 Processing helix chain 'C' and resid 442 through 448 removed outlier: 3.645A pdb=" N ALA C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 466 Processing helix chain 'C' and resid 467 through 475 removed outlier: 3.770A pdb=" N SER C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 503 removed outlier: 4.014A pdb=" N GLN C 497 " --> pdb=" O GLU C 493 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 525 removed outlier: 3.716A pdb=" N ILE C 513 " --> pdb=" O ASP C 509 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 563 Processing helix chain 'C' and resid 566 through 575 removed outlier: 4.116A pdb=" N ASP C 572 " --> pdb=" O SER C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 583 removed outlier: 3.599A pdb=" N HIS C 579 " --> pdb=" O GLY C 575 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 581 " --> pdb=" O VAL C 577 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 587 removed outlier: 3.674A pdb=" N PHE C 587 " --> pdb=" O SER C 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 584 through 587' Processing helix chain 'C' and resid 588 through 592 Processing helix chain 'C' and resid 593 through 614 removed outlier: 3.593A pdb=" N HIS C 597 " --> pdb=" O GLU C 593 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 17 Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.580A pdb=" N MET D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU D 109 " --> pdb=" O GLU D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 109' Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 179 through 191 removed outlier: 3.524A pdb=" N ILE D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 232 Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.580A pdb=" N ILE D 253 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 270 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.695A pdb=" N ALA D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 306 No H-bonds generated for 'chain 'D' and resid 305 through 306' Processing helix chain 'D' and resid 307 through 317 removed outlier: 3.621A pdb=" N THR D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.740A pdb=" N TYR D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 367 removed outlier: 3.509A pdb=" N HIS D 365 " --> pdb=" O ASP D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 387 Processing helix chain 'D' and resid 395 through 421 removed outlier: 4.034A pdb=" N SER D 400 " --> pdb=" O HIS D 396 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASN D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 425 Processing helix chain 'D' and resid 426 through 443 removed outlier: 4.035A pdb=" N GLU D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS D 441 " --> pdb=" O GLU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 466 removed outlier: 3.757A pdb=" N LEU D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 468 No H-bonds generated for 'chain 'D' and resid 467 through 468' Processing helix chain 'D' and resid 469 through 473 Processing helix chain 'D' and resid 477 through 484 Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.660A pdb=" N ILE E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 244 Processing helix chain 'E' and resid 261 through 273 removed outlier: 3.904A pdb=" N ILE E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 removed outlier: 4.056A pdb=" N ALA E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE E 297 " --> pdb=" O VAL E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 325 through 332 removed outlier: 3.501A pdb=" N ALA E 328 " --> pdb=" O PRO E 325 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU E 330 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 346 removed outlier: 3.664A pdb=" N LEU E 339 " --> pdb=" O THR E 335 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 340 " --> pdb=" O GLY E 336 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN E 346 " --> pdb=" O TYR E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 372 removed outlier: 3.527A pdb=" N ALA E 361 " --> pdb=" O SER E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 393 removed outlier: 3.762A pdb=" N ALA E 389 " --> pdb=" O GLY E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 432 Processing helix chain 'E' and resid 442 through 448 removed outlier: 3.791A pdb=" N ALA E 446 " --> pdb=" O ASP E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 475 Processing helix chain 'E' and resid 477 through 503 removed outlier: 3.924A pdb=" N VAL E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN E 500 " --> pdb=" O GLU E 496 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU E 501 " --> pdb=" O GLN E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 539 through 563 removed outlier: 3.733A pdb=" N ASN E 563 " --> pdb=" O LYS E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 575 removed outlier: 3.593A pdb=" N LEU E 570 " --> pdb=" O ASN E 566 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 575 " --> pdb=" O ALA E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 584 removed outlier: 3.724A pdb=" N HIS E 579 " --> pdb=" O GLY E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 587 No H-bonds generated for 'chain 'E' and resid 585 through 587' Processing helix chain 'E' and resid 592 through 615 removed outlier: 3.876A pdb=" N GLU E 599 " --> pdb=" O GLU E 595 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 604 " --> pdb=" O PHE E 600 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 605 " --> pdb=" O GLU E 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 16 removed outlier: 4.044A pdb=" N VAL F 16 " --> pdb=" O ASN F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 20 Processing helix chain 'F' and resid 140 through 144 Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.559A pdb=" N ASN F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 249 through 252 Processing helix chain 'F' and resid 253 through 271 removed outlier: 4.464A pdb=" N ARG F 257 " --> pdb=" O ILE F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 295 removed outlier: 3.804A pdb=" N TYR F 284 " --> pdb=" O ASP F 280 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 removed outlier: 3.682A pdb=" N TYR F 304 " --> pdb=" O ARG F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 317 removed outlier: 3.515A pdb=" N ILE F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 354 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.601A pdb=" N HIS F 365 " --> pdb=" O ASP F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 387 removed outlier: 3.505A pdb=" N ALA F 386 " --> pdb=" O LEU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 421 removed outlier: 3.795A pdb=" N SER F 400 " --> pdb=" O HIS F 396 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN F 401 " --> pdb=" O GLY F 397 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA F 418 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 442 Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 469 through 473 Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'G' and resid 9 through 103 removed outlier: 3.679A pdb=" N VAL G 13 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU G 86 " --> pdb=" O ASN G 82 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS G 87 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL G 88 " --> pdb=" O MET G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 112 removed outlier: 3.507A pdb=" N LEU G 107 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 133 removed outlier: 3.616A pdb=" N LYS G 118 " --> pdb=" O ARG G 114 " (cutoff:3.500A) Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 142 through 144 No H-bonds generated for 'chain 'G' and resid 142 through 144' Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'G' and resid 154 through 164 Processing helix chain 'G' and resid 202 through 214 removed outlier: 3.950A pdb=" N LEU G 207 " --> pdb=" O LEU G 203 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS G 208 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU G 212 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 224 removed outlier: 3.675A pdb=" N GLU G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 61 removed outlier: 3.520A pdb=" N ILE H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS H 52 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN H 61 " --> pdb=" O PHE H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 65 through 104 removed outlier: 4.176A pdb=" N GLY H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA H 81 " --> pdb=" O GLN H 77 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU H 82 " --> pdb=" O GLY H 78 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS H 90 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 41 removed outlier: 3.628A pdb=" N ASN I 14 " --> pdb=" O PRO I 10 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU I 17 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN I 21 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA I 39 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 49 removed outlier: 3.708A pdb=" N ILE I 45 " --> pdb=" O GLN I 41 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU I 46 " --> pdb=" O GLU I 42 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS I 47 " --> pdb=" O TYR I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 87 removed outlier: 4.102A pdb=" N THR I 55 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN I 57 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS I 67 " --> pdb=" O LYS I 63 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 113 removed outlier: 3.569A pdb=" N SER I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS I 104 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE I 110 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA I 111 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN I 112 " --> pdb=" O SER I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 133 removed outlier: 4.304A pdb=" N ILE I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU I 132 " --> pdb=" O ALA I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 152 Processing helix chain 'I' and resid 154 through 164 removed outlier: 3.509A pdb=" N ARG I 158 " --> pdb=" O ASP I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 211 Processing helix chain 'I' and resid 214 through 224 removed outlier: 4.213A pdb=" N LEU I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU I 221 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU I 222 " --> pdb=" O ILE I 218 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY I 224 " --> pdb=" O LEU I 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 6 Processing helix chain 'J' and resid 7 through 28 removed outlier: 3.690A pdb=" N GLN J 12 " --> pdb=" O ALA J 8 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA J 13 " --> pdb=" O THR J 9 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 39 Processing helix chain 'J' and resid 40 through 63 removed outlier: 4.394A pdb=" N ASP J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER J 45 " --> pdb=" O LYS J 41 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU J 53 " --> pdb=" O GLN J 49 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU J 54 " --> pdb=" O LYS J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 90 removed outlier: 3.590A pdb=" N GLY J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 103 removed outlier: 3.859A pdb=" N LYS J 96 " --> pdb=" O ASP J 92 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE J 97 " --> pdb=" O ASP J 93 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE J 103 " --> pdb=" O ILE J 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 13 Processing helix chain 'K' and resid 14 through 108 removed outlier: 3.759A pdb=" N MET K 20 " --> pdb=" O GLU K 16 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU K 37 " --> pdb=" O LYS K 33 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE K 50 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR K 76 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA K 81 " --> pdb=" O LYS K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.694A pdb=" N ASN K 113 " --> pdb=" O ILE K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 133 removed outlier: 4.045A pdb=" N ILE K 120 " --> pdb=" O GLU K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'K' and resid 154 through 164 Processing helix chain 'K' and resid 202 through 214 removed outlier: 3.809A pdb=" N GLU K 212 " --> pdb=" O LYS K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 223 removed outlier: 3.739A pdb=" N ILE K 218 " --> pdb=" O ALA K 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 53 removed outlier: 3.835A pdb=" N LEU L 11 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS L 47 " --> pdb=" O ILE L 43 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE L 48 " --> pdb=" O ASP L 44 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP L 51 " --> pdb=" O LYS L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 62 removed outlier: 4.455A pdb=" N PHE L 57 " --> pdb=" O GLU L 53 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU L 58 " --> pdb=" O LEU L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 75 removed outlier: 3.634A pdb=" N LEU L 68 " --> pdb=" O GLY L 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY L 75 " --> pdb=" O LYS L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 81 Processing helix chain 'L' and resid 81 through 103 removed outlier: 3.674A pdb=" N LYS L 85 " --> pdb=" O ALA L 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU L 88 " --> pdb=" O LYS L 84 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS L 89 " --> pdb=" O LYS L 85 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS L 90 " --> pdb=" O ILE L 86 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL L 94 " --> pdb=" O LYS L 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 73 removed outlier: 3.699A pdb=" N ARG M 34 " --> pdb=" O SER M 30 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU M 39 " --> pdb=" O LYS M 35 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG M 42 " --> pdb=" O ALA M 38 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA M 53 " --> pdb=" O ARG M 49 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN M 55 " --> pdb=" O ASP M 51 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL M 71 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR M 73 " --> pdb=" O ALA M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 87 removed outlier: 3.922A pdb=" N GLU M 85 " --> pdb=" O TYR M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 177 removed outlier: 3.511A pdb=" N GLN M 133 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG M 134 " --> pdb=" O GLN M 130 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA M 135 " --> pdb=" O GLN M 131 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU M 137 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE M 138 " --> pdb=" O ARG M 134 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU M 144 " --> pdb=" O SER M 140 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU M 149 " --> pdb=" O THR M 145 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA M 150 " --> pdb=" O LEU M 146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA M 155 " --> pdb=" O SER M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 222 removed outlier: 3.502A pdb=" N ASP M 193 " --> pdb=" O ASN M 189 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU M 198 " --> pdb=" O GLU M 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 23 removed outlier: 4.301A pdb=" N GLY N 19 " --> pdb=" O ASP N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 60 Processing helix chain 'N' and resid 71 through 77 removed outlier: 3.567A pdb=" N ILE N 77 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 84 Processing helix chain 'N' and resid 106 through 113 removed outlier: 4.131A pdb=" N ARG N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL N 112 " --> pdb=" O VAL N 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 36 removed outlier: 3.558A pdb=" N GLU O 36 " --> pdb=" O SER O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 89 removed outlier: 4.278A pdb=" N ILE O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL O 63 " --> pdb=" O ASP O 59 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE O 85 " --> pdb=" O LYS O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 105 removed outlier: 3.702A pdb=" N ASN O 104 " --> pdb=" O PRO O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 114 Processing helix chain 'O' and resid 126 through 167 Processing helix chain 'O' and resid 202 through 208 removed outlier: 3.860A pdb=" N PHE O 206 " --> pdb=" O LEU O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 242 through 250 removed outlier: 4.228A pdb=" N PHE O 246 " --> pdb=" O ASN O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 263 through 319 removed outlier: 4.386A pdb=" N GLN O 269 " --> pdb=" O GLU O 265 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU O 270 " --> pdb=" O LEU O 266 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS O 271 " --> pdb=" O ILE O 267 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL O 286 " --> pdb=" O GLN O 282 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL O 297 " --> pdb=" O LYS O 293 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP O 298 " --> pdb=" O THR O 294 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL O 316 " --> pdb=" O TYR O 312 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 348 removed outlier: 3.602A pdb=" N CYS O 340 " --> pdb=" O ASN O 336 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE O 348 " --> pdb=" O LEU O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 349 through 353 removed outlier: 3.722A pdb=" N GLY O 353 " --> pdb=" O PHE O 350 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 22 removed outlier: 3.800A pdb=" N GLU P 15 " --> pdb=" O THR P 11 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE P 16 " --> pdb=" O HIS P 12 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE P 20 " --> pdb=" O ILE P 16 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG P 21 " --> pdb=" O ARG P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 33 removed outlier: 4.136A pdb=" N LEU P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA P 31 " --> pdb=" O TRP P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 51 Processing helix chain 'P' and resid 74 through 78 Processing helix chain 'P' and resid 79 through 87 Processing helix chain 'P' and resid 92 through 104 removed outlier: 4.316A pdb=" N VAL P 96 " --> pdb=" O CYS P 92 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU P 104 " --> pdb=" O ILE P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 118 removed outlier: 3.847A pdb=" N PHE P 117 " --> pdb=" O THR P 113 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN P 118 " --> pdb=" O VAL P 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 113 through 118' Processing helix chain 'P' and resid 120 through 131 removed outlier: 4.332A pdb=" N LEU P 124 " --> pdb=" O ASP P 120 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE P 128 " --> pdb=" O LEU P 124 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP P 129 " --> pdb=" O GLU P 125 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 152 removed outlier: 4.144A pdb=" N GLN P 152 " --> pdb=" O SER P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 167 removed outlier: 4.081A pdb=" N VAL P 161 " --> pdb=" O ASN P 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 170 through 175 Processing helix chain 'P' and resid 180 through 195 removed outlier: 3.730A pdb=" N LEU P 190 " --> pdb=" O CYS P 186 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN P 191 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU P 192 " --> pdb=" O ARG P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 205 removed outlier: 4.110A pdb=" N ARG P 200 " --> pdb=" O ILE P 196 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP P 201 " --> pdb=" O PRO P 197 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL P 202 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU P 205 " --> pdb=" O ASP P 201 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 209 Processing helix chain 'P' and resid 210 through 223 Processing helix chain 'P' and resid 240 through 254 removed outlier: 3.533A pdb=" N TYR P 244 " --> pdb=" O ILE P 240 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU P 248 " --> pdb=" O TYR P 244 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 265 removed outlier: 4.049A pdb=" N GLU P 262 " --> pdb=" O VAL P 258 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU P 263 " --> pdb=" O PHE P 259 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL P 264 " --> pdb=" O ALA P 260 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 273 Processing helix chain 'P' and resid 273 through 281 removed outlier: 3.868A pdb=" N LYS P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 280 " --> pdb=" O LYS P 276 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR P 281 " --> pdb=" O LEU P 277 " (cutoff:3.500A) Processing helix chain 'P' and resid 283 through 299 removed outlier: 4.069A pdb=" N SER P 287 " --> pdb=" O LYS P 283 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG P 288 " --> pdb=" O GLU P 284 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LEU P 289 " --> pdb=" O LYS P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 308 through 317 Processing helix chain 'P' and resid 318 through 328 removed outlier: 4.200A pdb=" N GLN P 323 " --> pdb=" O LEU P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 334 through 351 removed outlier: 3.529A pdb=" N SER P 340 " --> pdb=" O ARG P 336 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU P 349 " --> pdb=" O ILE P 345 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR P 350 " --> pdb=" O LEU P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 365 Processing helix chain 'P' and resid 371 through 376 Processing helix chain 'P' and resid 382 through 388 removed outlier: 4.305A pdb=" N ARG P 386 " --> pdb=" O GLU P 382 " (cutoff:3.500A) Processing helix chain 'P' and resid 392 through 404 Processing helix chain 'P' and resid 407 through 425 removed outlier: 3.598A pdb=" N ALA P 415 " --> pdb=" O LEU P 411 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL P 422 " --> pdb=" O VAL P 418 " (cutoff:3.500A) Processing helix chain 'P' and resid 428 through 436 removed outlier: 3.762A pdb=" N GLY P 436 " --> pdb=" O ILE P 432 " (cutoff:3.500A) Processing helix chain 'P' and resid 437 through 445 Processing helix chain 'P' and resid 449 through 469 removed outlier: 3.628A pdb=" N ARG P 453 " --> pdb=" O ASP P 449 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP P 468 " --> pdb=" O MET P 464 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 34 removed outlier: 3.502A pdb=" N THR Q 32 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 78 removed outlier: 3.841A pdb=" N ILE Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG Q 60 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG Q 61 " --> pdb=" O ASN Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 93 removed outlier: 3.949A pdb=" N TYR Q 91 " --> pdb=" O ASP Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 126 removed outlier: 4.344A pdb=" N GLU Q 119 " --> pdb=" O SER Q 115 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET Q 124 " --> pdb=" O ARG Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 146 removed outlier: 3.736A pdb=" N VAL Q 133 " --> pdb=" O ASP Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 205 Processing helix chain 'Q' and resid 242 through 254 removed outlier: 3.832A pdb=" N GLU Q 254 " --> pdb=" O ARG Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 280 removed outlier: 3.627A pdb=" N ARG Q 270 " --> pdb=" O SER Q 266 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN Q 280 " --> pdb=" O LYS Q 276 " (cutoff:3.500A) Processing helix chain 'Q' and resid 281 through 324 removed outlier: 4.084A pdb=" N LEU Q 288 " --> pdb=" O LEU Q 284 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS Q 289 " --> pdb=" O TYR Q 285 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA Q 301 " --> pdb=" O SER Q 297 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS Q 304 " --> pdb=" O TYR Q 300 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU Q 305 " --> pdb=" O ALA Q 301 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP Q 307 " --> pdb=" O ALA Q 303 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SER Q 308 " --> pdb=" O LYS Q 304 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN Q 311 " --> pdb=" O ASP Q 307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 345 through 354 Processing helix chain 'Q' and resid 384 through 386 No H-bonds generated for 'chain 'Q' and resid 384 through 386' Processing helix chain 'Q' and resid 387 through 397 removed outlier: 3.704A pdb=" N SER Q 392 " --> pdb=" O ALA Q 388 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR Q 397 " --> pdb=" O ILE Q 393 " (cutoff:3.500A) Processing helix chain 'Q' and resid 407 through 423 removed outlier: 4.169A pdb=" N PHE Q 415 " --> pdb=" O THR Q 411 " (cutoff:3.500A) Proline residue: Q 416 - end of helix removed outlier: 3.801A pdb=" N PHE Q 423 " --> pdb=" O PHE Q 419 " (cutoff:3.500A) Processing helix chain 'Q' and resid 425 through 447 removed outlier: 3.543A pdb=" N ALA Q 435 " --> pdb=" O LEU Q 431 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS Q 444 " --> pdb=" O VAL Q 440 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LYS Q 445 " --> pdb=" O LEU Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 452 through 454 No H-bonds generated for 'chain 'Q' and resid 452 through 454' Processing helix chain 'Q' and resid 455 through 461 Processing helix chain 'Q' and resid 461 through 478 removed outlier: 3.646A pdb=" N ILE Q 465 " --> pdb=" O GLY Q 461 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU Q 466 " --> pdb=" O ARG Q 462 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU Q 467 " --> pdb=" O TYR Q 463 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR Q 474 " --> pdb=" O VAL Q 470 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Q 478 " --> pdb=" O TYR Q 474 " (cutoff:3.500A) Processing helix chain 'Q' and resid 519 through 524 removed outlier: 3.671A pdb=" N TRP Q 522 " --> pdb=" O ASP Q 519 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY Q 524 " --> pdb=" O ALA Q 521 " (cutoff:3.500A) Processing helix chain 'Q' and resid 525 through 553 removed outlier: 3.836A pdb=" N LEU Q 529 " --> pdb=" O THR Q 525 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER Q 534 " --> pdb=" O LEU Q 530 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS Q 538 " --> pdb=" O SER Q 534 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU Q 539 " --> pdb=" O TYR Q 535 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE Q 541 " --> pdb=" O MET Q 537 " (cutoff:3.500A) Processing helix chain 'Q' and resid 554 through 563 removed outlier: 3.723A pdb=" N ASN Q 558 " --> pdb=" O PHE Q 554 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS Q 559 " --> pdb=" O SER Q 555 " (cutoff:3.500A) Processing helix chain 'Q' and resid 568 through 596 Proline residue: Q 574 - end of helix removed outlier: 4.252A pdb=" N MET Q 579 " --> pdb=" O GLY Q 575 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE Q 582 " --> pdb=" O PHE Q 578 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR Q 585 " --> pdb=" O GLY Q 581 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP Q 594 " --> pdb=" O ILE Q 590 " (cutoff:3.500A) Processing helix chain 'Q' and resid 613 through 618 Processing helix chain 'Q' and resid 627 through 644 removed outlier: 3.679A pdb=" N ALA Q 631 " --> pdb=" O TYR Q 627 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS Q 632 " --> pdb=" O PRO Q 628 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL Q 633 " --> pdb=" O HIS Q 629 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL Q 635 " --> pdb=" O ALA Q 631 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE Q 636 " --> pdb=" O LYS Q 632 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS Q 644 " --> pdb=" O MET Q 640 " (cutoff:3.500A) Processing helix chain 'Q' and resid 646 through 652 removed outlier: 3.895A pdb=" N VAL Q 651 " --> pdb=" O TRP Q 647 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS Q 652 " --> pdb=" O LEU Q 648 " (cutoff:3.500A) Processing helix chain 'Q' and resid 708 through 733 removed outlier: 3.622A pdb=" N MET Q 712 " --> pdb=" O PHE Q 708 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL Q 727 " --> pdb=" O CYS Q 723 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR Q 733 " --> pdb=" O HIS Q 729 " (cutoff:3.500A) Processing helix chain 'Q' and resid 733 through 759 removed outlier: 4.413A pdb=" N TRP Q 737 " --> pdb=" O TYR Q 733 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN Q 756 " --> pdb=" O THR Q 752 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE Q 757 " --> pdb=" O MET Q 753 " (cutoff:3.500A) Processing helix chain 'Q' and resid 765 through 784 Processing helix chain 'Q' and resid 786 through 810 removed outlier: 3.537A pdb=" N LEU Q 795 " --> pdb=" O THR Q 791 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU Q 804 " --> pdb=" O LEU Q 800 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER Q 807 " --> pdb=" O VAL Q 803 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS Q 808 " --> pdb=" O GLU Q 804 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 9 removed outlier: 3.756A pdb=" N ASP S 9 " --> pdb=" O PHE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 23 removed outlier: 3.826A pdb=" N GLU S 14 " --> pdb=" O ASN S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 36 removed outlier: 3.621A pdb=" N ASN S 32 " --> pdb=" O ASN S 28 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS S 36 " --> pdb=" O ASN S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 48 removed outlier: 3.617A pdb=" N SER S 48 " --> pdb=" O LEU S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 86 removed outlier: 3.733A pdb=" N LYS S 75 " --> pdb=" O TYR S 71 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU S 76 " --> pdb=" O ALA S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 113 removed outlier: 3.573A pdb=" N ASP S 96 " --> pdb=" O ARG S 92 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR S 97 " --> pdb=" O LYS S 93 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE S 98 " --> pdb=" O PHE S 94 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY S 101 " --> pdb=" O TYR S 97 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR S 102 " --> pdb=" O ILE S 98 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 127 Processing helix chain 'S' and resid 128 through 132 removed outlier: 3.567A pdb=" N GLY S 131 " --> pdb=" O HIS S 128 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 156 removed outlier: 4.229A pdb=" N GLU S 150 " --> pdb=" O GLU S 146 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR S 151 " --> pdb=" O SER S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 158 through 162 Processing helix chain 'S' and resid 173 through 197 Processing helix chain 'S' and resid 201 through 226 removed outlier: 4.228A pdb=" N GLU S 206 " --> pdb=" O GLU S 202 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS S 207 " --> pdb=" O PRO S 203 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN S 209 " --> pdb=" O LYS S 205 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE S 223 " --> pdb=" O ARG S 219 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA S 224 " --> pdb=" O SER S 220 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN S 226 " --> pdb=" O ASN S 222 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 229 No H-bonds generated for 'chain 'S' and resid 227 through 229' Processing helix chain 'S' and resid 234 through 242 Processing helix chain 'S' and resid 251 through 259 removed outlier: 3.638A pdb=" N HIS S 255 " --> pdb=" O LEU S 251 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 271 Processing helix chain 'S' and resid 283 through 300 removed outlier: 3.685A pdb=" N GLU S 294 " --> pdb=" O GLN S 290 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU S 295 " --> pdb=" O LEU S 291 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 332 removed outlier: 3.719A pdb=" N LYS S 314 " --> pdb=" O TRP S 310 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS S 329 " --> pdb=" O TRP S 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 38 removed outlier: 3.968A pdb=" N ILE T 30 " --> pdb=" O LEU T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 54 removed outlier: 3.579A pdb=" N PHE T 50 " --> pdb=" O ASN T 46 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 91 removed outlier: 4.284A pdb=" N TRP T 59 " --> pdb=" O SER T 55 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA T 60 " --> pdb=" O PRO T 56 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU T 62 " --> pdb=" O MET T 58 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE T 64 " --> pdb=" O ALA T 60 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA T 65 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL T 68 " --> pdb=" O ILE T 64 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER T 84 " --> pdb=" O PHE T 80 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER T 85 " --> pdb=" O ILE T 81 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE T 87 " --> pdb=" O GLY T 83 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY T 88 " --> pdb=" O SER T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 122 removed outlier: 4.993A pdb=" N ILE T 102 " --> pdb=" O THR T 98 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER T 103 " --> pdb=" O LYS T 99 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE T 104 " --> pdb=" O ASN T 100 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL T 110 " --> pdb=" O PHE T 106 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA T 111 " --> pdb=" O CYS T 107 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE T 117 " --> pdb=" O TYR T 113 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA T 118 " --> pdb=" O GLY T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 123 through 125 No H-bonds generated for 'chain 'T' and resid 123 through 125' Processing helix chain 'T' and resid 135 through 175 removed outlier: 3.576A pdb=" N LEU T 139 " --> pdb=" O SER T 135 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR T 140 " --> pdb=" O LYS T 136 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR T 141 " --> pdb=" O SER T 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA T 162 " --> pdb=" O ILE T 158 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE T 172 " --> pdb=" O ALA T 168 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA T 175 " --> pdb=" O ALA T 171 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 209 removed outlier: 3.938A pdb=" N ILE T 189 " --> pdb=" O LEU T 185 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU T 194 " --> pdb=" O PHE T 190 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY T 195 " --> pdb=" O GLY T 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS T 208 " --> pdb=" O LEU T 204 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA T 209 " --> pdb=" O MET T 205 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 48 removed outlier: 3.771A pdb=" N GLY U 19 " --> pdb=" O ALA U 15 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY U 22 " --> pdb=" O PHE U 18 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET U 27 " --> pdb=" O CYS U 23 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU U 29 " --> pdb=" O ALA U 25 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE U 43 " --> pdb=" O ALA U 39 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE U 48 " --> pdb=" O GLY U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 59 Processing helix chain 'U' and resid 60 through 81 removed outlier: 4.206A pdb=" N LEU U 69 " --> pdb=" O MET U 65 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA U 70 " --> pdb=" O SER U 66 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE U 71 " --> pdb=" O GLY U 67 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE U 80 " --> pdb=" O VAL U 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 92 through 128 removed outlier: 3.826A pdb=" N HIS U 98 " --> pdb=" O ASN U 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE U 107 " --> pdb=" O LEU U 103 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU U 110 " --> pdb=" O GLY U 106 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET U 118 " --> pdb=" O TYR U 114 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N MET U 128 " --> pdb=" O VAL U 124 " (cutoff:3.500A) Processing helix chain 'U' and resid 129 through 132 removed outlier: 7.032A pdb=" N ARG U 132 " --> pdb=" O HIS U 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 129 through 132' Processing helix chain 'U' and resid 133 through 161 removed outlier: 3.613A pdb=" N LEU U 139 " --> pdb=" O VAL U 135 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU U 147 " --> pdb=" O PHE U 143 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY U 148 " --> pdb=" O SER U 144 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 45 removed outlier: 4.505A pdb=" N PHE V 12 " --> pdb=" O TYR V 8 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY V 13 " --> pdb=" O ALA V 9 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N CYS V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA V 18 " --> pdb=" O ALA V 14 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE V 21 " --> pdb=" O CYS V 17 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE V 22 " --> pdb=" O ALA V 18 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE V 23 " --> pdb=" O SER V 19 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR V 24 " --> pdb=" O ALA V 20 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY V 38 " --> pdb=" O LYS V 34 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL V 44 " --> pdb=" O CYS V 40 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU V 45 " --> pdb=" O ALA V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 77 removed outlier: 3.800A pdb=" N ILE V 58 " --> pdb=" O ILE V 54 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE V 63 " --> pdb=" O MET V 59 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA V 64 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER V 77 " --> pdb=" O LEU V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 83 through 122 removed outlier: 3.507A pdb=" N ILE V 89 " --> pdb=" O TYR V 85 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE V 106 " --> pdb=" O LEU V 102 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY V 112 " --> pdb=" O ILE V 108 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA V 114 " --> pdb=" O ILE V 110 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG V 117 " --> pdb=" O ASP V 113 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY V 118 " --> pdb=" O ALA V 114 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER V 119 " --> pdb=" O GLY V 115 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER V 120 " --> pdb=" O VAL V 116 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN V 121 " --> pdb=" O ARG V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 154 removed outlier: 3.534A pdb=" N LEU V 131 " --> pdb=" O VAL V 127 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE V 132 " --> pdb=" O GLY V 128 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU V 133 " --> pdb=" O MET V 129 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU V 139 " --> pdb=" O PHE V 135 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY V 140 " --> pdb=" O ALA V 136 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU V 141 " --> pdb=" O GLU V 137 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL V 146 " --> pdb=" O TYR V 142 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG V 153 " --> pdb=" O LEU V 149 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA V 154 " --> pdb=" O LEU V 150 " (cutoff:3.500A) Processing helix chain 'W' and resid 8 through 44 removed outlier: 4.322A pdb=" N PHE W 12 " --> pdb=" O TYR W 8 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY W 13 " --> pdb=" O ALA W 9 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE W 21 " --> pdb=" O CYS W 17 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR W 24 " --> pdb=" O ALA W 20 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY W 38 " --> pdb=" O LYS W 34 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL W 44 " --> pdb=" O CYS W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 76 removed outlier: 3.518A pdb=" N ILE W 58 " --> pdb=" O ILE W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 122 removed outlier: 3.515A pdb=" N GLY W 87 " --> pdb=" O ALA W 83 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU W 99 " --> pdb=" O LEU W 95 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER W 100 " --> pdb=" O SER W 96 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP W 113 " --> pdb=" O GLY W 109 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA W 114 " --> pdb=" O ILE W 110 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER W 120 " --> pdb=" O VAL W 116 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN W 121 " --> pdb=" O ARG W 117 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN W 122 " --> pdb=" O GLY W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 125 through 153 removed outlier: 4.369A pdb=" N LEU W 131 " --> pdb=" O VAL W 127 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE W 135 " --> pdb=" O LEU W 131 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA W 136 " --> pdb=" O ILE W 132 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU W 137 " --> pdb=" O LEU W 133 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL W 146 " --> pdb=" O TYR W 142 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA W 147 " --> pdb=" O GLY W 143 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU W 148 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU W 149 " --> pdb=" O ILE W 145 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU W 150 " --> pdb=" O VAL W 146 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN W 151 " --> pdb=" O ALA W 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 44 removed outlier: 3.787A pdb=" N PHE X 12 " --> pdb=" O TYR X 8 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY X 13 " --> pdb=" O ALA X 9 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA X 18 " --> pdb=" O ALA X 14 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE X 21 " --> pdb=" O CYS X 17 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR X 24 " --> pdb=" O ALA X 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL X 37 " --> pdb=" O ALA X 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY X 38 " --> pdb=" O LYS X 34 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL X 44 " --> pdb=" O CYS X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 52 removed outlier: 4.009A pdb=" N LEU X 50 " --> pdb=" O PRO X 47 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE X 51 " --> pdb=" O ASP X 48 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 77 removed outlier: 3.531A pdb=" N ILE X 58 " --> pdb=" O ILE X 54 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR X 66 " --> pdb=" O ILE X 62 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY X 67 " --> pdb=" O ILE X 63 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU X 68 " --> pdb=" O ALA X 64 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU X 73 " --> pdb=" O VAL X 69 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER X 77 " --> pdb=" O LEU X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 121 removed outlier: 3.935A pdb=" N PHE X 88 " --> pdb=" O LEU X 84 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE X 89 " --> pdb=" O TYR X 85 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLN X 90 " --> pdb=" O THR X 86 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU X 91 " --> pdb=" O GLY X 87 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP X 113 " --> pdb=" O GLY X 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA X 114 " --> pdb=" O ILE X 110 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG X 117 " --> pdb=" O ASP X 113 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY X 118 " --> pdb=" O ALA X 114 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN X 121 " --> pdb=" O ARG X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 129 removed outlier: 3.621A pdb=" N GLY X 128 " --> pdb=" O ARG X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 154 removed outlier: 4.111A pdb=" N LEU X 133 " --> pdb=" O MET X 129 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR X 142 " --> pdb=" O VAL X 138 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY X 143 " --> pdb=" O LEU X 139 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU X 144 " --> pdb=" O GLY X 140 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 23 removed outlier: 4.072A pdb=" N ILE Y 21 " --> pdb=" O CYS Y 17 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE Y 23 " --> pdb=" O SER Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 46 removed outlier: 4.164A pdb=" N GLY Y 38 " --> pdb=" O LYS Y 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS Y 40 " --> pdb=" O GLY Y 36 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA Y 41 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR Y 42 " --> pdb=" O GLY Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 54 through 77 removed outlier: 3.626A pdb=" N ILE Y 62 " --> pdb=" O ILE Y 58 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE Y 63 " --> pdb=" O MET Y 59 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA Y 64 " --> pdb=" O ALA Y 60 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE Y 65 " --> pdb=" O GLY Y 61 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER Y 77 " --> pdb=" O LEU Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 120 removed outlier: 3.550A pdb=" N LEU Y 95 " --> pdb=" O LEU Y 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER Y 100 " --> pdb=" O SER Y 96 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE Y 110 " --> pdb=" O PHE Y 106 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL Y 111 " --> pdb=" O ALA Y 107 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP Y 113 " --> pdb=" O GLY Y 109 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA Y 114 " --> pdb=" O ILE Y 110 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER Y 119 " --> pdb=" O GLY Y 115 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER Y 120 " --> pdb=" O VAL Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 124 through 157 removed outlier: 4.243A pdb=" N GLY Y 128 " --> pdb=" O ARG Y 124 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU Y 131 " --> pdb=" O VAL Y 127 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE Y 132 " --> pdb=" O GLY Y 128 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE Y 135 " --> pdb=" O LEU Y 131 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA Y 136 " --> pdb=" O ILE Y 132 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU Y 137 " --> pdb=" O LEU Y 133 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR Y 142 " --> pdb=" O VAL Y 138 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY Y 143 " --> pdb=" O LEU Y 139 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU Y 144 " --> pdb=" O GLY Y 140 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU Y 149 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR Y 155 " --> pdb=" O ASN Y 151 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN Y 156 " --> pdb=" O SER Y 152 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP Y 157 " --> pdb=" O ARG Y 153 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 43 removed outlier: 4.345A pdb=" N PHE Z 12 " --> pdb=" O TYR Z 8 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY Z 13 " --> pdb=" O ALA Z 9 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS Z 17 " --> pdb=" O GLY Z 13 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA Z 18 " --> pdb=" O ALA Z 14 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR Z 24 " --> pdb=" O ALA Z 20 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY Z 38 " --> pdb=" O LYS Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 45 No H-bonds generated for 'chain 'Z' and resid 44 through 45' Processing helix chain 'Z' and resid 46 through 53 removed outlier: 3.530A pdb=" N LEU Z 49 " --> pdb=" O ARG Z 46 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE Z 51 " --> pdb=" O ASP Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 54 through 61 removed outlier: 3.549A pdb=" N ILE Z 58 " --> pdb=" O ILE Z 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 76 removed outlier: 3.669A pdb=" N ILE Z 65 " --> pdb=" O GLY Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 84 through 120 removed outlier: 5.023A pdb=" N GLN Z 90 " --> pdb=" O THR Z 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU Z 91 " --> pdb=" O GLY Z 87 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA Z 114 " --> pdb=" O ILE Z 110 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG Z 117 " --> pdb=" O ASP Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 134 Processing helix chain 'Z' and resid 136 through 155 removed outlier: 3.805A pdb=" N GLY Z 143 " --> pdb=" O LEU Z 139 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU Z 144 " --> pdb=" O GLY Z 140 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG Z 153 " --> pdb=" O LEU Z 149 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA Z 154 " --> pdb=" O LEU Z 150 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR Z 155 " --> pdb=" O ASN Z 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 46 removed outlier: 4.231A pdb=" N PHE a 12 " --> pdb=" O TYR a 8 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY a 13 " --> pdb=" O ALA a 9 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA a 18 " --> pdb=" O ALA a 14 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE a 21 " --> pdb=" O CYS a 17 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY a 27 " --> pdb=" O PHE a 23 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY a 38 " --> pdb=" O LYS a 34 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL a 44 " --> pdb=" O CYS a 40 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU a 45 " --> pdb=" O ALA a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 53 removed outlier: 4.475A pdb=" N LYS a 52 " --> pdb=" O ASP a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 76 removed outlier: 3.544A pdb=" N GLY a 61 " --> pdb=" O VAL a 57 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL a 70 " --> pdb=" O TYR a 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU a 73 " --> pdb=" O VAL a 69 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS a 75 " --> pdb=" O SER a 71 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR a 76 " --> pdb=" O VAL a 72 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 118 removed outlier: 3.514A pdb=" N GLY a 87 " --> pdb=" O ALA a 83 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE a 110 " --> pdb=" O PHE a 106 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY a 118 " --> pdb=" O ALA a 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 136 removed outlier: 4.242A pdb=" N ILE a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 155 Processing helix chain 'b' and resid 8 through 46 removed outlier: 3.928A pdb=" N PHE b 12 " --> pdb=" O TYR b 8 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA b 20 " --> pdb=" O GLY b 16 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE b 21 " --> pdb=" O CYS b 17 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE b 22 " --> pdb=" O ALA b 18 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE b 23 " --> pdb=" O SER b 19 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR b 24 " --> pdb=" O ALA b 20 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY b 38 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL b 44 " --> pdb=" O CYS b 40 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU b 45 " --> pdb=" O ALA b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 54 through 61 Processing helix chain 'b' and resid 61 through 76 removed outlier: 4.139A pdb=" N ILE b 65 " --> pdb=" O GLY b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 120 removed outlier: 3.658A pdb=" N ILE b 89 " --> pdb=" O TYR b 85 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN b 90 " --> pdb=" O THR b 86 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU b 91 " --> pdb=" O GLY b 87 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY b 92 " --> pdb=" O PHE b 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER b 120 " --> pdb=" O VAL b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 123 No H-bonds generated for 'chain 'b' and resid 121 through 123' Processing helix chain 'b' and resid 124 through 157 removed outlier: 3.568A pdb=" N GLY b 128 " --> pdb=" O ARG b 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU b 131 " --> pdb=" O VAL b 127 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE b 132 " --> pdb=" O GLY b 128 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY b 140 " --> pdb=" O ALA b 136 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY b 143 " --> pdb=" O LEU b 139 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU b 144 " --> pdb=" O GLY b 140 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE b 145 " --> pdb=" O LEU b 141 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL b 146 " --> pdb=" O TYR b 142 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR b 155 " --> pdb=" O ASN b 151 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP b 157 " --> pdb=" O ARG b 153 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 44 removed outlier: 4.397A pdb=" N PHE c 12 " --> pdb=" O TYR c 8 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY c 13 " --> pdb=" O ALA c 9 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA c 20 " --> pdb=" O GLY c 16 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE c 21 " --> pdb=" O CYS c 17 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU c 26 " --> pdb=" O ILE c 22 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY c 31 " --> pdb=" O GLY c 27 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR c 42 " --> pdb=" O GLY c 38 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL c 44 " --> pdb=" O CYS c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 76 removed outlier: 3.657A pdb=" N ILE c 58 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY c 61 " --> pdb=" O VAL c 57 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE c 62 " --> pdb=" O ILE c 58 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE c 63 " --> pdb=" O MET c 59 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA c 64 " --> pdb=" O ALA c 60 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR c 66 " --> pdb=" O ILE c 62 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY c 67 " --> pdb=" O ILE c 63 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU c 68 " --> pdb=" O ALA c 64 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER c 71 " --> pdb=" O GLY c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 87 Processing helix chain 'c' and resid 88 through 120 removed outlier: 3.677A pdb=" N VAL c 97 " --> pdb=" O ALA c 93 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER c 120 " --> pdb=" O VAL c 116 " (cutoff:3.500A) Processing helix chain 'c' and resid 125 through 138 removed outlier: 4.431A pdb=" N PHE c 135 " --> pdb=" O LEU c 131 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA c 136 " --> pdb=" O ILE c 132 " (cutoff:3.500A) Processing helix chain 'c' and resid 138 through 157 removed outlier: 4.013A pdb=" N TYR c 142 " --> pdb=" O VAL c 138 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY c 143 " --> pdb=" O LEU c 139 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP c 157 " --> pdb=" O ARG c 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 24 removed outlier: 3.653A pdb=" N GLY d 9 " --> pdb=" O TYR d 5 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL d 14 " --> pdb=" O VAL d 10 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE d 23 " --> pdb=" O VAL d 19 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 41 removed outlier: 4.658A pdb=" N SER d 35 " --> pdb=" O ALA d 31 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL d 37 " --> pdb=" O TRP d 33 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE d 38 " --> pdb=" O ARG d 34 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU d 39 " --> pdb=" O SER d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 50 removed outlier: 4.280A pdb=" N TRP d 48 " --> pdb=" O MET d 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 223 through 226 removed outlier: 4.168A pdb=" N CYS e 226 " --> pdb=" O LEU e 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 223 through 226' Processing helix chain 'e' and resid 227 through 246 removed outlier: 3.578A pdb=" N ALA e 231 " --> pdb=" O LEU e 227 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU e 232 " --> pdb=" O ILE e 228 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN e 246 " --> pdb=" O SER e 242 " (cutoff:3.500A) Processing helix chain 'e' and resid 250 through 255 removed outlier: 4.558A pdb=" N LEU e 254 " --> pdb=" O THR e 250 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU e 255 " --> pdb=" O TYR e 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 250 through 255' Processing helix chain 'f' and resid 9 through 19 removed outlier: 3.662A pdb=" N PHE f 19 " --> pdb=" O VAL f 15 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 33 removed outlier: 4.364A pdb=" N VAL f 26 " --> pdb=" O VAL f 22 " (cutoff:3.500A) Processing helix chain 'f' and resid 51 through 77 removed outlier: 4.162A pdb=" N VAL f 55 " --> pdb=" O VAL f 51 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL f 61 " --> pdb=" O LEU f 57 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR f 62 " --> pdb=" O ALA f 58 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU f 63 " --> pdb=" O ALA f 59 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL f 64 " --> pdb=" O LEU f 60 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN f 72 " --> pdb=" O PHE f 68 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL f 73 " --> pdb=" O CYS f 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 31 removed outlier: 3.650A pdb=" N ALA A 37 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 removed outlier: 6.221A pdb=" N ILE A 278 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 318 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR A 280 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 277 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 279 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 173 removed outlier: 4.132A pdb=" N GLY A 159 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 removed outlier: 6.572A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 225 through 226 removed outlier: 3.733A pdb=" N GLU A 225 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 303 removed outlier: 4.003A pdb=" N THR A 302 " --> pdb=" O LYS A 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 437 through 438 Processing sheet with id=AA9, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.877A pdb=" N VAL I 188 " --> pdb=" O ASN I 201 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA I 137 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 31 through 35 removed outlier: 5.948A pdb=" N ILE B 40 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL B 34 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 75 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE B 70 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 76 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 65 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 53 " --> pdb=" O GLY B 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=AB3, first strand: chain 'B' and resid 112 through 113 removed outlier: 3.557A pdb=" N LEU B 278 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.881A pdb=" N ARG B 166 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU B 148 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 172 through 173 removed outlier: 6.071A pdb=" N PHE B 359 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 26 through 31 removed outlier: 6.588A pdb=" N ILE C 36 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL C 30 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE C 63 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR C 69 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 93 through 96 Processing sheet with id=AB8, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.750A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 139 through 141 removed outlier: 3.747A pdb=" N GLY C 189 " --> pdb=" O PHE C 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 152 removed outlier: 6.585A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 157 through 161 removed outlier: 4.499A pdb=" N GLY C 159 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 225 through 226 removed outlier: 3.728A pdb=" N GLU C 225 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AC5, first strand: chain 'C' and resid 437 through 439 Processing sheet with id=AC6, first strand: chain 'D' and resid 31 through 35 removed outlier: 5.536A pdb=" N ILE D 40 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL D 34 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU D 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA D 75 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE D 70 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 94 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 92 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU D 26 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE K 197 " --> pdb=" O ASN K 192 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA K 137 " --> pdb=" O GLU K 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 101 through 104 Processing sheet with id=AC8, first strand: chain 'D' and resid 111 through 113 removed outlier: 6.959A pdb=" N ARG D 111 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU D 242 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE D 113 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N LEU D 244 " --> pdb=" O PHE D 113 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 144 through 145 removed outlier: 3.724A pdb=" N ILE D 145 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG D 321 " --> pdb=" O ILE D 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AD2, first strand: chain 'D' and resid 172 through 174 removed outlier: 5.950A pdb=" N ILE D 172 " --> pdb=" O LEU D 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 26 through 30 removed outlier: 6.414A pdb=" N ILE E 36 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 37 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN E 71 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 93 through 96 Processing sheet with id=AD5, first strand: chain 'E' and resid 104 through 105 removed outlier: 6.164A pdb=" N TYR E 105 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR E 321 " --> pdb=" O TYR E 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 139 through 141 Processing sheet with id=AD7, first strand: chain 'E' and resid 151 through 152 removed outlier: 6.415A pdb=" N GLU E 199 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER E 207 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 157 through 161 removed outlier: 4.424A pdb=" N GLY E 159 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE E 172 " --> pdb=" O GLY E 159 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 225 through 226 removed outlier: 3.888A pdb=" N GLU E 225 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 302 through 303 removed outlier: 3.954A pdb=" N THR E 302 " --> pdb=" O LYS E 308 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS E 308 " --> pdb=" O THR E 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 375 through 377 removed outlier: 6.211A pdb=" N PHE E 380 " --> pdb=" O ALA E 376 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 437 through 438 Processing sheet with id=AE4, first strand: chain 'F' and resid 93 through 94 removed outlier: 3.667A pdb=" N VAL G 190 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 188 " --> pdb=" O ASN G 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA G 137 " --> pdb=" O VAL G 173 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 31 through 35 removed outlier: 5.756A pdb=" N ILE F 40 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL F 34 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA F 75 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE F 76 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 101 through 104 removed outlier: 3.750A pdb=" N ASP F 130 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 111 through 114 removed outlier: 3.938A pdb=" N ARG F 111 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER F 209 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE F 277 " --> pdb=" O SER F 209 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 211 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU F 278 " --> pdb=" O ILE F 332 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 151 through 152 Processing sheet with id=AE9, first strand: chain 'M' and resid 93 through 98 removed outlier: 3.651A pdb=" N LYS M 93 " --> pdb=" O TYR M 112 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 7 through 11 removed outlier: 5.848A pdb=" N LEU N 7 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE N 66 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU N 92 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU N 67 " --> pdb=" O LEU N 92 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE N 94 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE N 69 " --> pdb=" O ILE N 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 28 through 29 Processing sheet with id=AF3, first strand: chain 'O' and resid 46 through 47 removed outlier: 3.904A pdb=" N ILE O 330 " --> pdb=" O ILE O 12 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP O 10 " --> pdb=" O VAL O 332 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU O 13 " --> pdb=" O TYR O 388 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR O 388 " --> pdb=" O LEU O 13 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 191 through 192 Processing sheet with id=AF5, first strand: chain 'O' and resid 198 through 199 removed outlier: 3.930A pdb=" N VAL O 198 " --> pdb=" O VAL O 232 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 14 through 22 removed outlier: 3.589A pdb=" N VAL Q 17 " --> pdb=" O GLY Q 339 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY Q 339 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA Q 337 " --> pdb=" O PHE Q 19 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE Q 21 " --> pdb=" O LEU Q 335 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN Q 40 " --> pdb=" O TRP Q 340 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 212 through 217 removed outlier: 3.826A pdb=" N PHE Q 212 " --> pdb=" O PHE Q 239 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE Q 239 " --> pdb=" O PHE Q 212 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS Q 214 " --> pdb=" O ILE Q 237 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE Q 236 " --> pdb=" O GLY Q 189 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY Q 189 " --> pdb=" O PHE Q 236 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL Q 238 " --> pdb=" O VAL Q 187 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL Q 187 " --> pdb=" O VAL Q 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL Q 190 " --> pdb=" O ASN Q 259 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN Q 259 " --> pdb=" O VAL Q 190 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 222 through 223 removed outlier: 4.524A pdb=" N VAL Q 222 " --> pdb=" O LYS Q 231 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS Q 231 " --> pdb=" O VAL Q 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 3433 hydrogen bonds defined for protein. 10011 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: 22.00 Time building geometry restraints manager: 23.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18754 1.33 - 1.45: 9511 1.45 - 1.57: 36939 1.57 - 1.69: 0 1.69 - 1.81: 462 Bond restraints: 65666 Sorted by residual: bond pdb=" C ILE E 185 " pdb=" N ALA E 186 " ideal model delta sigma weight residual 1.331 1.294 0.036 1.48e-02 4.57e+03 6.05e+00 bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N MET W 1 " pdb=" CA MET W 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N MET O 1 " pdb=" CA MET O 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N MET Z 1 " pdb=" CA MET Z 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 ... (remaining 65661 not shown) Histogram of bond angle deviations from ideal: 96.54 - 104.11: 856 104.11 - 111.67: 30449 111.67 - 119.23: 24106 119.23 - 126.79: 32836 126.79 - 134.36: 597 Bond angle restraints: 88844 Sorted by residual: angle pdb=" N VAL C 264 " pdb=" CA VAL C 264 " pdb=" C VAL C 264 " ideal model delta sigma weight residual 111.81 108.06 3.75 8.60e-01 1.35e+00 1.90e+01 angle pdb=" N ILE M 79 " pdb=" CA ILE M 79 " pdb=" C ILE M 79 " ideal model delta sigma weight residual 113.53 109.26 4.27 9.80e-01 1.04e+00 1.90e+01 angle pdb=" N VAL E 502 " pdb=" CA VAL E 502 " pdb=" C VAL E 502 " ideal model delta sigma weight residual 113.71 109.75 3.96 9.50e-01 1.11e+00 1.74e+01 angle pdb=" C TYR S 102 " pdb=" N MET S 103 " pdb=" CA MET S 103 " ideal model delta sigma weight residual 121.18 113.77 7.41 1.98e+00 2.55e-01 1.40e+01 angle pdb=" N VAL d 32 " pdb=" CA VAL d 32 " pdb=" C VAL d 32 " ideal model delta sigma weight residual 112.96 109.28 3.68 1.00e+00 1.00e+00 1.36e+01 ... (remaining 88839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 36888 17.82 - 35.65: 2328 35.65 - 53.47: 297 53.47 - 71.30: 56 71.30 - 89.12: 42 Dihedral angle restraints: 39611 sinusoidal: 15701 harmonic: 23910 Sorted by residual: dihedral pdb=" CA THR I 79 " pdb=" C THR I 79 " pdb=" N ILE I 80 " pdb=" CA ILE I 80 " ideal model delta harmonic sigma weight residual 180.00 154.28 25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA LYS C 308 " pdb=" C LYS C 308 " pdb=" N GLU C 309 " pdb=" CA GLU C 309 " ideal model delta harmonic sigma weight residual 180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA TYR F 146 " pdb=" C TYR F 146 " pdb=" N PRO F 147 " pdb=" CA PRO F 147 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 39608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 6968 0.034 - 0.067: 2386 0.067 - 0.101: 601 0.101 - 0.135: 279 0.135 - 0.168: 9 Chirality restraints: 10243 Sorted by residual: chirality pdb=" CA MET P 211 " pdb=" N MET P 211 " pdb=" C MET P 211 " pdb=" CB MET P 211 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA ILE D 172 " pdb=" N ILE D 172 " pdb=" C ILE D 172 " pdb=" CB ILE D 172 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA MET S 103 " pdb=" N MET S 103 " pdb=" C MET S 103 " pdb=" CB MET S 103 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 10240 not shown) Planarity restraints: 11334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 309 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO A 310 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 774 " 0.022 2.00e-02 2.50e+03 1.48e-02 3.84e+00 pdb=" CG PHE Q 774 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 774 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 774 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 774 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 774 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE Q 774 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 143 " 0.018 2.00e-02 2.50e+03 1.44e-02 3.63e+00 pdb=" CG PHE Q 143 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 143 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 143 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE Q 143 " 0.004 2.00e-02 2.50e+03 ... (remaining 11331 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 393 2.48 - 3.08: 50883 3.08 - 3.69: 96823 3.69 - 4.29: 139550 4.29 - 4.90: 226946 Nonbonded interactions: 514595 Sorted by model distance: nonbonded pdb=" O LYS Q 90 " pdb=" OH TYR Q 99 " model vdw 1.871 2.440 nonbonded pdb=" O LEU C 269 " pdb=" OG SER C 273 " model vdw 1.890 2.440 nonbonded pdb=" NH1 ARG b 153 " pdb=" O CYS c 75 " model vdw 1.951 2.520 nonbonded pdb=" OG1 THR Q 215 " pdb=" O ALA Q 235 " model vdw 1.961 2.440 nonbonded pdb=" OH TYR N 101 " pdb=" OD1 ASP N 106 " model vdw 1.973 2.440 ... (remaining 514590 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 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 9 through 195 or resid 207 through 487)) selection = chain 'D' selection = (chain 'F' and (resid 9 through 195 or resid 207 through 487)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = (chain 'Y' and resid 1 through 159) selection = chain 'Z' selection = chain 'a' selection = (chain 'b' and resid 1 through 159) selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 279 5.16 5 C 41330 2.51 5 N 10738 2.21 5 O 12150 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 17.360 Check model and map are aligned: 0.740 Process input model: 127.450 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.460 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 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 : 0.003 0.036 65666 Z= 0.211 Angle : 0.559 8.925 88844 Z= 0.321 Chirality : 0.039 0.168 10243 Planarity : 0.003 0.065 11334 Dihedral : 11.989 89.124 24269 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.86 (0.09), residues: 8221 helix: 0.57 (0.08), residues: 4376 sheet: -2.42 (0.20), residues: 562 loop : -1.78 (0.11), residues: 3283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1551 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1551 time to evaluate : 6.006 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1551 average time/residue: 0.6239 time to fit residues: 1610.8481 Evaluate side-chains 684 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 684 time to evaluate : 6.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 815 random chunks: chunk 688 optimal weight: 40.0000 chunk 617 optimal weight: 20.0000 chunk 342 optimal weight: 40.0000 chunk 211 optimal weight: 6.9990 chunk 416 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 638 optimal weight: 40.0000 chunk 247 optimal weight: 8.9990 chunk 388 optimal weight: 7.9990 chunk 475 optimal weight: 9.9990 chunk 740 optimal weight: 20.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN A 491 ASN A 579 HIS C 213 HIS C 491 ASN ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 HIS ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** E 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN K 49 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN L 18 HIS L 61 ASN L 77 GLN M 183 ASN O 21 GLN ** O 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 274 HIS O 305 HIS ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN P 323 GLN P 446 HIS ** P 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS ** Q 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 375 HIS ** Q 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 527 ASN Q 718 HIS ** S 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 318 GLN U 159 ASN ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 82 GLN b 156 GLN c 151 ASN ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.152 65666 Z= 0.510 Angle : 0.940 14.059 88844 Z= 0.491 Chirality : 0.051 0.337 10243 Planarity : 0.007 0.094 11334 Dihedral : 5.508 24.702 8920 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.55 (0.09), residues: 8221 helix: -0.15 (0.07), residues: 4452 sheet: -2.26 (0.21), residues: 535 loop : -1.99 (0.11), residues: 3234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 680 time to evaluate : 6.042 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 outliers start: 34 outliers final: 10 residues processed: 714 average time/residue: 0.6104 time to fit residues: 740.3365 Evaluate side-chains 441 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 431 time to evaluate : 6.023 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4525 time to fit residues: 16.6832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 815 random chunks: chunk 411 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 615 optimal weight: 5.9990 chunk 503 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 741 optimal weight: 0.8980 chunk 800 optimal weight: 4.9990 chunk 660 optimal weight: 20.0000 chunk 735 optimal weight: 30.0000 chunk 252 optimal weight: 6.9990 chunk 594 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN D 54 ASN D 186 GLN D 190 GLN E 349 ASN E 528 GLN G 21 GLN G 36 GLN I 74 GLN J 110 HIS ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN O 153 ASN P 450 GLN P 451 GLN Q 201 GLN ** Q 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 428 HIS Q 527 ASN ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 45 GLN ** S 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 258 GLN S 322 ASN ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 GLN ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 53 ASN Y 80 GLN ** Y 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 53 ASN b 53 ASN ** d 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 65666 Z= 0.277 Angle : 0.664 10.543 88844 Z= 0.344 Chirality : 0.044 0.203 10243 Planarity : 0.004 0.068 11334 Dihedral : 4.939 25.304 8920 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.09 (0.09), residues: 8221 helix: 0.21 (0.08), residues: 4479 sheet: -1.79 (0.21), residues: 554 loop : -1.82 (0.11), residues: 3188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 597 time to evaluate : 6.025 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 outliers start: 17 outliers final: 1 residues processed: 613 average time/residue: 0.6267 time to fit residues: 660.0681 Evaluate side-chains 417 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 416 time to evaluate : 7.307 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4817 time to fit residues: 9.1418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 815 random chunks: chunk 732 optimal weight: 0.9980 chunk 557 optimal weight: 30.0000 chunk 384 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 353 optimal weight: 40.0000 chunk 497 optimal weight: 0.8980 chunk 744 optimal weight: 9.9990 chunk 787 optimal weight: 20.0000 chunk 388 optimal weight: 9.9990 chunk 705 optimal weight: 0.9990 chunk 212 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 HIS ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 528 GLN ** E 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN P 450 GLN ** P 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS Q 527 ASN ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 HIS S 322 ASN ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 GLN Y 121 GLN Y 151 ASN d 30 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 65666 Z= 0.166 Angle : 0.592 11.390 88844 Z= 0.304 Chirality : 0.042 0.220 10243 Planarity : 0.004 0.060 11334 Dihedral : 4.565 24.490 8920 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.71 (0.09), residues: 8221 helix: 0.47 (0.08), residues: 4486 sheet: -1.38 (0.21), residues: 577 loop : -1.61 (0.11), residues: 3158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 613 time to evaluate : 6.152 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 outliers start: 2 outliers final: 0 residues processed: 615 average time/residue: 0.6307 time to fit residues: 667.2926 Evaluate side-chains 420 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 6.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 815 random chunks: chunk 656 optimal weight: 5.9990 chunk 447 optimal weight: 0.4980 chunk 11 optimal weight: 9.9990 chunk 586 optimal weight: 9.9990 chunk 325 optimal weight: 3.9990 chunk 672 optimal weight: 0.2980 chunk 544 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 402 optimal weight: 0.9980 chunk 707 optimal weight: 9.9990 chunk 198 optimal weight: 0.0060 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN F 232 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 461 GLN ** Q 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 375 HIS Q 527 ASN Q 580 GLN ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 GLN Y 151 ASN ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 65666 Z= 0.162 Angle : 0.577 11.296 88844 Z= 0.294 Chirality : 0.041 0.246 10243 Planarity : 0.004 0.060 11334 Dihedral : 4.364 24.578 8920 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.51 (0.09), residues: 8221 helix: 0.59 (0.08), residues: 4497 sheet: -1.11 (0.21), residues: 594 loop : -1.50 (0.11), residues: 3130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 578 time to evaluate : 6.477 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 outliers start: 1 outliers final: 0 residues processed: 579 average time/residue: 0.6026 time to fit residues: 602.1928 Evaluate side-chains 426 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 6.000 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 815 random chunks: chunk 265 optimal weight: 30.0000 chunk 709 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 462 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 788 optimal weight: 40.0000 chunk 654 optimal weight: 20.0000 chunk 365 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 chunk 413 optimal weight: 4.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 HIS E 140 GLN ** E 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN K 36 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 ASN ** Q 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 185 ASN ** Q 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 527 ASN Q 629 HIS ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 322 ASN S 333 ASN ** T 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 GLN Y 80 GLN Y 151 ASN ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 GLN ** e 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.7224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 65666 Z= 0.306 Angle : 0.683 17.016 88844 Z= 0.353 Chirality : 0.044 0.259 10243 Planarity : 0.005 0.069 11334 Dihedral : 4.751 25.946 8920 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.09), residues: 8221 helix: 0.43 (0.08), residues: 4510 sheet: -1.02 (0.22), residues: 573 loop : -1.58 (0.11), residues: 3138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 552 time to evaluate : 6.106 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 outliers start: 2 outliers final: 1 residues processed: 553 average time/residue: 0.6079 time to fit residues: 582.0390 Evaluate side-chains 384 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 383 time to evaluate : 6.088 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5722 time to fit residues: 8.9716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 815 random chunks: chunk 760 optimal weight: 40.0000 chunk 88 optimal weight: 0.8980 chunk 449 optimal weight: 20.0000 chunk 575 optimal weight: 6.9990 chunk 446 optimal weight: 30.0000 chunk 663 optimal weight: 10.0000 chunk 440 optimal weight: 10.0000 chunk 785 optimal weight: 30.0000 chunk 491 optimal weight: 20.0000 chunk 478 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 overall best weight: 6.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 GLN F 18 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 ASN ** O 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 311 GLN ** P 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 527 ASN ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 255 HIS S 322 ASN ** T 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 159 ASN Y 80 GLN Y 151 ASN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 GLN d 55 GLN ** e 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 259 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.7961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 65666 Z= 0.358 Angle : 0.713 11.710 88844 Z= 0.370 Chirality : 0.045 0.212 10243 Planarity : 0.005 0.057 11334 Dihedral : 5.008 25.656 8920 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.87 (0.09), residues: 8221 helix: 0.27 (0.08), residues: 4500 sheet: -1.04 (0.21), residues: 568 loop : -1.68 (0.11), residues: 3153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 6.348 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 outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.6018 time to fit residues: 538.0401 Evaluate side-chains 372 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 6.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 815 random chunks: chunk 485 optimal weight: 8.9990 chunk 313 optimal weight: 9.9990 chunk 469 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 499 optimal weight: 20.0000 chunk 535 optimal weight: 30.0000 chunk 388 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 617 optimal weight: 20.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 ASN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 21 GLN ** O 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 527 ASN ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 GLN ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 100 ASN T 132 ASN ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 GLN Y 151 ASN d 30 GLN ** e 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.8365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.105 65666 Z= 0.294 Angle : 0.682 13.583 88844 Z= 0.352 Chirality : 0.044 0.210 10243 Planarity : 0.005 0.078 11334 Dihedral : 4.946 25.339 8920 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.81 (0.09), residues: 8221 helix: 0.31 (0.08), residues: 4511 sheet: -1.05 (0.22), residues: 559 loop : -1.63 (0.11), residues: 3151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 513 time to evaluate : 6.184 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 outliers start: 1 outliers final: 0 residues processed: 514 average time/residue: 0.6293 time to fit residues: 568.1117 Evaluate side-chains 374 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 6.092 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 815 random chunks: chunk 714 optimal weight: 50.0000 chunk 752 optimal weight: 10.0000 chunk 686 optimal weight: 7.9990 chunk 732 optimal weight: 4.9990 chunk 440 optimal weight: 6.9990 chunk 318 optimal weight: 6.9990 chunk 574 optimal weight: 30.0000 chunk 224 optimal weight: 6.9990 chunk 661 optimal weight: 20.0000 chunk 692 optimal weight: 20.0000 chunk 729 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** E 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 527 ASN Q 571 ASN Q 580 GLN ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 213 GLN ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 159 ASN d 30 GLN ** e 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.8887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.097 65666 Z= 0.366 Angle : 0.735 12.003 88844 Z= 0.381 Chirality : 0.045 0.296 10243 Planarity : 0.005 0.094 11334 Dihedral : 5.184 25.937 8920 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.01 (0.09), residues: 8221 helix: 0.15 (0.08), residues: 4534 sheet: -0.90 (0.23), residues: 507 loop : -1.78 (0.11), residues: 3180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 6.187 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 outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.6416 time to fit residues: 557.2211 Evaluate side-chains 362 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 6.029 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 815 random chunks: chunk 480 optimal weight: 0.8980 chunk 774 optimal weight: 5.9990 chunk 472 optimal weight: 0.4980 chunk 367 optimal weight: 8.9990 chunk 538 optimal weight: 9.9990 chunk 811 optimal weight: 20.0000 chunk 747 optimal weight: 40.0000 chunk 646 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 499 optimal weight: 6.9990 chunk 396 optimal weight: 10.0000 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** E 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 348 ASN ** P 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 443 ASN P 451 GLN ** Q 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 527 ASN ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 HIS ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 GLN W 122 GLN Y 151 ASN ** e 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.9089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 65666 Z= 0.267 Angle : 0.686 18.129 88844 Z= 0.350 Chirality : 0.044 0.335 10243 Planarity : 0.004 0.066 11334 Dihedral : 5.003 28.003 8920 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.81 (0.09), residues: 8221 helix: 0.32 (0.08), residues: 4518 sheet: -0.68 (0.23), residues: 502 loop : -1.72 (0.11), residues: 3201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16442 Ramachandran restraints generated. 8221 Oldfield, 0 Emsley, 8221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 486 time to evaluate : 6.196 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 outliers start: 1 outliers final: 1 residues processed: 486 average time/residue: 0.6553 time to fit residues: 563.3041 Evaluate side-chains 370 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 369 time to evaluate : 6.174 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5887 time to fit residues: 9.4144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 815 random chunks: chunk 513 optimal weight: 6.9990 chunk 688 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 596 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 647 optimal weight: 0.5980 chunk 271 optimal weight: 7.9990 chunk 664 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN E 528 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 354 ASN ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 443 ASN Q 273 GLN ** Q 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 527 ASN ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 151 ASN ** e 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.082493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.063739 restraints weight = 411398.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.061617 restraints weight = 312558.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.061959 restraints weight = 272307.261| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.9327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 65666 Z= 0.271 Angle : 0.668 12.302 88844 Z= 0.344 Chirality : 0.044 0.291 10243 Planarity : 0.004 0.078 11334 Dihedral : 4.948 25.196 8920 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.77 (0.09), residues: 8221 helix: 0.35 (0.08), residues: 4536 sheet: -0.66 (0.23), residues: 494 loop : -1.70 (0.11), residues: 3191 =============================================================================== Job complete usr+sys time: 11611.95 seconds wall clock time: 207 minutes 58.72 seconds (12478.72 seconds total)