Starting phenix.real_space_refine on Wed Nov 15 14:53:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdb_31539/11_2023/7fdb_31539.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdb_31539/11_2023/7fdb_31539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdb_31539/11_2023/7fdb_31539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdb_31539/11_2023/7fdb_31539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdb_31539/11_2023/7fdb_31539.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdb_31539/11_2023/7fdb_31539.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. Process input model Symmetric amino acids flipped Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A ASP 616": "OD1" <-> "OD2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 588": "OE1" <-> "OE2" Residue "E PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 196": "OD1" <-> "OD2" Residue "N GLU 42": "OE1" <-> "OE2" Residue "P PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 344": "OE1" <-> "OE2" Residue "Q TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 170": "OE1" <-> "OE2" Residue "T TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 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: "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: 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: "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: 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: "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: 24.00, per 1000 atoms: 0.37 Number of scatterers: 64497 At special positions: 0 Unit cell: (165.24, 190.08, 271.08, 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: 20.17 Conformation dependent library (CDL) restraints added in 8.3 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: 306 helices and 44 sheets defined 61.0% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 111 through 120 Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 287 through 300 removed outlier: 5.139A pdb=" N MET A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 327 through 346 removed outlier: 3.583A pdb=" N ALA A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.848A pdb=" N TRP A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 381 through 382 No H-bonds generated for 'chain 'A' and resid 381 through 382' Processing helix chain 'A' and resid 383 through 394 Processing helix chain 'A' and resid 425 through 433 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 463 through 475 removed outlier: 4.618A pdb=" N LYS A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 503 removed outlier: 3.837A pdb=" N ARG A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 532 through 537 removed outlier: 3.868A pdb=" N PHE A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 563 Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 576 through 585 removed outlier: 4.058A pdb=" N LYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 616 removed outlier: 4.498A pdb=" N ASP A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.585A pdb=" N LEU B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'B' and resid 218 through 233 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.748A pdb=" N ARG B 252 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 253' Processing helix chain 'B' and resid 253 through 271 removed outlier: 4.435A pdb=" N ARG B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 307 through 317 removed outlier: 3.677A pdb=" N ASP B 311 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 395 through 421 removed outlier: 3.692A pdb=" N VAL B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'C' and resid 262 through 272 removed outlier: 4.132A pdb=" N SER C 266 " --> pdb=" O LYS C 262 " (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 325 through 346 removed outlier: 3.501A pdb=" N ARG C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 372 Processing helix chain 'C' and resid 383 through 394 removed outlier: 3.585A pdb=" N ARG C 394 " --> pdb=" O SER C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 442 through 448 removed outlier: 3.704A pdb=" N ALA C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 475 removed outlier: 3.787A pdb=" N LYS C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 503 removed outlier: 4.559A pdb=" N GLU C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU C 494 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU C 501 " --> pdb=" O GLN C 497 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 502 " --> pdb=" O VAL C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 526 removed outlier: 3.995A pdb=" N LEU C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 564 removed outlier: 3.509A pdb=" N GLY C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 575 Processing helix chain 'C' and resid 575 through 587 removed outlier: 3.612A pdb=" N HIS C 579 " --> pdb=" O GLY C 575 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 616 Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 218 through 232 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 249 through 270 removed outlier: 4.245A pdb=" N ILE D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 281 through 291 Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.564A pdb=" N GLY D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 317 removed outlier: 3.858A pdb=" N ASP D 311 " --> pdb=" O TYR D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 354 Processing helix chain 'D' and resid 361 through 368 removed outlier: 3.747A 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: 3.752A pdb=" N SER D 400 " --> pdb=" O HIS D 396 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 3.900A 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 442 Processing helix chain 'D' and resid 453 through 464 removed outlier: 3.621A pdb=" N LEU D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 486 removed outlier: 4.116A pdb=" N ASP D 486 " --> pdb=" O ASP D 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 237 through 244 Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 287 through 295 Processing helix chain 'E' and resid 296 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 345 removed outlier: 4.534A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 removed outlier: 3.678A pdb=" N TRP E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 392 removed outlier: 4.627A pdb=" N ALA E 386 " --> pdb=" O ALA E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 removed outlier: 3.548A pdb=" N GLY E 433 " --> pdb=" O THR E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 448 removed outlier: 3.737A pdb=" N ALA E 446 " --> pdb=" O ASP E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 475 removed outlier: 4.330A pdb=" N VAL E 466 " --> pdb=" O LYS E 462 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS E 469 " --> pdb=" O ASN E 465 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N PHE E 470 " --> pdb=" O VAL E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 501 removed outlier: 4.491A pdb=" N GLN E 497 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 539 through 563 removed outlier: 3.881A pdb=" N ASN E 563 " --> pdb=" O LYS E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 575 Processing helix chain 'E' and resid 575 through 584 removed outlier: 3.970A 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 616 removed outlier: 3.676A pdb=" N SER E 614 " --> pdb=" O ARG E 610 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP E 616 " --> pdb=" O ALA E 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 19 removed outlier: 3.722A pdb=" N GLY F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) 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: 3.615A pdb=" N ALA F 222 " --> pdb=" O ASN F 218 " (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 253 Processing helix chain 'F' and resid 254 through 269 Processing helix chain 'F' and resid 280 through 295 removed outlier: 3.613A pdb=" N TYR F 284 " --> pdb=" O ASP F 280 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 307 through 318 removed outlier: 4.050A pdb=" N ASP F 311 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG F 318 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 354 removed outlier: 3.915A pdb=" N TYR F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE F 353 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR F 354 " --> pdb=" O THR F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 367 removed outlier: 3.537A pdb=" N HIS F 365 " --> pdb=" O ASP F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 removed outlier: 4.005A pdb=" N ILE F 387 " --> pdb=" O LYS F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 418 Processing helix chain 'F' and resid 426 through 444 Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 477 through 486 removed outlier: 4.780A pdb=" N ASP F 486 " --> pdb=" O ASP F 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 111 removed outlier: 3.766A pdb=" N ASN G 14 " --> pdb=" O PRO G 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 25 " --> pdb=" O GLN G 21 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN G 57 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 133 removed outlier: 4.189A pdb=" N ILE G 120 " --> pdb=" O GLU G 116 " (cutoff:3.500A) 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 164 removed outlier: 5.015A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 Processing helix chain 'G' and resid 214 through 224 Processing helix chain 'H' and resid 3 through 63 removed outlier: 4.924A pdb=" N THR H 9 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU H 10 " --> pdb=" O GLY H 6 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU H 53 " --> pdb=" O GLN H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.868A pdb=" N VAL H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 90 removed outlier: 3.668A pdb=" N LYS H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 104 Processing helix chain 'I' and resid 9 through 112 removed outlier: 3.678A pdb=" N VAL I 13 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU I 17 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN I 18 " --> pdb=" O ASN I 14 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN I 112 " --> pdb=" O SER I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 133 Proline residue: I 119 - end of helix Processing helix chain 'I' and resid 142 through 144 No H-bonds generated for 'chain 'I' and resid 142 through 144' Processing helix chain 'I' and resid 145 through 164 removed outlier: 3.542A pdb=" N ILE I 149 " --> pdb=" O ASP I 145 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASP I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP I 155 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY I 161 " --> pdb=" O MET I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 214 removed outlier: 4.076A pdb=" N GLU I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU I 213 " --> pdb=" O LEU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 224 Processing helix chain 'J' and resid 4 through 63 removed outlier: 3.601A pdb=" N ALA J 8 " --> pdb=" O LYS J 4 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU J 11 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS J 60 " --> pdb=" O GLU J 56 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN J 61 " --> pdb=" O PHE J 57 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY J 63 " --> pdb=" O GLN J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 103 removed outlier: 4.034A pdb=" N LYS J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY J 75 " --> pdb=" O LYS J 71 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 112 removed outlier: 3.677A pdb=" N LYS K 63 " --> pdb=" O ASP K 59 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER K 72 " --> pdb=" O LYS K 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN K 112 " --> pdb=" O SER K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 133 removed outlier: 3.595A pdb=" N ILE K 120 " --> pdb=" O GLU K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 164 removed outlier: 5.067A pdb=" N ASP K 154 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG K 158 " --> pdb=" O ASP K 154 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY K 161 " --> pdb=" O MET K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 214 Processing helix chain 'K' and resid 214 through 223 Processing helix chain 'L' and resid 5 through 40 removed outlier: 3.998A pdb=" N THR L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL L 21 " --> pdb=" O ALA L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 44 Processing helix chain 'L' and resid 45 through 63 removed outlier: 3.905A pdb=" N LYS L 50 " --> pdb=" O TYR L 46 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP L 51 " --> pdb=" O LYS L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 103 removed outlier: 4.338A pdb=" N LYS L 70 " --> pdb=" O GLY L 66 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU L 79 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS L 90 " --> pdb=" O ILE L 86 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 66 removed outlier: 3.712A pdb=" N MET M 18 " --> pdb=" O THR M 14 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN M 55 " --> pdb=" O ASP M 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG M 59 " --> pdb=" O GLN M 55 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE M 66 " --> pdb=" O GLN M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 75 removed outlier: 4.021A pdb=" N GLU M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL M 71 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR M 73 " --> pdb=" O ALA M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 86 removed outlier: 4.219A pdb=" N GLN M 82 " --> pdb=" O ASN M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 142 removed outlier: 3.923A pdb=" N GLU M 137 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER M 140 " --> pdb=" O LYS M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 176 removed outlier: 3.719A pdb=" N HIS M 175 " --> pdb=" O ASN M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 220 removed outlier: 3.619A pdb=" N THR M 181 " --> pdb=" O ILE M 177 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA M 186 " --> pdb=" O GLU M 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 24 removed outlier: 4.359A pdb=" N GLY N 19 " --> pdb=" O ASP N 15 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 59 Processing helix chain 'N' and resid 71 through 77 Processing helix chain 'N' and resid 77 through 84 Processing helix chain 'N' and resid 102 through 105 Processing helix chain 'N' and resid 106 through 114 removed outlier: 3.527A pdb=" N LYS N 114 " --> pdb=" O LYS N 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 38 Processing helix chain 'O' and resid 57 through 89 removed outlier: 4.209A pdb=" N ILE O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL O 63 " --> pdb=" O ASP O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 105 Processing helix chain 'O' and resid 126 through 165 removed outlier: 3.621A pdb=" N LYS O 165 " --> pdb=" O ALA O 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 184 Processing helix chain 'O' and resid 202 through 208 removed outlier: 3.620A pdb=" N LYS O 208 " --> pdb=" O SER O 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 242 through 253 removed outlier: 3.735A pdb=" N PHE O 246 " --> pdb=" O ASN O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 263 through 319 removed outlier: 3.813A pdb=" N ILE O 267 " --> pdb=" O SER O 263 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE O 301 " --> pdb=" O VAL O 297 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN O 302 " --> pdb=" O ASP O 298 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE O 304 " --> pdb=" O PHE O 300 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS O 307 " --> pdb=" O TRP O 303 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL O 316 " --> pdb=" O TYR O 312 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 353 removed outlier: 3.965A pdb=" N GLU O 343 " --> pdb=" O LYS O 339 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE O 348 " --> pdb=" O LEU O 344 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE O 350 " --> pdb=" O ASP O 346 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEU O 351 " --> pdb=" O ALA O 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 22 removed outlier: 4.320A pdb=" N ILE P 16 " --> pdb=" O HIS P 12 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG P 17 " --> pdb=" O PHE P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 51 Processing helix chain 'P' and resid 76 through 87 removed outlier: 3.863A pdb=" N LEU P 80 " --> pdb=" O THR P 76 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE P 81 " --> pdb=" O LEU P 77 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU P 83 " --> pdb=" O PRO P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 105 removed outlier: 4.452A pdb=" N SER P 95 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 118 Processing helix chain 'P' and resid 122 through 129 removed outlier: 4.087A pdb=" N GLN P 126 " --> pdb=" O LYS P 122 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU P 127 " --> pdb=" O GLN P 123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP P 129 " --> pdb=" O GLU P 125 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 151 removed outlier: 3.563A pdb=" N VAL P 139 " --> pdb=" O ASP P 135 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE P 144 " --> pdb=" O LEU P 140 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN P 145 " --> pdb=" O ILE P 141 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL P 146 " --> pdb=" O SER P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 166 removed outlier: 4.122A pdb=" N LYS P 166 " --> pdb=" O GLU P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 174 removed outlier: 3.844A pdb=" N ASN P 172 " --> pdb=" O ASN P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 194 removed outlier: 3.507A pdb=" N TYR P 184 " --> pdb=" O MET P 180 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL P 185 " --> pdb=" O ASP P 181 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU P 190 " --> pdb=" O CYS P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 205 removed outlier: 3.616A pdb=" N VAL P 202 " --> pdb=" O GLU P 198 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 220 removed outlier: 4.078A pdb=" N LEU P 214 " --> pdb=" O PHE P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 240 through 254 removed outlier: 3.871A pdb=" N THR P 254 " --> pdb=" O ILE P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 267 removed outlier: 4.001A pdb=" N ALA P 260 " --> pdb=" O ASN P 256 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN P 265 " --> pdb=" O ASN P 261 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 279 removed outlier: 4.303A pdb=" N ASP P 273 " --> pdb=" O ASP P 270 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU P 274 " --> pdb=" O PHE P 271 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 291 removed outlier: 4.344A pdb=" N LEU P 289 " --> pdb=" O LYS P 285 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE P 291 " --> pdb=" O SER P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 291 through 299 removed outlier: 3.684A pdb=" N GLN P 296 " --> pdb=" O SER P 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 308 through 317 removed outlier: 3.589A pdb=" N LEU P 312 " --> pdb=" O VAL P 308 " (cutoff:3.500A) Processing helix chain 'P' and resid 318 through 328 removed outlier: 3.549A pdb=" N SER P 326 " --> pdb=" O VAL P 322 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU P 327 " --> pdb=" O GLN P 323 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG P 328 " --> pdb=" O SER P 324 " (cutoff:3.500A) Processing helix chain 'P' and resid 332 through 334 No H-bonds generated for 'chain 'P' and resid 332 through 334' Processing helix chain 'P' and resid 335 through 351 removed outlier: 3.950A pdb=" N GLU P 349 " --> pdb=" O ILE P 345 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR P 350 " --> pdb=" O LEU P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 354 through 366 Processing helix chain 'P' and resid 377 through 382 Processing helix chain 'P' and resid 383 through 391 removed outlier: 3.618A pdb=" N LEU P 387 " --> pdb=" O ASN P 383 " (cutoff:3.500A) Processing helix chain 'P' and resid 392 through 404 removed outlier: 3.580A pdb=" N LYS P 400 " --> pdb=" O LYS P 396 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL P 404 " --> pdb=" O LYS P 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 407 through 420 removed outlier: 3.671A pdb=" N ALA P 415 " --> pdb=" O LEU P 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 421 through 425 removed outlier: 6.298A pdb=" N TYR P 425 " --> pdb=" O VAL P 422 " (cutoff:3.500A) Processing helix chain 'P' and resid 426 through 434 removed outlier: 3.920A pdb=" N ARG P 430 " --> pdb=" O PRO P 426 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL P 431 " --> pdb=" O ARG P 427 " (cutoff:3.500A) Processing helix chain 'P' and resid 438 through 447 Processing helix chain 'P' and resid 449 through 469 removed outlier: 5.487A pdb=" N ASN P 455 " --> pdb=" O GLN P 451 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU P 458 " --> pdb=" O TYR P 454 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU P 463 " --> pdb=" O ALA P 459 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N MET P 464 " --> pdb=" O VAL P 460 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL P 465 " --> pdb=" O GLN P 461 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 26 removed outlier: 3.692A pdb=" N ILE Q 25 " --> pdb=" O PRO Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 28 No H-bonds generated for 'chain 'Q' and resid 27 through 28' Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.246A pdb=" N LEU Q 33 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU Q 36 " --> pdb=" O THR Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 79 removed outlier: 4.325A pdb=" N GLU Q 58 " --> pdb=" O THR Q 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG Q 61 " --> pdb=" O ASN Q 57 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASN Q 64 " --> pdb=" O ARG Q 60 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU Q 66 " --> pdb=" O LEU Q 62 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER Q 74 " --> pdb=" O ARG Q 70 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU Q 75 " --> pdb=" O TYR Q 71 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS Q 79 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 92 removed outlier: 3.712A pdb=" N LYS Q 90 " --> pdb=" O GLY Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 129 removed outlier: 3.930A pdb=" N ASP Q 109 " --> pdb=" O SER Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 146 removed outlier: 3.771A pdb=" N GLN Q 134 " --> pdb=" O GLN Q 130 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN Q 146 " --> pdb=" O ARG Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 207 Processing helix chain 'Q' and resid 245 through 257 Processing helix chain 'Q' and resid 267 through 285 removed outlier: 3.789A pdb=" N SER Q 271 " --> pdb=" O ASN Q 267 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN Q 272 " --> pdb=" O GLU Q 268 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN Q 280 " --> pdb=" O LYS Q 276 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP Q 283 " --> pdb=" O LYS Q 279 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR Q 285 " --> pdb=" O LEU Q 281 " (cutoff:3.500A) Processing helix chain 'Q' and resid 285 through 325 removed outlier: 4.295A pdb=" N LYS Q 289 " --> pdb=" O TYR Q 285 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR Q 293 " --> pdb=" O LYS Q 289 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR Q 294 " --> pdb=" O THR Q 290 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU Q 295 " --> pdb=" O THR Q 291 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS Q 304 " --> pdb=" O TYR Q 300 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU Q 305 " --> pdb=" O ALA Q 301 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP Q 307 " --> pdb=" O ALA Q 303 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SER Q 308 " --> pdb=" O LYS Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 344 through 346 No H-bonds generated for 'chain 'Q' and resid 344 through 346' Processing helix chain 'Q' and resid 347 through 354 Processing helix chain 'Q' and resid 355 through 357 No H-bonds generated for 'chain 'Q' and resid 355 through 357' Processing helix chain 'Q' and resid 387 through 397 removed outlier: 3.944A pdb=" N TYR Q 397 " --> pdb=" O ILE Q 393 " (cutoff:3.500A) Processing helix chain 'Q' and resid 407 through 421 removed outlier: 3.639A pdb=" N THR Q 411 " --> pdb=" O ALA Q 407 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE Q 412 " --> pdb=" O GLY Q 408 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL Q 413 " --> pdb=" O LEU Q 409 " (cutoff:3.500A) Proline residue: Q 416 - end of helix Processing helix chain 'Q' and resid 425 through 447 removed outlier: 4.688A pdb=" N LYS Q 444 " --> pdb=" O VAL Q 440 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS Q 445 " --> pdb=" O LEU Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 452 through 460 removed outlier: 3.731A pdb=" N MET Q 457 " --> pdb=" O GLU Q 453 " (cutoff:3.500A) Processing helix chain 'Q' and resid 461 through 480 removed outlier: 3.585A pdb=" N PHE Q 471 " --> pdb=" O LEU Q 467 " (cutoff:3.500A) Processing helix chain 'Q' and resid 519 through 523 Processing helix chain 'Q' and resid 525 through 552 removed outlier: 3.919A pdb=" N LEU Q 529 " --> pdb=" O THR Q 525 " (cutoff:3.500A) Processing helix chain 'Q' and resid 553 through 555 No H-bonds generated for 'chain 'Q' and resid 553 through 555' Processing helix chain 'Q' and resid 556 through 563 removed outlier: 3.799A pdb=" N TYR Q 561 " --> pdb=" O ALA Q 557 " (cutoff:3.500A) Processing helix chain 'Q' and resid 568 through 596 Proline residue: Q 574 - end of helix removed outlier: 4.061A pdb=" N ILE Q 582 " --> pdb=" O PHE Q 578 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR Q 585 " --> pdb=" O GLY Q 581 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS Q 593 " --> pdb=" O CYS Q 589 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP Q 594 " --> pdb=" O ILE Q 590 " (cutoff:3.500A) Processing helix chain 'Q' and resid 612 through 617 removed outlier: 4.013A pdb=" N PHE Q 616 " --> pdb=" O LEU Q 612 " (cutoff:3.500A) Processing helix chain 'Q' and resid 629 through 640 removed outlier: 4.996A pdb=" N VAL Q 635 " --> pdb=" O ALA Q 631 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE Q 636 " --> pdb=" O LYS Q 632 " (cutoff:3.500A) Processing helix chain 'Q' and resid 643 through 650 removed outlier: 3.847A pdb=" N LEU Q 650 " --> pdb=" O PRO Q 646 " (cutoff:3.500A) Processing helix chain 'Q' and resid 710 through 712 No H-bonds generated for 'chain 'Q' and resid 710 through 712' Processing helix chain 'Q' and resid 713 through 733 removed outlier: 4.398A pdb=" N ILE Q 717 " --> pdb=" O ILE Q 713 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS Q 718 " --> pdb=" O HIS Q 714 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL Q 727 " --> pdb=" O CYS Q 723 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR Q 733 " --> pdb=" O HIS Q 729 " (cutoff:3.500A) Processing helix chain 'Q' and resid 733 through 759 removed outlier: 4.242A pdb=" N TRP Q 737 " --> pdb=" O TYR Q 733 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE Q 757 " --> pdb=" O MET Q 753 " (cutoff:3.500A) Processing helix chain 'Q' and resid 765 through 810 removed outlier: 3.736A pdb=" N ALA Q 779 " --> pdb=" O ALA Q 775 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU Q 785 " --> pdb=" O THR Q 781 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N MET Q 788 " --> pdb=" O VAL Q 784 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU Q 789 " --> pdb=" O LEU Q 785 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU Q 795 " --> pdb=" O THR Q 791 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N HIS Q 796 " --> pdb=" O SER Q 792 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER Q 797 " --> pdb=" O ALA Q 793 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER Q 807 " --> pdb=" O VAL Q 803 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS Q 808 " --> pdb=" O GLU Q 804 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 22 Processing helix chain 'S' and resid 26 through 36 removed outlier: 4.448A pdb=" N ASN S 32 " --> pdb=" O ASN S 28 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU S 33 " --> pdb=" O GLN S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 46 Processing helix chain 'S' and resid 64 through 87 removed outlier: 3.932A pdb=" N LYS S 75 " --> pdb=" O TYR S 71 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU S 76 " --> pdb=" O ALA S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 113 removed outlier: 3.559A pdb=" N GLY S 101 " --> pdb=" O TYR S 97 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR S 102 " --> pdb=" O ILE S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 127 Processing helix chain 'S' and resid 128 through 132 Processing helix chain 'S' and resid 148 through 156 Processing helix chain 'S' and resid 175 through 199 removed outlier: 4.729A pdb=" N ARG S 181 " --> pdb=" O ILE S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 201 through 229 removed outlier: 4.190A pdb=" N LEU S 211 " --> pdb=" O CYS S 207 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 242 Processing helix chain 'S' and resid 251 through 259 Processing helix chain 'S' and resid 261 through 271 Processing helix chain 'S' and resid 283 through 302 removed outlier: 3.590A pdb=" N HIS S 287 " --> pdb=" O ASN S 283 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP S 298 " --> pdb=" O GLU S 294 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA S 299 " --> pdb=" O LEU S 295 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE S 300 " --> pdb=" O CYS S 296 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 332 removed outlier: 4.531A pdb=" N TRP S 310 " --> pdb=" O ILE S 306 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 39 removed outlier: 3.684A pdb=" N LEU T 26 " --> pdb=" O TYR T 22 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE T 27 " --> pdb=" O TYR T 23 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL T 28 " --> pdb=" O LEU T 24 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL T 29 " --> pdb=" O VAL T 25 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE T 30 " --> pdb=" O LEU T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 54 removed outlier: 3.611A pdb=" N PHE T 50 " --> pdb=" O ASN T 46 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 93 removed outlier: 3.663A pdb=" N TRP T 59 " --> pdb=" O SER T 55 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA T 65 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU T 66 " --> pdb=" O LEU T 62 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS T 67 " --> pdb=" O GLY T 63 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL T 68 " --> pdb=" O ILE T 64 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER T 71 " --> pdb=" O CYS T 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER T 84 " --> pdb=" O PHE T 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY T 88 " --> pdb=" O SER T 84 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA T 89 " --> pdb=" O SER T 85 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG T 92 " --> pdb=" O GLY T 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 125 removed outlier: 4.082A pdb=" N LYS T 99 " --> pdb=" O ARG T 95 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE T 102 " --> pdb=" O THR T 98 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER T 103 " --> pdb=" O LYS T 99 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE T 104 " --> pdb=" O ASN T 100 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE T 105 " --> pdb=" O LEU T 101 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE T 106 " --> pdb=" O ILE T 102 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS T 107 " --> pdb=" O SER T 103 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL T 110 " --> pdb=" O PHE T 106 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA T 111 " --> pdb=" O CYS T 107 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE T 112 " --> pdb=" O GLU T 108 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR T 113 " --> pdb=" O VAL T 109 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE T 117 " --> pdb=" O TYR T 113 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA T 118 " --> pdb=" O GLY T 114 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL T 120 " --> pdb=" O ILE T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 138 through 175 removed outlier: 3.553A pdb=" N ALA T 175 " --> pdb=" O ALA T 171 " (cutoff:3.500A) Processing helix chain 'T' and resid 177 through 180 Processing helix chain 'T' and resid 181 through 207 removed outlier: 4.341A pdb=" N VAL T 186 " --> pdb=" O VAL T 182 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE T 187 " --> pdb=" O LYS T 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU T 188 " --> pdb=" O ILE T 184 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE T 190 " --> pdb=" O VAL T 186 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY T 191 " --> pdb=" O ILE T 187 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU T 194 " --> pdb=" O PHE T 190 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY T 195 " --> pdb=" O GLY T 191 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU T 196 " --> pdb=" O SER T 192 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL T 201 " --> pdb=" O LEU T 197 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY T 202 " --> pdb=" O GLY T 198 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 50 removed outlier: 3.933A pdb=" N PHE U 18 " --> pdb=" O TYR U 14 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY U 19 " --> pdb=" O ALA U 15 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 removed outlier: 3.939A pdb=" N LEU U 60 " --> pdb=" O MET U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 64 No H-bonds generated for 'chain 'U' and resid 62 through 64' Processing helix chain 'U' and resid 65 through 81 removed outlier: 4.355A pdb=" N LEU U 69 " --> pdb=" O MET U 65 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA U 70 " --> pdb=" O SER U 66 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL U 76 " --> pdb=" O TYR U 72 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE U 80 " --> pdb=" O VAL U 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 91 through 128 removed outlier: 4.175A pdb=" N PHE U 107 " --> pdb=" O LEU U 103 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA U 108 " --> pdb=" O CYS U 104 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS U 109 " --> pdb=" O VAL U 105 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU U 110 " --> pdb=" O GLY U 106 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET U 128 " --> pdb=" O VAL U 124 " (cutoff:3.500A) Processing helix chain 'U' and resid 133 through 161 removed outlier: 4.106A pdb=" N VAL U 138 " --> pdb=" O PHE U 134 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU U 139 " --> pdb=" O VAL U 135 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE U 140 " --> pdb=" O GLY U 136 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU U 141 " --> pdb=" O ILE U 137 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY U 151 " --> pdb=" O LEU U 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 16 Processing helix chain 'V' and resid 19 through 45 removed outlier: 4.019A pdb=" N VAL V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY V 38 " --> pdb=" O LYS V 34 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU V 45 " --> pdb=" O ALA V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 53 No H-bonds generated for 'chain 'V' and resid 51 through 53' Processing helix chain 'V' and resid 54 through 77 removed outlier: 3.504A pdb=" N TYR V 66 " --> pdb=" O ILE V 62 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY V 67 " --> pdb=" O ILE V 63 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU V 68 " --> pdb=" O ALA V 64 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR V 76 " --> pdb=" O VAL V 72 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER V 77 " --> pdb=" O LEU V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 83 through 120 removed outlier: 3.924A pdb=" N LEU V 95 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER V 96 " --> pdb=" O GLY V 92 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL V 97 " --> pdb=" O ALA V 93 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY V 98 " --> pdb=" O GLY V 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA V 114 " --> pdb=" O ILE V 110 " (cutoff:3.500A) Processing helix chain 'V' and resid 122 through 124 No H-bonds generated for 'chain 'V' and resid 122 through 124' Processing helix chain 'V' and resid 125 through 139 removed outlier: 4.418A pdb=" N ILE V 130 " --> pdb=" O PHE V 126 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU V 131 " --> pdb=" O VAL V 127 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE V 132 " --> pdb=" O GLY V 128 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE V 135 " --> pdb=" O LEU V 131 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU V 139 " --> pdb=" O PHE V 135 " (cutoff:3.500A) Processing helix chain 'V' and resid 141 through 156 removed outlier: 3.832A pdb=" N VAL V 146 " --> pdb=" O TYR V 142 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN V 156 " --> pdb=" O SER V 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 8 through 17 removed outlier: 3.802A pdb=" N PHE W 12 " --> pdb=" O TYR W 8 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY W 13 " --> pdb=" O ALA W 9 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS W 17 " --> pdb=" O GLY W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 46 removed outlier: 4.437A pdb=" N ILE W 21 " --> pdb=" O CYS W 17 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL W 37 " --> pdb=" O ALA W 33 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY W 38 " --> pdb=" O LYS W 34 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE W 39 " --> pdb=" O SER W 35 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS W 40 " --> pdb=" O GLY W 36 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA W 41 " --> pdb=" O VAL W 37 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR W 42 " --> pdb=" O GLY W 38 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL W 44 " --> pdb=" O CYS W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 53 No H-bonds generated for 'chain 'W' and resid 51 through 53' Processing helix chain 'W' and resid 54 through 65 removed outlier: 3.666A pdb=" N ILE W 65 " --> pdb=" O GLY W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 75 removed outlier: 3.763A pdb=" N VAL W 70 " --> pdb=" O TYR W 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 122 removed outlier: 4.756A pdb=" N ALA W 114 " --> pdb=" O ILE W 110 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG W 117 " --> pdb=" O ASP W 113 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN W 121 " --> pdb=" O ARG W 117 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN W 122 " --> pdb=" O GLY W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 125 through 155 removed outlier: 3.797A pdb=" N MET W 129 " --> pdb=" O LEU W 125 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU W 131 " --> pdb=" O VAL W 127 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE W 135 " --> pdb=" O LEU W 131 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA W 136 " --> pdb=" O ILE W 132 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU W 137 " --> pdb=" O LEU W 133 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL W 146 " --> pdb=" O TYR W 142 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA W 147 " --> pdb=" O GLY W 143 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU W 148 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU W 149 " --> pdb=" O ILE W 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 46 removed outlier: 4.252A pdb=" N GLY X 13 " --> pdb=" O ALA X 9 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA X 18 " --> pdb=" O ALA X 14 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA X 20 " --> pdb=" O GLY X 16 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE X 21 " --> pdb=" O CYS X 17 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL X 37 " --> pdb=" O ALA X 33 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL X 44 " --> pdb=" O CYS X 40 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU X 45 " --> pdb=" O ALA X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 47 through 53 removed outlier: 4.456A pdb=" N PHE X 51 " --> pdb=" O ASP X 48 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 77 removed outlier: 4.122A pdb=" N ILE X 58 " --> pdb=" O ILE X 54 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET X 59 " --> pdb=" O VAL X 55 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA X 60 " --> pdb=" O PRO X 56 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY X 61 " --> pdb=" O VAL X 57 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR X 66 " --> pdb=" O ILE X 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY X 67 " --> pdb=" O ILE X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 119 removed outlier: 3.943A pdb=" N ILE X 89 " --> pdb=" O TYR X 85 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN X 90 " --> pdb=" O THR X 86 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU X 91 " --> pdb=" O GLY X 87 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER X 96 " --> pdb=" O GLY X 92 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP X 113 " --> pdb=" O GLY X 109 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA X 114 " --> pdb=" O ILE X 110 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER X 119 " --> pdb=" O GLY X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 138 removed outlier: 3.954A pdb=" N LEU X 133 " --> pdb=" O MET X 129 " (cutoff:3.500A) Processing helix chain 'X' and resid 138 through 156 removed outlier: 3.992A pdb=" N TYR X 142 " --> pdb=" O VAL X 138 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY X 143 " --> pdb=" O LEU X 139 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU X 144 " --> pdb=" O GLY X 140 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN X 156 " --> pdb=" O SER X 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 44 removed outlier: 3.828A pdb=" N PHE Y 12 " --> pdb=" O TYR Y 8 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY Y 13 " --> pdb=" O ALA Y 9 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR Y 24 " --> pdb=" O ALA Y 20 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY Y 38 " --> pdb=" O LYS Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 54 through 62 removed outlier: 3.577A pdb=" N ILE Y 58 " --> pdb=" O ILE Y 54 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET Y 59 " --> pdb=" O VAL Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 78 removed outlier: 4.326A pdb=" N GLY Y 67 " --> pdb=" O ILE Y 63 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU Y 68 " --> pdb=" O ALA Y 64 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL Y 70 " --> pdb=" O TYR Y 66 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 120 removed outlier: 3.876A pdb=" N VAL Y 111 " --> pdb=" O ALA Y 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP Y 113 " --> pdb=" O GLY Y 109 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA Y 114 " --> pdb=" O ILE Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 121 through 124 removed outlier: 6.931A pdb=" N ARG Y 124 " --> pdb=" O GLN Y 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 121 through 124' Processing helix chain 'Y' and resid 125 through 157 removed outlier: 3.890A pdb=" N ILE Y 130 " --> pdb=" O PHE Y 126 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU Y 131 " --> pdb=" O VAL Y 127 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE Y 132 " --> pdb=" O GLY Y 128 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU Y 133 " --> pdb=" O MET Y 129 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE Y 134 " --> pdb=" O ILE Y 130 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE Y 135 " --> pdb=" O LEU Y 131 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA Y 136 " --> pdb=" O ILE Y 132 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU Y 137 " --> pdb=" O LEU Y 133 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY Y 143 " --> pdb=" O LEU Y 139 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU Y 144 " --> pdb=" O GLY Y 140 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE Y 145 " --> pdb=" O LEU Y 141 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL Y 146 " --> pdb=" O TYR Y 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 37 removed outlier: 3.655A pdb=" N GLY Z 13 " --> pdb=" O ALA Z 9 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS Z 17 " --> pdb=" O GLY Z 13 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA Z 18 " --> pdb=" O ALA Z 14 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 45 removed outlier: 4.204A pdb=" N LEU Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 54 through 64 removed outlier: 4.265A pdb=" N ALA Z 60 " --> pdb=" O PRO Z 56 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY Z 61 " --> pdb=" O VAL Z 57 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE Z 62 " --> pdb=" O ILE Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 65 through 76 removed outlier: 3.941A pdb=" N VAL Z 70 " --> pdb=" O TYR Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 83 through 122 removed outlier: 3.552A pdb=" N ILE Z 89 " --> pdb=" O TYR Z 85 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP Z 113 " --> pdb=" O GLY Z 109 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG Z 117 " --> pdb=" O ASP Z 113 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY Z 118 " --> pdb=" O ALA Z 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 153 removed outlier: 4.079A pdb=" N LEU Z 131 " --> pdb=" O VAL Z 127 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE Z 132 " --> pdb=" O GLY Z 128 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Z 133 " --> pdb=" O MET Z 129 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE Z 134 " --> pdb=" O ILE Z 130 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA Z 136 " --> pdb=" O ILE Z 132 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU Z 137 " --> pdb=" O LEU Z 133 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG Z 153 " --> pdb=" O LEU Z 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 46 removed outlier: 4.197A pdb=" N GLY a 13 " --> pdb=" O ALA a 9 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE a 15 " --> pdb=" O PHE a 11 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS a 17 " --> pdb=" O GLY a 13 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA a 18 " --> pdb=" O ALA a 14 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL a 37 " --> pdb=" O ALA a 33 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY a 38 " --> pdb=" O LYS a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 78 removed outlier: 3.571A pdb=" N ILE a 58 " --> pdb=" O ILE a 54 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY a 67 " --> pdb=" O ILE a 63 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL a 70 " --> pdb=" O TYR a 66 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR a 76 " --> pdb=" O VAL a 72 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 117 removed outlier: 3.626A pdb=" N LEU a 91 " --> pdb=" O GLY a 87 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER a 96 " --> pdb=" O GLY a 92 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL a 97 " --> pdb=" O ALA a 93 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY a 98 " --> pdb=" O GLY a 94 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 124 No H-bonds generated for 'chain 'a' and resid 122 through 124' Processing helix chain 'a' and resid 125 through 156 removed outlier: 4.062A pdb=" N ILE a 130 " --> pdb=" O PHE a 126 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU a 131 " --> pdb=" O VAL a 127 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU a 139 " --> pdb=" O PHE a 135 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY a 140 " --> pdb=" O ALA a 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU a 141 " --> pdb=" O GLU a 137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL a 146 " --> pdb=" O TYR a 142 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN a 156 " --> pdb=" O SER a 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 46 removed outlier: 4.189A pdb=" N PHE b 12 " --> pdb=" O TYR b 8 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY b 13 " --> pdb=" O ALA b 9 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA b 18 " --> pdb=" O ALA b 14 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA b 20 " --> pdb=" O GLY b 16 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE b 21 " --> pdb=" O CYS b 17 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE b 22 " --> pdb=" O ALA b 18 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE b 23 " --> pdb=" O SER b 19 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY b 38 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL b 44 " --> pdb=" O CYS b 40 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU b 45 " --> pdb=" O ALA b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 54 through 76 removed outlier: 3.869A pdb=" N ILE b 58 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY b 67 " --> pdb=" O ILE b 63 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU b 68 " --> pdb=" O ALA b 64 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL b 70 " --> pdb=" O TYR b 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL b 72 " --> pdb=" O LEU b 68 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU b 73 " --> pdb=" O VAL b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 122 removed outlier: 3.587A pdb=" N GLY b 92 " --> pdb=" O PHE b 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY b 109 " --> pdb=" O GLY b 105 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE b 110 " --> pdb=" O PHE b 106 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG b 117 " --> pdb=" O ASP b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 133 removed outlier: 4.119A pdb=" N ILE b 132 " --> pdb=" O GLY b 128 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU b 133 " --> pdb=" O MET b 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 157 removed outlier: 3.955A pdb=" N GLU b 137 " --> pdb=" O LEU b 133 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY b 143 " --> pdb=" O LEU b 139 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 44 removed outlier: 3.728A pdb=" N GLY c 31 " --> pdb=" O GLY c 27 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL c 37 " --> pdb=" O ALA c 33 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR c 42 " --> pdb=" O GLY c 38 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL c 44 " --> pdb=" O CYS c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 50 removed outlier: 3.519A pdb=" N LEU c 50 " --> pdb=" O PRO c 47 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 63 removed outlier: 3.901A pdb=" N ILE c 58 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE c 63 " --> pdb=" O MET c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 65 through 76 Processing helix chain 'c' and resid 88 through 122 removed outlier: 3.953A pdb=" N GLY c 92 " --> pdb=" O PHE c 88 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL c 116 " --> pdb=" O GLY c 112 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG c 117 " --> pdb=" O ASP c 113 " (cutoff:3.500A) Processing helix chain 'c' and resid 125 through 143 removed outlier: 3.735A pdb=" N MET c 129 " --> pdb=" O LEU c 125 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU c 131 " --> pdb=" O VAL c 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL c 138 " --> pdb=" O ILE c 134 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU c 139 " --> pdb=" O PHE c 135 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY c 143 " --> pdb=" O LEU c 139 " (cutoff:3.500A) Processing helix chain 'c' and resid 143 through 156 Processing helix chain 'd' and resid 3 through 24 removed outlier: 4.231A pdb=" N VAL d 7 " --> pdb=" O SER d 3 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL d 8 " --> pdb=" O PHE d 4 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE d 12 " --> pdb=" O VAL d 8 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL d 13 " --> pdb=" O GLY d 9 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL d 14 " --> pdb=" O VAL d 10 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER d 15 " --> pdb=" O PHE d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 52 removed outlier: 3.947A pdb=" N TRP d 33 " --> pdb=" O ASN d 29 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG d 34 " --> pdb=" O GLN d 30 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ILE d 38 " --> pdb=" O ARG d 34 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU d 39 " --> pdb=" O SER d 35 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET d 44 " --> pdb=" O THR d 40 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE d 50 " --> pdb=" O LEU d 46 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR d 51 " --> pdb=" O MET d 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 229 through 246 Processing helix chain 'e' and resid 250 through 254 Processing helix chain 'f' and resid 9 through 33 removed outlier: 3.845A pdb=" N VAL f 21 " --> pdb=" O SER f 17 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL f 22 " --> pdb=" O ALA f 18 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE f 23 " --> pdb=" O PHE f 19 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU f 24 " --> pdb=" O GLY f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 51 through 74 removed outlier: 4.014A pdb=" N VAL f 55 " --> pdb=" O VAL f 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA f 59 " --> pdb=" O VAL f 55 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU f 60 " --> pdb=" O TYR f 56 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL f 61 " --> pdb=" O LEU f 57 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR f 62 " --> pdb=" O ALA f 58 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE f 65 " --> pdb=" O VAL f 61 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN f 72 " --> pdb=" O PHE f 68 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 31 removed outlier: 7.100A pdb=" N LYS A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE A 63 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A 69 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 60 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU A 47 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 48 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 25 " --> pdb=" O VAL A 85 " (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: 6.400A pdb=" N TYR A 105 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N THR A 321 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 280 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 279 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS A 397 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 225 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 6.400A pdb=" N TYR A 105 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N THR A 321 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 280 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 279 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR A 252 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL A 416 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 254 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS A 253 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 441 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 11.175A pdb=" N PHE A 438 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N SER A 457 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY A 440 " --> pdb=" O ASN A 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 173 removed outlier: 6.377A pdb=" N HIS A 170 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER A 160 " --> pdb=" O HIS A 170 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 172 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 160 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.904A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 207 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 232 through 233 removed outlier: 4.532A pdb=" N CYS A 246 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.713A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE B 70 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 76 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 92 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 95 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU B 26 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE I 197 " --> pdb=" O ASN I 192 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA I 137 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AB1, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.915A pdb=" N SER B 239 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 212 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.336A pdb=" N ARG B 321 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.265A pdb=" N GLU B 149 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE B 164 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 334 through 336 Processing sheet with id=AB5, first strand: chain 'B' and resid 299 through 301 Processing sheet with id=AB6, first strand: chain 'C' and resid 25 through 31 removed outlier: 3.556A pdb=" N ALA C 26 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE C 36 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL C 30 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 37 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LYS C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE C 63 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 6.224A 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: 6.902A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 277 " --> pdb=" O ASN C 349 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 398 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS C 397 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 225 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.902A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 277 " --> pdb=" O ASN C 349 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 252 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 170 through 173 removed outlier: 3.529A pdb=" N GLY C 159 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 152 removed outlier: 6.928A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 232 through 233 removed outlier: 4.385A pdb=" N CYS C 246 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 92 through 95 removed outlier: 3.572A pdb=" N THR D 92 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 53 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE D 70 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 75 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 33 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE E 63 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL E 60 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN E 71 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 86 " --> pdb=" O LYS E 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 101 through 104 Processing sheet with id=AC6, first strand: chain 'D' and resid 172 through 174 removed outlier: 6.218A pdb=" N ILE D 172 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 278 " --> pdb=" O ILE D 332 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 95 through 96 Processing sheet with id=AC8, first strand: chain 'E' and resid 104 through 105 removed outlier: 6.232A pdb=" N TYR E 105 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR E 321 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA E 277 " --> pdb=" O SER E 351 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE E 353 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE E 279 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS E 397 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU E 225 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 104 through 105 removed outlier: 6.232A pdb=" N TYR E 105 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR E 321 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA E 277 " --> pdb=" O SER E 351 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE E 353 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE E 279 " --> pdb=" O ILE E 353 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 170 through 171 Processing sheet with id=AD2, first strand: chain 'E' and resid 198 through 200 removed outlier: 3.830A pdb=" N LEU E 198 " --> pdb=" O PHE E 209 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE E 209 " --> pdb=" O LEU E 198 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 302 through 303 Processing sheet with id=AD4, first strand: chain 'F' and resid 33 through 35 removed outlier: 6.596A pdb=" N ARG F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE F 70 " --> pdb=" O ARG F 74 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE F 76 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 92 " --> pdb=" O THR F 56 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 102 through 104 Processing sheet with id=AD6, first strand: chain 'F' and resid 112 through 113 removed outlier: 6.385A pdb=" N ILE F 210 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE F 241 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE F 212 " --> pdb=" O PHE F 241 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N SER F 209 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE F 277 " --> pdb=" O SER F 209 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL F 211 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 334 through 336 removed outlier: 6.209A pdb=" N ILE F 172 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 172 through 174 removed outlier: 3.706A pdb=" N VAL G 173 " --> pdb=" O ALA G 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 173 through 174 Processing sheet with id=AE1, first strand: chain 'M' and resid 92 through 93 Processing sheet with id=AE2, first strand: chain 'M' and resid 96 through 101 Processing sheet with id=AE3, first strand: chain 'N' and resid 38 through 40 removed outlier: 6.998A pdb=" N PHE N 38 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL N 10 " --> pdb=" O PHE N 38 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TYR N 40 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA N 12 " --> pdb=" O TYR N 40 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU N 7 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU N 68 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA N 9 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN N 70 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE N 11 " --> pdb=" O ASN N 70 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE N 69 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 45 through 47 removed outlier: 4.667A pdb=" N LYS O 328 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE O 14 " --> pdb=" O LYS O 328 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 231 through 236 removed outlier: 3.818A pdb=" N LEU O 195 " --> pdb=" O ARG O 258 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 14 through 16 removed outlier: 4.534A pdb=" N GLN Q 40 " --> pdb=" O TRP Q 340 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 190 through 192 Processing sheet with id=AE8, first strand: chain 'Q' and resid 213 through 214 3647 hydrogen bonds defined for protein. 10653 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: 25.48 Time building geometry restraints manager: 22.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 20933 1.34 - 1.46: 13149 1.46 - 1.58: 31122 1.58 - 1.70: 0 1.70 - 1.82: 462 Bond restraints: 65666 Sorted by residual: 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 3.10e+00 bond pdb=" N MET c 1 " pdb=" CA MET c 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N MET P 1 " pdb=" CA MET P 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N MET a 1 " pdb=" CA MET a 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 ... (remaining 65661 not shown) Histogram of bond angle deviations from ideal: 97.37 - 104.70: 914 104.70 - 112.03: 32421 112.03 - 119.36: 22518 119.36 - 126.69: 32366 126.69 - 134.02: 625 Bond angle restraints: 88844 Sorted by residual: angle pdb=" N SER O 171 " pdb=" CA SER O 171 " pdb=" C SER O 171 " ideal model delta sigma weight residual 114.04 107.30 6.74 1.24e+00 6.50e-01 2.96e+01 angle pdb=" N LEU S 248 " pdb=" CA LEU S 248 " pdb=" C LEU S 248 " ideal model delta sigma weight residual 114.04 107.94 6.10 1.24e+00 6.50e-01 2.42e+01 angle pdb=" N ILE P 177 " pdb=" CA ILE P 177 " pdb=" C ILE P 177 " ideal model delta sigma weight residual 111.90 108.45 3.45 8.10e-01 1.52e+00 1.81e+01 angle pdb=" N ILE Q 368 " pdb=" CA ILE Q 368 " pdb=" C ILE Q 368 " ideal model delta sigma weight residual 113.71 109.71 4.00 9.50e-01 1.11e+00 1.77e+01 angle pdb=" N ILE P 291 " pdb=" CA ILE P 291 " pdb=" C ILE P 291 " ideal model delta sigma weight residual 113.20 109.19 4.01 9.60e-01 1.09e+00 1.74e+01 ... (remaining 88839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 36259 17.98 - 35.95: 2716 35.95 - 53.93: 417 53.93 - 71.90: 132 71.90 - 89.88: 87 Dihedral angle restraints: 39611 sinusoidal: 15701 harmonic: 23910 Sorted by residual: dihedral pdb=" CA VAL Q 364 " pdb=" C VAL Q 364 " pdb=" N PRO Q 365 " pdb=" CA PRO Q 365 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLU P 90 " pdb=" C GLU P 90 " pdb=" N ASP P 91 " pdb=" CA ASP P 91 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA SER P 376 " pdb=" C SER P 376 " pdb=" N GLU P 377 " pdb=" CA GLU P 377 " ideal model delta harmonic sigma weight residual -180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 39608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 7033 0.032 - 0.064: 2226 0.064 - 0.097: 669 0.097 - 0.129: 296 0.129 - 0.161: 19 Chirality restraints: 10243 Sorted by residual: chirality pdb=" CB THR W 24 " pdb=" CA THR W 24 " pdb=" OG1 THR W 24 " pdb=" CG2 THR W 24 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA PRO O 323 " pdb=" N PRO O 323 " pdb=" C PRO O 323 " pdb=" CB PRO O 323 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.41e-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 2.35 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 10240 not shown) Planarity restraints: 11334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 231 " -0.040 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO E 232 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 232 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 232 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 135 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C LYS Q 135 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS Q 135 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN Q 136 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE U 61 " -0.035 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO U 62 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO U 62 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO U 62 " -0.030 5.00e-02 4.00e+02 ... (remaining 11331 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 359 2.39 - 3.02: 45603 3.02 - 3.64: 104919 3.64 - 4.27: 150560 4.27 - 4.90: 242197 Nonbonded interactions: 543638 Sorted by model distance: nonbonded pdb=" O ARG P 288 " pdb=" OG SER P 292 " model vdw 1.761 2.440 nonbonded pdb=" O ALA F 213 " pdb=" OG1 THR F 279 " model vdw 1.902 2.440 nonbonded pdb=" OG SER C 160 " pdb=" OG SER C 169 " model vdw 1.909 2.440 nonbonded pdb=" OG1 THR N 58 " pdb=" OE1 GLU N 59 " model vdw 1.925 2.440 nonbonded pdb=" O ILE Q 25 " pdb=" OG SER Q 29 " model vdw 1.931 2.440 ... (remaining 543633 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' and (resid 9 through 195 or resid 207 through 487)) selection = chain 'F' } 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 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 14.950 Check model and map are aligned: 0.710 Set scattering table: 0.460 Process input model: 129.390 Find NCS groups from input model: 2.830 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3256 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 0.037 65666 Z= 0.190 Angle : 0.569 12.023 88844 Z= 0.326 Chirality : 0.038 0.161 10243 Planarity : 0.004 0.064 11334 Dihedral : 13.839 89.877 24269 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.35 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.78 (0.09), residues: 8221 helix: 0.56 (0.08), residues: 4447 sheet: -0.76 (0.23), residues: 525 loop : -2.02 (0.11), residues: 3249 *********************** 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 1218 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1218 time to evaluate : 5.380 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1218 average time/residue: 0.6692 time to fit residues: 1316.6203 Evaluate side-chains 598 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 598 time to evaluate : 5.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4275 ------------------------------------------------------------------------------- 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: 4.9990 chunk 617 optimal weight: 30.0000 chunk 342 optimal weight: 20.0000 chunk 211 optimal weight: 0.6980 chunk 416 optimal weight: 10.0000 chunk 330 optimal weight: 2.9990 chunk 638 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 388 optimal weight: 4.9990 chunk 475 optimal weight: 30.0000 chunk 740 optimal weight: 0.0570 overall best weight: 2.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN C 109 GLN C 170 HIS ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS G 49 ASN G 94 GLN I 12 GLN I 122 GLN K 18 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN M 100 ASN ** M 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 ASN O 136 ASN ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 234 ASN ** P 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 341 ASN ** P 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 273 GLN Q 571 ASN Q 796 HIS ** S 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 HIS U 159 ASN V 80 GLN W 80 GLN X 90 GLN ** X 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 121 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3679 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 65666 Z= 0.237 Angle : 0.683 12.784 88844 Z= 0.355 Chirality : 0.044 0.309 10243 Planarity : 0.005 0.108 11334 Dihedral : 4.904 28.891 8920 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.23 % Favored : 94.76 % Rotamer: Outliers : 0.30 % Allowed : 5.27 % Favored : 94.43 % 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: -0.70 (0.09), residues: 8221 helix: 0.58 (0.08), residues: 4525 sheet: -0.84 (0.23), residues: 480 loop : -1.93 (0.11), residues: 3216 *********************** 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 795 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 774 time to evaluate : 5.478 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 21 outliers final: 6 residues processed: 792 average time/residue: 0.6464 time to fit residues: 852.6108 Evaluate side-chains 524 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 518 time to evaluate : 5.401 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4819 time to fit residues: 12.8227 ------------------------------------------------------------------------------- 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: 1.9990 chunk 229 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 chunk 503 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 741 optimal weight: 20.0000 chunk 800 optimal weight: 10.0000 chunk 660 optimal weight: 2.9990 chunk 735 optimal weight: 0.8980 chunk 252 optimal weight: 8.9990 chunk 594 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN B 401 ASN C 455 ASN D 12 ASN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 GLN F 190 GLN F 365 HIS F 396 HIS ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN O 103 ASN O 190 HIS P 118 GLN ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 323 GLN Q 68 GLN Q 201 GLN ** Q 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 796 HIS S 128 HIS ** S 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 129 HIS U 159 ASN X 80 GLN X 121 GLN Y 151 ASN ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3912 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 65666 Z= 0.217 Angle : 0.646 11.077 88844 Z= 0.336 Chirality : 0.043 0.327 10243 Planarity : 0.005 0.099 11334 Dihedral : 4.805 29.769 8920 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.76 % Favored : 95.23 % Rotamer: Outliers : 0.13 % Allowed : 5.07 % Favored : 94.80 % 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: -0.64 (0.09), residues: 8221 helix: 0.65 (0.08), residues: 4518 sheet: -0.85 (0.22), residues: 506 loop : -1.92 (0.11), residues: 3197 *********************** 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 702 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 693 time to evaluate : 5.474 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 revert: symmetry clash 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: 9 outliers final: 0 residues processed: 701 average time/residue: 0.6478 time to fit residues: 760.9298 Evaluate side-chains 505 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 5.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4317 ------------------------------------------------------------------------------- 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: 20.0000 chunk 557 optimal weight: 9.9990 chunk 384 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 353 optimal weight: 5.9990 chunk 497 optimal weight: 2.9990 chunk 744 optimal weight: 10.0000 chunk 787 optimal weight: 0.9990 chunk 388 optimal weight: 30.0000 chunk 705 optimal weight: 30.0000 chunk 212 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 563 ASN C 491 ASN ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 HIS F 365 HIS F 401 ASN F 402 GLN ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN K 165 GLN L 110 HIS ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 171 ASN ** M 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN O 176 HIS ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 ASN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 714 HIS Q 718 HIS ** Q 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 796 HIS S 29 GLN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 159 ASN V 122 GLN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 122 GLN X 151 ASN Y 151 ASN ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 90 GLN c 121 GLN ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4431 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 65666 Z= 0.288 Angle : 0.757 16.691 88844 Z= 0.396 Chirality : 0.046 0.312 10243 Planarity : 0.006 0.091 11334 Dihedral : 5.124 33.299 8920 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.12 % Favored : 94.87 % Rotamer: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.01 % 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: -1.02 (0.09), residues: 8221 helix: 0.31 (0.08), residues: 4502 sheet: -0.86 (0.22), residues: 502 loop : -2.07 (0.10), residues: 3217 *********************** 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 718 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 711 time to evaluate : 5.489 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: 7 outliers final: 2 residues processed: 717 average time/residue: 0.6241 time to fit residues: 758.0463 Evaluate side-chains 492 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 490 time to evaluate : 5.448 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4996 time to fit residues: 9.2774 ------------------------------------------------------------------------------- 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: 40.0000 chunk 447 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 586 optimal weight: 5.9990 chunk 325 optimal weight: 0.8980 chunk 672 optimal weight: 20.0000 chunk 544 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 402 optimal weight: 9.9990 chunk 707 optimal weight: 7.9990 chunk 198 optimal weight: 0.5980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN B 232 ASN B 396 HIS ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN ** K 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 ASN O 35 ASN O 287 GLN ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 64 ASN Q 68 GLN ** Q 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 571 ASN Q 745 GLN Q 796 HIS S 81 ASN ** S 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 159 ASN V 122 GLN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 122 GLN Y 151 ASN ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4557 moved from start: 0.6602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 65666 Z= 0.239 Angle : 0.673 10.984 88844 Z= 0.352 Chirality : 0.044 0.387 10243 Planarity : 0.005 0.124 11334 Dihedral : 5.015 30.219 8920 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.91 (0.09), residues: 8221 helix: 0.42 (0.08), residues: 4508 sheet: -0.80 (0.22), residues: 510 loop : -2.06 (0.10), residues: 3203 *********************** 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 693 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 690 time to evaluate : 5.436 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 outliers start: 3 outliers final: 1 residues processed: 693 average time/residue: 0.6239 time to fit residues: 733.9670 Evaluate side-chains 488 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 487 time to evaluate : 5.465 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4508 time to fit residues: 8.3844 ------------------------------------------------------------------------------- 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: 9.9990 chunk 709 optimal weight: 30.0000 chunk 155 optimal weight: 9.9990 chunk 462 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 788 optimal weight: 30.0000 chunk 654 optimal weight: 40.0000 chunk 365 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 260 optimal weight: 0.1980 chunk 413 optimal weight: 6.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 474 ASN ** A 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 HIS C 109 GLN ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 232 ASN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN G 49 ASN I 11 ASN ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 ASN I 201 ASN J 34 GLN J 61 ASN K 21 GLN ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 ASN O 367 GLN ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 GLN Q 185 ASN ** Q 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 499 HIS Q 801 HIS S 35 GLN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 159 ASN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 GLN ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 GLN a 90 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 259 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5022 moved from start: 0.8329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 65666 Z= 0.299 Angle : 0.787 15.356 88844 Z= 0.411 Chirality : 0.048 0.364 10243 Planarity : 0.006 0.095 11334 Dihedral : 5.354 28.698 8920 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 26.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.00 % Favored : 93.95 % Rotamer: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.68 % 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: -1.21 (0.09), residues: 8221 helix: 0.21 (0.08), residues: 4509 sheet: -1.06 (0.22), residues: 519 loop : -2.23 (0.10), residues: 3193 *********************** 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 716 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 711 time to evaluate : 5.479 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 715 average time/residue: 0.6348 time to fit residues: 774.5725 Evaluate side-chains 513 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 5.426 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5429 time to fit residues: 8.4321 ------------------------------------------------------------------------------- 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: 30.0000 chunk 88 optimal weight: 4.9990 chunk 449 optimal weight: 9.9990 chunk 575 optimal weight: 10.0000 chunk 446 optimal weight: 20.0000 chunk 663 optimal weight: 40.0000 chunk 440 optimal weight: 9.9990 chunk 785 optimal weight: 8.9990 chunk 491 optimal weight: 30.0000 chunk 478 optimal weight: 10.0000 chunk 362 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 GLN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS B 64 GLN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 GLN D 50 ASN ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** E 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN F 273 HIS ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN J 34 GLN ** J 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN ** K 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 171 ASN M 183 ASN N 55 ASN O 367 GLN O 373 GLN ** O 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 HIS P 118 GLN P 126 GLN ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 210 ASN ** Q 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 384 ASN ** Q 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 756 GLN Q 801 HIS S 7 ASN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN ** S 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 302 GLN S 334 GLN ** T 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 GLN X 121 GLN Y 80 GLN ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 80 GLN b 122 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 1.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.173 65666 Z= 0.501 Angle : 1.115 20.982 88844 Z= 0.589 Chirality : 0.059 0.742 10243 Planarity : 0.009 0.175 11334 Dihedral : 6.812 37.872 8920 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 43.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.94 % Favored : 91.98 % Rotamer: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.28 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.08), residues: 8221 helix: -0.85 (0.07), residues: 4521 sheet: -2.01 (0.21), residues: 516 loop : -2.72 (0.10), residues: 3184 *********************** 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 727 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 722 time to evaluate : 5.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 727 average time/residue: 0.6265 time to fit residues: 778.8285 Evaluate side-chains 477 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 476 time to evaluate : 5.489 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4648 time to fit residues: 8.4307 ------------------------------------------------------------------------------- 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: 9.9990 chunk 313 optimal weight: 0.8980 chunk 469 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 499 optimal weight: 30.0000 chunk 535 optimal weight: 0.6980 chunk 388 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 617 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS A 527 GLN ** A 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 GLN F 162 ASN F 246 ASN F 273 HIS ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN M 207 GLN ** P 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 447 HIS ** Q 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 715 GLN Q 796 HIS ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 ASN ** V 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 80 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5573 moved from start: 1.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 65666 Z= 0.228 Angle : 0.742 14.671 88844 Z= 0.387 Chirality : 0.047 0.363 10243 Planarity : 0.005 0.091 11334 Dihedral : 5.672 31.525 8920 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 0.01 % Allowed : 1.46 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.54 (0.09), residues: 8221 helix: -0.05 (0.07), residues: 4544 sheet: -1.55 (0.22), residues: 489 loop : -2.34 (0.10), residues: 3188 *********************** 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 681 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 680 time to evaluate : 5.599 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 outliers start: 1 outliers final: 0 residues processed: 681 average time/residue: 0.6391 time to fit residues: 742.1718 Evaluate side-chains 495 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 5.462 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5252 ------------------------------------------------------------------------------- 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: 30.0000 chunk 752 optimal weight: 8.9990 chunk 686 optimal weight: 20.0000 chunk 732 optimal weight: 8.9990 chunk 440 optimal weight: 20.0000 chunk 318 optimal weight: 5.9990 chunk 574 optimal weight: 0.9990 chunk 224 optimal weight: 10.0000 chunk 661 optimal weight: 50.0000 chunk 692 optimal weight: 10.0000 chunk 729 optimal weight: 50.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 455 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN K 14 ASN ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 ASN ** P 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 GLN ** Q 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 796 HIS ** S 29 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 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 340 ASN ** T 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 159 ASN ** V 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 ASN ** W 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 53 ASN ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 80 GLN ** b 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 1.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 65666 Z= 0.397 Angle : 0.952 13.906 88844 Z= 0.502 Chirality : 0.054 0.721 10243 Planarity : 0.008 0.123 11334 Dihedral : 6.304 38.140 8920 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 38.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.43 % Favored : 91.51 % Rotamer: Outliers : 0.03 % Allowed : 1.21 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.09), residues: 8221 helix: -0.49 (0.07), residues: 4525 sheet: -1.81 (0.21), residues: 530 loop : -2.59 (0.10), residues: 3166 *********************** 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 661 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 659 time to evaluate : 5.492 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 outliers start: 2 outliers final: 0 residues processed: 661 average time/residue: 0.6225 time to fit residues: 712.9735 Evaluate side-chains 470 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 470 time to evaluate : 5.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5133 ------------------------------------------------------------------------------- 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: 2.9990 chunk 774 optimal weight: 30.0000 chunk 472 optimal weight: 8.9990 chunk 367 optimal weight: 10.0000 chunk 538 optimal weight: 5.9990 chunk 811 optimal weight: 20.0000 chunk 747 optimal weight: 30.0000 chunk 646 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 499 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN D 162 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN I 12 GLN ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 GLN P 447 HIS ** Q 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 159 ASN ** V 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 GLN ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 34 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 1.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 65666 Z= 0.343 Angle : 0.852 14.824 88844 Z= 0.449 Chirality : 0.050 0.355 10243 Planarity : 0.007 0.101 11334 Dihedral : 6.138 39.244 8920 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 31.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.88 % Favored : 93.08 % Rotamer: Outliers : 0.06 % Allowed : 0.56 % Favored : 99.39 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.03 % 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: -1.99 (0.09), residues: 8221 helix: -0.37 (0.07), residues: 4544 sheet: -1.92 (0.20), residues: 538 loop : -2.60 (0.10), residues: 3139 ********************** 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 660 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 656 time to evaluate : 5.565 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 outliers start: 4 outliers final: 0 residues processed: 659 average time/residue: 0.6288 time to fit residues: 717.1557 Evaluate side-chains 488 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 5.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5097 ------------------------------------------------------------------------------- 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: 8.9990 chunk 688 optimal weight: 0.9990 chunk 198 optimal weight: 0.1980 chunk 596 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 647 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 chunk 664 optimal weight: 40.0000 chunk 81 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** C 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 GLN I 122 GLN J 34 GLN ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 175 GLN Q 68 GLN ** Q 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 796 HIS ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 159 ASN ** V 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 GLN ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.079322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.060270 restraints weight = 577147.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.061033 restraints weight = 434075.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.061409 restraints weight = 327835.624| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 1.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 65666 Z= 0.276 Angle : 0.784 12.574 88844 Z= 0.412 Chirality : 0.048 0.412 10243 Planarity : 0.006 0.128 11334 Dihedral : 5.876 32.514 8920 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 29.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.65 % Favored : 92.31 % Rotamer: Outliers : 0.03 % Allowed : 0.50 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.01 % 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: -1.80 (0.09), residues: 8221 helix: -0.22 (0.07), residues: 4541 sheet: -1.75 (0.21), residues: 534 loop : -2.53 (0.10), residues: 3146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13570.69 seconds wall clock time: 241 minutes 27.20 seconds (14487.20 seconds total)