Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 27 19:00:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rrd_4987/08_2023/6rrd_4987.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rrd_4987/08_2023/6rrd_4987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rrd_4987/08_2023/6rrd_4987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rrd_4987/08_2023/6rrd_4987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rrd_4987/08_2023/6rrd_4987.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rrd_4987/08_2023/6rrd_4987.pdb" } resolution = 3.1 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= 0.006 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 98 5.49 5 S 238 5.16 5 C 32476 2.51 5 N 8903 2.21 5 O 9915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ARG 26": "NH1" <-> "NH2" Residue "Q ARG 27": "NH1" <-> "NH2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 204": "NH1" <-> "NH2" Residue "Q ARG 305": "NH1" <-> "NH2" Residue "Q ARG 324": "NH1" <-> "NH2" Residue "Q ARG 350": "NH1" <-> "NH2" Residue "Q TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 411": "NH1" <-> "NH2" Residue "Q ARG 421": "NH1" <-> "NH2" Residue "Q ARG 478": "NH1" <-> "NH2" Residue "Q ARG 504": "NH1" <-> "NH2" Residue "S ARG 44": "NH1" <-> "NH2" Residue "S TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S ARG 221": "NH1" <-> "NH2" Residue "S ARG 257": "NH1" <-> "NH2" Residue "S PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 407": "NH1" <-> "NH2" Residue "S ARG 419": "NH1" <-> "NH2" Residue "S ARG 434": "NH1" <-> "NH2" Residue "S TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 472": "NH1" <-> "NH2" Residue "S ARG 484": "NH1" <-> "NH2" Residue "S PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 542": "NH1" <-> "NH2" Residue "S ARG 746": "NH1" <-> "NH2" Residue "S ARG 762": "NH1" <-> "NH2" Residue "S TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 17": "NH1" <-> "NH2" Residue "R ARG 29": "NH1" <-> "NH2" Residue "R ARG 30": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 209": "NH1" <-> "NH2" Residue "R ARG 241": "NH1" <-> "NH2" Residue "R ARG 283": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "R PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 381": "NH1" <-> "NH2" Residue "R ARG 397": "NH1" <-> "NH2" Residue "R ARG 441": "NH1" <-> "NH2" Residue "M PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 6": "NH1" <-> "NH2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "O PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 51631 Number of models: 1 Model: "" Number of chains: 21 Chain: "T" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1019 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "U" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1010 Classifications: {'DNA': 48} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "Q" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3936 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4963 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 21, 'TRANS': 588} Chain breaks: 7 Chain: "R" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2771 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 3 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 942 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 856 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 11565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1465, 11565 Classifications: {'peptide': 1465} Link IDs: {'PTRANS': 59, 'TRANS': 1405} Chain breaks: 7 Chain: "B" Number of atoms: 9365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9365 Classifications: {'peptide': 1180} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 59, 'TRANS': 1120} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1600 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 2 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "O" Number of atoms: 4139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4139 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P DT T 40 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 40 " occ=0.00 residue: pdb=" P DG U 12 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG U 12 " occ=0.00 residue: pdb=" P DA U 19 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA U 19 " occ=0.00 residue: pdb=" P DA U 31 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA U 31 " occ=0.00 Time building chain proxies: 23.97, per 1000 atoms: 0.46 Number of scatterers: 51631 At special positions: 0 Unit cell: (158.232, 216.528, 190.503, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 238 16.00 P 98 15.00 O 9915 8.00 N 8903 7.00 C 32476 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: 18.74 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 601 " pdb="ZN ZN Q 601 " - pdb=" ND1 HIS Q 33 " 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11720 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 60 sheets defined 37.5% alpha, 13.6% beta 8 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 14.45 Creating SS restraints... Processing helix chain 'Q' and resid 78 through 82 Processing helix chain 'Q' and resid 85 through 89 removed outlier: 4.037A pdb=" N SER Q 88 " --> pdb=" O GLN Q 85 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS Q 89 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 85 through 89' Processing helix chain 'Q' and resid 100 through 122 removed outlier: 3.949A pdb=" N LEU Q 105 " --> pdb=" O LYS Q 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP Q 118 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU Q 119 " --> pdb=" O GLN Q 115 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE Q 120 " --> pdb=" O ILE Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 147 removed outlier: 3.744A pdb=" N ALA Q 133 " --> pdb=" O PHE Q 129 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE Q 135 " --> pdb=" O HIS Q 131 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE Q 136 " --> pdb=" O VAL Q 132 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU Q 141 " --> pdb=" O TRP Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 167 removed outlier: 3.877A pdb=" N LEU Q 165 " --> pdb=" O THR Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 182 Processing helix chain 'Q' and resid 194 through 199 removed outlier: 4.209A pdb=" N ILE Q 198 " --> pdb=" O GLN Q 194 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU Q 199 " --> pdb=" O ALA Q 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 194 through 199' Processing helix chain 'Q' and resid 224 through 237 removed outlier: 3.718A pdb=" N ASN Q 228 " --> pdb=" O GLY Q 224 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE Q 230 " --> pdb=" O LEU Q 226 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE Q 237 " --> pdb=" O THR Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 261 removed outlier: 3.538A pdb=" N LEU Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS Q 255 " --> pdb=" O GLY Q 251 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL Q 257 " --> pdb=" O LEU Q 253 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET Q 258 " --> pdb=" O LEU Q 254 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS Q 260 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 278 removed outlier: 4.311A pdb=" N PHE Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Q 273 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 320 removed outlier: 3.673A pdb=" N LEU Q 312 " --> pdb=" O SER Q 308 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR Q 313 " --> pdb=" O TYR Q 309 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE Q 314 " --> pdb=" O PHE Q 310 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN Q 315 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU Q 318 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE Q 320 " --> pdb=" O TRP Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 339 removed outlier: 3.691A pdb=" N ILE Q 331 " --> pdb=" O PRO Q 327 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU Q 332 " --> pdb=" O LEU Q 328 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU Q 336 " --> pdb=" O LEU Q 332 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER Q 337 " --> pdb=" O SER Q 333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 346 through 357 removed outlier: 3.756A pdb=" N VAL Q 353 " --> pdb=" O GLY Q 349 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR Q 357 " --> pdb=" O VAL Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 364 through 369 removed outlier: 3.868A pdb=" N PHE Q 367 " --> pdb=" O SER Q 364 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN Q 368 " --> pdb=" O ASP Q 365 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP Q 369 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 364 through 369' Processing helix chain 'Q' and resid 370 through 381 Processing helix chain 'Q' and resid 407 through 417 removed outlier: 3.618A pdb=" N ILE Q 416 " --> pdb=" O LYS Q 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 441 through 446 Processing helix chain 'Q' and resid 476 through 490 removed outlier: 3.815A pdb=" N HIS Q 482 " --> pdb=" O ARG Q 478 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN Q 486 " --> pdb=" O HIS Q 482 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL Q 489 " --> pdb=" O SER Q 485 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP Q 490 " --> pdb=" O GLN Q 486 " (cutoff:3.500A) Processing helix chain 'Q' and resid 495 through 510 removed outlier: 4.029A pdb=" N CYS Q 501 " --> pdb=" O GLN Q 497 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE Q 505 " --> pdb=" O CYS Q 501 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN Q 507 " --> pdb=" O SER Q 503 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA Q 508 " --> pdb=" O ARG Q 504 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU Q 510 " --> pdb=" O LYS Q 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 571 through 576 Processing helix chain 'S' and resid 590 through 601 removed outlier: 3.785A pdb=" N ARG S 601 " --> pdb=" O LYS S 597 " (cutoff:3.500A) Processing helix chain 'S' and resid 601 through 613 removed outlier: 3.870A pdb=" N SER S 605 " --> pdb=" O ARG S 601 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL S 607 " --> pdb=" O ARG S 603 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU S 610 " --> pdb=" O ARG S 606 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU S 612 " --> pdb=" O GLN S 608 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS S 613 " --> pdb=" O ASN S 609 " (cutoff:3.500A) Processing helix chain 'S' and resid 619 through 640 removed outlier: 3.925A pdb=" N LEU S 623 " --> pdb=" O GLU S 619 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR S 628 " --> pdb=" O GLN S 624 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER S 631 " --> pdb=" O GLY S 627 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE S 632 " --> pdb=" O TYR S 628 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA S 633 " --> pdb=" O ARG S 629 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN S 635 " --> pdb=" O SER S 631 " (cutoff:3.500A) Processing helix chain 'S' and resid 671 through 686 removed outlier: 3.972A pdb=" N PHE S 675 " --> pdb=" O SER S 671 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER S 676 " --> pdb=" O ILE S 672 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR S 686 " --> pdb=" O PHE S 682 " (cutoff:3.500A) Processing helix chain 'S' and resid 713 through 720 removed outlier: 4.224A pdb=" N LYS S 717 " --> pdb=" O ILE S 713 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU S 718 " --> pdb=" O PHE S 714 " (cutoff:3.500A) Processing helix chain 'S' and resid 730 through 742 removed outlier: 3.728A pdb=" N LYS S 734 " --> pdb=" O GLU S 730 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL S 737 " --> pdb=" O THR S 733 " (cutoff:3.500A) Processing helix chain 'S' and resid 752 through 760 removed outlier: 3.909A pdb=" N ASN S 758 " --> pdb=" O GLU S 754 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE S 760 " --> pdb=" O ILE S 756 " (cutoff:3.500A) Processing helix chain 'S' and resid 760 through 766 removed outlier: 3.802A pdb=" N GLY S 766 " --> pdb=" O ARG S 762 " (cutoff:3.500A) Processing helix chain 'S' and resid 767 through 773 removed outlier: 4.070A pdb=" N ILE S 772 " --> pdb=" O TYR S 768 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER S 773 " --> pdb=" O GLN S 769 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 36 removed outlier: 3.999A pdb=" N GLN R 22 " --> pdb=" O LYS R 18 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN R 25 " --> pdb=" O TYR R 21 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE R 27 " --> pdb=" O TYR R 23 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG R 33 " --> pdb=" O ARG R 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 131 removed outlier: 3.537A pdb=" N LYS R 130 " --> pdb=" O PHE R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 163 Processing helix chain 'R' and resid 166 through 172 Processing helix chain 'R' and resid 175 through 179 removed outlier: 3.820A pdb=" N LEU R 178 " --> pdb=" O ILE R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 192 Processing helix chain 'R' and resid 209 through 226 removed outlier: 3.601A pdb=" N ASP R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 219 " --> pdb=" O THR R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 240 removed outlier: 3.785A pdb=" N ALA R 232 " --> pdb=" O ASN R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 253 removed outlier: 4.183A pdb=" N LEU R 250 " --> pdb=" O GLN R 246 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP R 251 " --> pdb=" O ILE R 247 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 246 through 253' Processing helix chain 'R' and resid 254 through 259 removed outlier: 3.779A pdb=" N LEU R 258 " --> pdb=" O GLY R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 278 removed outlier: 3.620A pdb=" N LEU R 271 " --> pdb=" O GLY R 267 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE R 277 " --> pdb=" O TRP R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 299 removed outlier: 3.868A pdb=" N GLN R 298 " --> pdb=" O VAL R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 322 removed outlier: 3.702A pdb=" N SER R 316 " --> pdb=" O TYR R 312 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 355 removed outlier: 3.541A pdb=" N TRP R 352 " --> pdb=" O LYS R 348 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU R 354 " --> pdb=" O SER R 350 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR R 355 " --> pdb=" O GLU R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 379 removed outlier: 3.522A pdb=" N ILE R 367 " --> pdb=" O GLU R 363 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS R 372 " --> pdb=" O TYR R 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 421 removed outlier: 3.659A pdb=" N VAL R 404 " --> pdb=" O LYS R 400 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE R 405 " --> pdb=" O ILE R 401 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS R 406 " --> pdb=" O ASN R 402 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS R 409 " --> pdb=" O ILE R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 427 through 440 removed outlier: 3.736A pdb=" N GLU R 432 " --> pdb=" O SER R 428 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'M' and resid 69 through 74 removed outlier: 3.715A pdb=" N SER M 73 " --> pdb=" O SER M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 106 No H-bonds generated for 'chain 'M' and resid 104 through 106' Processing helix chain 'A' and resid 22 through 28 removed outlier: 4.181A pdb=" N LEU A 27 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.819A pdb=" N GLY A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N HIS A 43 " --> pdb=" O ASN A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 43' Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.722A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.597A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 174 through 197 removed outlier: 3.566A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 removed outlier: 3.773A pdb=" N HIS A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.581A pdb=" N ILE A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.571A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.656A pdb=" N SER A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.951A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 3.676A pdb=" N GLN A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.533A pdb=" N LEU A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.977A pdb=" N GLN A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.781A pdb=" N VAL A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.044A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.815A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.593A pdb=" N MET A 600 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 621 Processing helix chain 'A' and resid 640 through 650 removed outlier: 3.629A pdb=" N GLU A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 681 removed outlier: 3.801A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.660A pdb=" N GLN A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.817A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.571A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 824 removed outlier: 3.570A pdb=" N LEU A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.745A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 849 removed outlier: 3.587A pdb=" N LYS A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 857 Processing helix chain 'A' and resid 857 through 862 removed outlier: 3.528A pdb=" N VAL A 861 " --> pdb=" O ALA A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.505A pdb=" N LYS A 877 " --> pdb=" O PRO A 873 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 3.696A pdb=" N GLY A 890 " --> pdb=" O ASN A 886 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.539A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1011 removed outlier: 3.532A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 3.702A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1078 removed outlier: 3.969A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1105 removed outlier: 3.563A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.553A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.708A pdb=" N ASP A1142 " --> pdb=" O GLU A1138 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A1150 " --> pdb=" O SER A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1176 removed outlier: 3.676A pdb=" N ALA A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1199 Proline residue: A1196 - end of helix removed outlier: 4.313A pdb=" N GLN A1199 " --> pdb=" O GLU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.992A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1256 Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 4.929A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1318 removed outlier: 3.557A pdb=" N GLN A1314 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A1315 " --> pdb=" O GLU A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1337 removed outlier: 3.534A pdb=" N VAL A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1452 removed outlier: 3.546A pdb=" N GLN A1447 " --> pdb=" O GLN A1443 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A1449 " --> pdb=" O ASP A1445 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1494 removed outlier: 4.082A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A1494 " --> pdb=" O GLU A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 4.088A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.572A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 removed outlier: 4.176A pdb=" N ILE A1541 " --> pdb=" O VAL A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1573 removed outlier: 3.702A pdb=" N GLY A1554 " --> pdb=" O LEU A1550 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL A1555 " --> pdb=" O LYS A1551 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N GLU A1556 " --> pdb=" O THR A1552 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A1557 " --> pdb=" O TYR A1553 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A1572 " --> pdb=" O ASN A1568 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.596A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A1585 " --> pdb=" O HIS A1581 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A1588 " --> pdb=" O LEU A1584 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 3.698A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1628 removed outlier: 4.110A pdb=" N THR A1623 " --> pdb=" O CYS A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1644 removed outlier: 3.756A pdb=" N ILE A1641 " --> pdb=" O PRO A1637 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A1642 " --> pdb=" O SER A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1652 removed outlier: 3.673A pdb=" N GLY A1652 " --> pdb=" O VAL A1649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1652' Processing helix chain 'B' and resid 17 through 26 removed outlier: 3.946A pdb=" N GLU B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.564A pdb=" N GLU B 40 " --> pdb=" O PRO B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 4.146A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 58 through 63 removed outlier: 4.483A pdb=" N ASN B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 removed outlier: 3.538A pdb=" N SER B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.557A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.679A pdb=" N ALA B 223 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B 224 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 226' Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.665A pdb=" N LYS B 278 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 3.842A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 310 through 317 removed outlier: 3.580A pdb=" N LYS B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 4.443A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.614A pdb=" N LEU B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.810A pdb=" N ARG B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 433 removed outlier: 3.506A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.699A pdb=" N MET B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.673A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.507A pdb=" N TRP B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.556A pdb=" N LYS B 602 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 614 " --> pdb=" O TYR B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 removed outlier: 3.780A pdb=" N ILE B 681 " --> pdb=" O PRO B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.564A pdb=" N ASN B 695 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 697 " --> pdb=" O THR B 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 697' Processing helix chain 'B' and resid 711 through 724 removed outlier: 3.724A pdb=" N LYS B 723 " --> pdb=" O CYS B 719 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 724 " --> pdb=" O GLN B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.730A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.533A pdb=" N ASN B 764 " --> pdb=" O GLY B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 835 through 840 removed outlier: 4.220A pdb=" N LYS B 839 " --> pdb=" O GLU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.648A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.751A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.718A pdb=" N GLU B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B1003 " --> pdb=" O GLN B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 removed outlier: 4.192A pdb=" N ASP B1042 " --> pdb=" O MET B1039 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B1043 " --> pdb=" O VAL B1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1039 through 1043' Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 3.631A pdb=" N LEU B1079 " --> pdb=" O GLU B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1093 removed outlier: 3.620A pdb=" N LEU B1088 " --> pdb=" O THR B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1192 removed outlier: 3.600A pdb=" N SER B1190 " --> pdb=" O ASP B1186 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.645A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.617A pdb=" N HIS C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.133A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 174 through 179 removed outlier: 3.728A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.703A pdb=" N SER C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.805A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 311 through 330 removed outlier: 3.504A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.737A pdb=" N THR D 12 " --> pdb=" O THR D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 removed outlier: 3.633A pdb=" N GLN D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 removed outlier: 3.575A pdb=" N ILE D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 removed outlier: 3.599A pdb=" N ILE E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.767A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.528A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.686A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 127 removed outlier: 3.757A pdb=" N VAL E 124 " --> pdb=" O MET E 121 " (cutoff:3.500A) Proline residue: E 125 - end of helix Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.684A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.509A pdb=" N GLN E 174 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 72 Processing helix chain 'F' and resid 88 through 102 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.621A pdb=" N ALA F 126 " --> pdb=" O MET F 122 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 13 through 21 removed outlier: 3.511A pdb=" N ILE G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 66 through 70 removed outlier: 3.888A pdb=" N VAL G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.551A pdb=" N ASP H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR H 93 " --> pdb=" O ALA H 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 93' Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.507A pdb=" N ASN J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.642A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.697A pdb=" N ARG J 48 " --> pdb=" O TYR J 44 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.717A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 141 removed outlier: 3.511A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 56 removed outlier: 4.061A pdb=" N PHE O 55 " --> pdb=" O MET O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 removed outlier: 4.508A pdb=" N ASN O 76 " --> pdb=" O GLY O 72 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA O 79 " --> pdb=" O ALA O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 102 removed outlier: 3.517A pdb=" N LEU O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE O 95 " --> pdb=" O LYS O 91 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU O 97 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP O 98 " --> pdb=" O ASN O 94 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE O 99 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER O 102 " --> pdb=" O ASP O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 107 removed outlier: 3.507A pdb=" N ILE O 107 " --> pdb=" O ILE O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 111 No H-bonds generated for 'chain 'O' and resid 109 through 111' Processing helix chain 'O' and resid 112 through 121 removed outlier: 4.160A pdb=" N ILE O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN O 121 " --> pdb=" O GLN O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 128 removed outlier: 3.612A pdb=" N GLU O 127 " --> pdb=" O LYS O 124 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU O 128 " --> pdb=" O TRP O 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 124 through 128' Processing helix chain 'O' and resid 132 through 147 Processing helix chain 'O' and resid 150 through 160 removed outlier: 4.176A pdb=" N MET O 156 " --> pdb=" O GLN O 152 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 183 removed outlier: 3.719A pdb=" N MET O 175 " --> pdb=" O CYS O 171 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 197 removed outlier: 3.551A pdb=" N ILE O 190 " --> pdb=" O SER O 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP O 191 " --> pdb=" O MET O 187 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR O 192 " --> pdb=" O GLY O 188 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA O 195 " --> pdb=" O ASP O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 220 removed outlier: 4.200A pdb=" N LEU O 208 " --> pdb=" O THR O 204 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL O 209 " --> pdb=" O ARG O 205 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER O 213 " --> pdb=" O VAL O 209 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU O 216 " --> pdb=" O THR O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 225 Processing helix chain 'O' and resid 226 through 242 removed outlier: 4.134A pdb=" N LEU O 232 " --> pdb=" O GLN O 228 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU O 235 " --> pdb=" O SER O 231 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE O 238 " --> pdb=" O ILE O 234 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER O 239 " --> pdb=" O GLU O 235 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 327 through 347 removed outlier: 3.506A pdb=" N THR O 337 " --> pdb=" O ASP O 333 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU O 345 " --> pdb=" O THR O 341 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 369 removed outlier: 3.544A pdb=" N VAL O 360 " --> pdb=" O GLU O 356 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE O 361 " --> pdb=" O GLY O 357 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR O 365 " --> pdb=" O PHE O 361 " (cutoff:3.500A) Processing helix chain 'O' and resid 382 through 390 removed outlier: 3.754A pdb=" N GLN O 390 " --> pdb=" O PHE O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 393 through 408 removed outlier: 3.926A pdb=" N PHE O 399 " --> pdb=" O LEU O 395 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL O 401 " --> pdb=" O ASP O 397 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR O 402 " --> pdb=" O SER O 398 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 430 removed outlier: 4.155A pdb=" N SER O 420 " --> pdb=" O LYS O 416 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER O 426 " --> pdb=" O GLN O 422 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 457 removed outlier: 3.830A pdb=" N ILE O 440 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU O 450 " --> pdb=" O LEU O 446 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG O 452 " --> pdb=" O SER O 448 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR O 453 " --> pdb=" O TRP O 449 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL O 454 " --> pdb=" O LEU O 450 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE O 455 " --> pdb=" O ASN O 451 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU O 456 " --> pdb=" O ARG O 452 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG O 457 " --> pdb=" O TYR O 453 " (cutoff:3.500A) Processing helix chain 'O' and resid 458 through 461 removed outlier: 4.162A pdb=" N VAL O 461 " --> pdb=" O GLU O 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 458 through 461' Processing helix chain 'O' and resid 466 through 471 removed outlier: 3.508A pdb=" N ARG O 469 " --> pdb=" O GLY O 466 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE O 470 " --> pdb=" O MET O 467 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS O 471 " --> pdb=" O GLU O 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 466 through 471' Processing helix chain 'O' and resid 472 through 485 removed outlier: 4.097A pdb=" N GLN O 478 " --> pdb=" O TYR O 474 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS O 485 " --> pdb=" O CYS O 481 " (cutoff:3.500A) Processing helix chain 'O' and resid 498 through 500 No H-bonds generated for 'chain 'O' and resid 498 through 500' Processing helix chain 'O' and resid 501 through 511 removed outlier: 5.436A pdb=" N GLN O 507 " --> pdb=" O ASP O 503 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG O 508 " --> pdb=" O LYS O 504 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE O 511 " --> pdb=" O GLN O 507 " (cutoff:3.500A) Processing helix chain 'O' and resid 521 through 528 removed outlier: 3.536A pdb=" N LEU O 526 " --> pdb=" O GLU O 522 " (cutoff:3.500A) Processing helix chain 'O' and resid 528 through 533 removed outlier: 3.904A pdb=" N GLN O 533 " --> pdb=" O ALA O 529 " (cutoff:3.500A) Processing helix chain 'O' and resid 543 through 548 Processing helix chain 'O' and resid 582 through 591 removed outlier: 3.570A pdb=" N ASP O 587 " --> pdb=" O GLN O 583 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU O 588 " --> pdb=" O GLN O 584 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN O 589 " --> pdb=" O PHE O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 602 through 607 Processing sheet with id=AA1, first strand: chain 'Q' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'S' and resid 63 through 66 removed outlier: 6.704A pdb=" N VAL S 547 " --> pdb=" O LEU S 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 182 through 183 removed outlier: 4.015A pdb=" N LEU S 214 " --> pdb=" O ILE S 236 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE S 236 " --> pdb=" O LEU S 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 186 through 187 Processing sheet with id=AA5, first strand: chain 'S' and resid 242 through 246 removed outlier: 6.560A pdb=" N ILE S 264 " --> pdb=" O LYS S 243 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ILE S 245 " --> pdb=" O GLY S 262 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLY S 262 " --> pdb=" O ILE S 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 318 through 319 removed outlier: 3.575A pdb=" N GLY S 349 " --> pdb=" O TRP S 324 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE S 326 " --> pdb=" O LEU S 347 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU S 347 " --> pdb=" O ILE S 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 371 through 375 removed outlier: 6.603A pdb=" N MET S 380 " --> pdb=" O VAL S 393 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TRP S 389 " --> pdb=" O ASP S 384 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 402 through 404 removed outlier: 3.893A pdb=" N ILE S 421 " --> pdb=" O SER S 418 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU S 420 " --> pdb=" O LEU S 442 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 450 through 457 removed outlier: 3.599A pdb=" N LEU S 464 " --> pdb=" O PHE S 481 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS S 479 " --> pdb=" O ALA S 466 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER S 495 " --> pdb=" O MET S 478 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL S 480 " --> pdb=" O GLY S 493 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY S 493 " --> pdb=" O VAL S 480 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER S 482 " --> pdb=" O SER S 491 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N SER S 491 " --> pdb=" O SER S 482 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 505 through 510 removed outlier: 3.642A pdb=" N GLY S 507 " --> pdb=" O LYS S 540 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AB3, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.683A pdb=" N ARG A1295 " --> pdb=" O ASP A1268 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A1270 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N HIS A1293 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A1272 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A1291 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU A1274 " --> pdb=" O SER A1289 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER A1289 " --> pdb=" O GLU A1274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 94 through 99 removed outlier: 4.017A pdb=" N LEU I 99 " --> pdb=" O THR I 109 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR I 109 " --> pdb=" O LEU I 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 30 through 31 removed outlier: 3.606A pdb=" N VAL M 52 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 30 through 31 removed outlier: 4.025A pdb=" N GLU M 50 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS M 45 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS M 48 " --> pdb=" O LYS M 45 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 81 through 82 removed outlier: 6.787A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLU N 141 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR M 91 " --> pdb=" O VAL M 78 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU M 80 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN M 89 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE M 12 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU M 90 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER M 14 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS M 92 " --> pdb=" O SER M 14 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLN M 16 " --> pdb=" O LYS M 92 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 60 through 61 Processing sheet with id=AB9, first strand: chain 'A' and resid 1631 through 1632 Processing sheet with id=AC1, first strand: chain 'A' and resid 80 through 86 removed outlier: 8.987A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS A 85 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AC3, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.849A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 7.285A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.021A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AC7, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.444A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.544A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.544A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AD2, first strand: chain 'A' and resid 1031 through 1032 Processing sheet with id=AD3, first strand: chain 'A' and resid 1506 through 1508 removed outlier: 3.939A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.770A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.556A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 29 through 30 removed outlier: 7.188A pdb=" N TRP G 117 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE G 89 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS G 119 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU G 87 " --> pdb=" O HIS G 119 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 70 through 73 removed outlier: 3.683A pdb=" N ILE B 73 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 95 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER B 144 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 100 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 154 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 150 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.876A pdb=" N ARG B 119 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AE1, first strand: chain 'B' and resid 400 through 403 Processing sheet with id=AE2, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.070A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 259 through 264 Processing sheet with id=AE4, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AE5, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AE6, first strand: chain 'B' and resid 571 through 572 removed outlier: 5.183A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.290A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AE9, first strand: chain 'B' and resid 824 through 825 removed outlier: 3.632A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AF2, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AF3, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AF4, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AF5, first strand: chain 'C' and resid 44 through 47 removed outlier: 5.558A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.728A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.453A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AF8, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.693A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.631A pdb=" N TYR C 266 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.157A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AG3, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.917A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 132 through 133 removed outlier: 5.354A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.678A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 60 through 66 removed outlier: 6.717A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) 1562 hydrogen bonds defined for protein. 4353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 20.94 Time building geometry restraints manager: 20.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14058 1.33 - 1.45: 10167 1.45 - 1.57: 28082 1.57 - 1.69: 192 1.69 - 1.81: 374 Bond restraints: 52873 Sorted by residual: bond pdb=" O3' DG T 11 " pdb=" P DC T 12 " ideal model delta sigma weight residual 1.607 1.682 -0.075 1.50e-02 4.44e+03 2.51e+01 bond pdb=" C ILE S 672 " pdb=" N PRO S 673 " ideal model delta sigma weight residual 1.336 1.387 -0.051 1.23e-02 6.61e+03 1.75e+01 bond pdb=" C LEU Q 199 " pdb=" N PRO Q 200 " ideal model delta sigma weight residual 1.336 1.384 -0.048 1.20e-02 6.94e+03 1.61e+01 bond pdb=" O3' DC T 30 " pdb=" P DC T 31 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.50e-02 4.44e+03 1.44e+01 bond pdb=" C GLU S 754 " pdb=" N PRO S 755 " ideal model delta sigma weight residual 1.336 1.381 -0.045 1.23e-02 6.61e+03 1.36e+01 ... (remaining 52868 not shown) Histogram of bond angle deviations from ideal: 95.63 - 103.33: 655 103.33 - 111.03: 19142 111.03 - 118.73: 22889 118.73 - 126.43: 28162 126.43 - 134.13: 1012 Bond angle restraints: 71860 Sorted by residual: angle pdb=" O3' DT T 13 " pdb=" C3' DT T 13 " pdb=" C2' DT T 13 " ideal model delta sigma weight residual 111.50 95.63 15.87 1.50e+00 4.44e-01 1.12e+02 angle pdb=" C SER N 113 " pdb=" N GLU N 114 " pdb=" CA GLU N 114 " ideal model delta sigma weight residual 122.44 110.21 12.23 1.19e+00 7.06e-01 1.06e+02 angle pdb=" N LYS Q 101 " pdb=" CA LYS Q 101 " pdb=" C LYS Q 101 " ideal model delta sigma weight residual 111.28 102.45 8.83 1.09e+00 8.42e-01 6.56e+01 angle pdb=" O3' DC T 12 " pdb=" C3' DC T 12 " pdb=" C2' DC T 12 " ideal model delta sigma weight residual 111.50 99.48 12.02 1.50e+00 4.44e-01 6.42e+01 angle pdb=" O3' DT U 64 " pdb=" C3' DT U 64 " pdb=" C2' DT U 64 " ideal model delta sigma weight residual 111.50 101.46 10.04 1.50e+00 4.44e-01 4.48e+01 ... (remaining 71855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.52: 31168 33.52 - 67.04: 524 67.04 - 100.56: 49 100.56 - 134.08: 0 134.08 - 167.60: 8 Dihedral angle restraints: 31749 sinusoidal: 13676 harmonic: 18073 Sorted by residual: dihedral pdb=" CA SER S 288 " pdb=" C SER S 288 " pdb=" N SER S 289 " pdb=" CA SER S 289 " 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 MET Q 236 " pdb=" C MET Q 236 " pdb=" N ILE Q 237 " pdb=" CA ILE Q 237 " ideal model delta harmonic sigma weight residual 180.00 151.83 28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA GLU Q 36 " pdb=" C GLU Q 36 " pdb=" N GLY Q 37 " pdb=" CA GLY Q 37 " ideal model delta harmonic sigma weight residual 180.00 152.61 27.39 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 31746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 7186 0.099 - 0.198: 775 0.198 - 0.297: 42 0.297 - 0.395: 9 0.395 - 0.494: 2 Chirality restraints: 8014 Sorted by residual: chirality pdb=" CB ILE R 175 " pdb=" CA ILE R 175 " pdb=" CG1 ILE R 175 " pdb=" CG2 ILE R 175 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CB ILE A1457 " pdb=" CA ILE A1457 " pdb=" CG1 ILE A1457 " pdb=" CG2 ILE A1457 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CB ILE R 140 " pdb=" CA ILE R 140 " pdb=" CG1 ILE R 140 " pdb=" CG2 ILE R 140 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 8011 not shown) Planarity restraints: 8879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA U 61 " -0.010 2.00e-02 2.50e+03 3.20e-02 2.82e+01 pdb=" N9 DA U 61 " -0.003 2.00e-02 2.50e+03 pdb=" C8 DA U 61 " 0.058 2.00e-02 2.50e+03 pdb=" N7 DA U 61 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA U 61 " -0.082 2.00e-02 2.50e+03 pdb=" C6 DA U 61 " 0.009 2.00e-02 2.50e+03 pdb=" N6 DA U 61 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DA U 61 " 0.032 2.00e-02 2.50e+03 pdb=" C2 DA U 61 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA U 61 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA U 61 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP S 438 " 0.024 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C TRP S 438 " -0.082 2.00e-02 2.50e+03 pdb=" O TRP S 438 " 0.031 2.00e-02 2.50e+03 pdb=" N LYS S 439 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 785 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ASP B 785 " -0.062 2.00e-02 2.50e+03 pdb=" O ASP B 785 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B 786 " 0.021 2.00e-02 2.50e+03 ... (remaining 8876 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 679 2.64 - 3.20: 43159 3.20 - 3.77: 77991 3.77 - 4.33: 111649 4.33 - 4.90: 179654 Nonbonded interactions: 413132 Sorted by model distance: nonbonded pdb=" O PRO N 112 " pdb=" O SER N 113 " model vdw 2.072 3.040 nonbonded pdb=" OD1 ASN Q 14 " pdb="ZN ZN Q 601 " model vdw 2.187 2.230 nonbonded pdb=" OE1 GLU A 646 " pdb=" OG1 THR B1084 " model vdw 2.216 2.440 nonbonded pdb=" OG1 THR A1458 " pdb=" OE1 GLU A1475 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR S 234 " pdb=" O VAL S 284 " model vdw 2.226 2.440 ... (remaining 413127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.670 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: 0.040 Extract box with map and model: 15.170 Check model and map are aligned: 0.710 Set scattering table: 0.430 Process input model: 135.310 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.008 0.109 52873 Z= 0.535 Angle : 1.090 15.874 71860 Z= 0.595 Chirality : 0.062 0.494 8014 Planarity : 0.007 0.081 8879 Dihedral : 12.672 167.596 20029 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.13 % Favored : 91.82 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.08), residues: 6079 helix: -4.28 (0.05), residues: 2146 sheet: -2.66 (0.16), residues: 792 loop : -2.63 (0.09), residues: 3141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1470 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1448 time to evaluate : 6.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 1458 average time/residue: 0.6678 time to fit residues: 1551.3122 Evaluate side-chains 773 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 766 time to evaluate : 5.858 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4280 time to fit residues: 13.2103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 523 optimal weight: 0.7980 chunk 469 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 316 optimal weight: 20.0000 chunk 251 optimal weight: 0.8980 chunk 485 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 295 optimal weight: 0.8980 chunk 361 optimal weight: 0.9980 chunk 563 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 71 GLN Q 84 GLN Q 194 GLN ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 228 ASN Q 272 GLN Q 283 ASN ** S 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 490 GLN S 579 ASN ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS R 276 GLN R 287 ASN I 91 ASN I 95 ASN A 31 GLN A 43 HIS A 382 GLN A1237 GLN A1319 ASN A1323 HIS A1447 GLN A1629 ASN B 62 ASN B 128 GLN B 147 ASN B 319 HIS B 462 GLN B 547 HIS ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1199 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 8 ASN E 146 HIS G 65 HIS G 216 HIS ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN L 53 HIS O 92 ASN ** O 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 52873 Z= 0.220 Angle : 0.679 11.191 71860 Z= 0.363 Chirality : 0.045 0.179 8014 Planarity : 0.005 0.053 8879 Dihedral : 12.790 179.337 7662 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.48 % Favored : 93.47 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.09), residues: 6079 helix: -2.80 (0.08), residues: 2183 sheet: -2.06 (0.17), residues: 751 loop : -2.19 (0.10), residues: 3145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 892 time to evaluate : 5.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 128 outliers final: 60 residues processed: 974 average time/residue: 0.5977 time to fit residues: 958.8645 Evaluate side-chains 757 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 697 time to evaluate : 4.518 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.4467 time to fit residues: 57.7867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 312 optimal weight: 5.9990 chunk 174 optimal weight: 0.4980 chunk 468 optimal weight: 1.9990 chunk 383 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 564 optimal weight: 3.9990 chunk 609 optimal weight: 5.9990 chunk 502 optimal weight: 0.0970 chunk 559 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 chunk 452 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 283 ASN S 348 HIS ** S 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 665 ASN S 687 GLN ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS I 91 ASN I 95 ASN ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 HIS A1237 GLN A1323 HIS ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN J 53 HIS L 66 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 52873 Z= 0.179 Angle : 0.609 12.152 71860 Z= 0.322 Chirality : 0.044 0.238 8014 Planarity : 0.004 0.047 8879 Dihedral : 12.834 179.727 7662 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.14 % Favored : 93.85 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.10), residues: 6079 helix: -1.86 (0.10), residues: 2195 sheet: -1.67 (0.18), residues: 755 loop : -1.94 (0.10), residues: 3129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 825 time to evaluate : 5.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 43 residues processed: 883 average time/residue: 0.5968 time to fit residues: 871.3296 Evaluate side-chains 712 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 669 time to evaluate : 5.503 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4432 time to fit residues: 42.7518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 557 optimal weight: 0.0060 chunk 424 optimal weight: 1.9990 chunk 292 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 269 optimal weight: 0.7980 chunk 378 optimal weight: 2.9990 chunk 566 optimal weight: 3.9990 chunk 599 optimal weight: 0.5980 chunk 295 optimal weight: 4.9990 chunk 536 optimal weight: 5.9990 chunk 161 optimal weight: 0.0770 overall best weight: 0.3112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 157 HIS Q 225 GLN ** S 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 687 GLN R 221 HIS R 407 HIS I 91 ASN I 95 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A1237 GLN A1323 HIS A1629 ASN B 147 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 ASN L 66 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 52873 Z= 0.149 Angle : 0.567 10.164 71860 Z= 0.299 Chirality : 0.043 0.263 8014 Planarity : 0.004 0.048 8879 Dihedral : 12.860 179.831 7662 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.10), residues: 6079 helix: -1.14 (0.10), residues: 2192 sheet: -1.48 (0.18), residues: 757 loop : -1.71 (0.11), residues: 3130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 787 time to evaluate : 6.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 38 residues processed: 845 average time/residue: 0.5812 time to fit residues: 825.5089 Evaluate side-chains 725 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 687 time to evaluate : 5.489 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4462 time to fit residues: 37.6087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 499 optimal weight: 4.9990 chunk 340 optimal weight: 0.3980 chunk 8 optimal weight: 7.9990 chunk 446 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 511 optimal weight: 0.6980 chunk 414 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 306 optimal weight: 0.5980 chunk 537 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 ASN R 221 HIS ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 HIS ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 106 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 ASN A1323 HIS A1447 GLN A1527 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 ASN G 20 HIS G 119 HIS L 66 GLN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 52873 Z= 0.253 Angle : 0.613 9.841 71860 Z= 0.321 Chirality : 0.045 0.218 8014 Planarity : 0.004 0.077 8879 Dihedral : 13.009 179.844 7662 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.10), residues: 6079 helix: -0.89 (0.11), residues: 2195 sheet: -1.36 (0.18), residues: 764 loop : -1.65 (0.11), residues: 3120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 721 time to evaluate : 4.809 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 54 residues processed: 787 average time/residue: 0.5606 time to fit residues: 737.2982 Evaluate side-chains 714 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 660 time to evaluate : 4.553 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.4369 time to fit residues: 52.2001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 201 optimal weight: 4.9990 chunk 539 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 599 optimal weight: 0.5980 chunk 497 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 14 ASN Q 33 HIS ** Q 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 624 GLN R 221 HIS R 223 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1447 GLN A1500 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS O 92 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 52873 Z= 0.380 Angle : 0.705 10.399 71860 Z= 0.368 Chirality : 0.048 0.251 8014 Planarity : 0.005 0.073 8879 Dihedral : 13.245 179.493 7662 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.10), residues: 6079 helix: -1.01 (0.11), residues: 2181 sheet: -1.35 (0.18), residues: 767 loop : -1.71 (0.11), residues: 3131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 680 time to evaluate : 4.693 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 60 residues processed: 755 average time/residue: 0.5800 time to fit residues: 731.2952 Evaluate side-chains 699 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 639 time to evaluate : 4.454 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.4268 time to fit residues: 54.6964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 578 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 341 optimal weight: 2.9990 chunk 438 optimal weight: 0.9980 chunk 339 optimal weight: 0.6980 chunk 504 optimal weight: 0.0070 chunk 334 optimal weight: 0.5980 chunk 597 optimal weight: 7.9990 chunk 373 optimal weight: 1.9990 chunk 364 optimal weight: 0.7980 chunk 275 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS I 91 ASN M 89 GLN A 93 GLN A 260 GLN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1447 GLN A1527 GLN B 147 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 GLN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 52873 Z= 0.169 Angle : 0.579 10.972 71860 Z= 0.303 Chirality : 0.043 0.244 8014 Planarity : 0.004 0.059 8879 Dihedral : 13.063 178.342 7662 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.11), residues: 6079 helix: -0.56 (0.11), residues: 2188 sheet: -1.24 (0.18), residues: 761 loop : -1.52 (0.11), residues: 3130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 742 time to evaluate : 4.372 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 22 residues processed: 771 average time/residue: 0.5578 time to fit residues: 721.7158 Evaluate side-chains 686 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 664 time to evaluate : 4.554 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4701 time to fit residues: 25.8197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 369 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 356 optimal weight: 0.7980 chunk 180 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 379 optimal weight: 0.8980 chunk 407 optimal weight: 0.2980 chunk 295 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 469 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 483 HIS S 608 GLN A 260 GLN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1447 GLN B 147 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 52873 Z= 0.181 Angle : 0.573 11.150 71860 Z= 0.300 Chirality : 0.043 0.208 8014 Planarity : 0.004 0.058 8879 Dihedral : 12.997 178.976 7662 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.11), residues: 6079 helix: -0.31 (0.11), residues: 2186 sheet: -1.13 (0.19), residues: 749 loop : -1.45 (0.11), residues: 3144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 697 time to evaluate : 4.909 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 720 average time/residue: 0.6096 time to fit residues: 735.2284 Evaluate side-chains 691 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 668 time to evaluate : 4.327 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4319 time to fit residues: 24.3360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 543 optimal weight: 0.0030 chunk 572 optimal weight: 8.9990 chunk 522 optimal weight: 0.8980 chunk 556 optimal weight: 1.9990 chunk 335 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 437 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 503 optimal weight: 0.9980 chunk 526 optimal weight: 0.3980 chunk 554 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 87 GLN ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 52873 Z= 0.172 Angle : 0.567 11.191 71860 Z= 0.295 Chirality : 0.043 0.183 8014 Planarity : 0.004 0.054 8879 Dihedral : 12.930 178.842 7662 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 6079 helix: -0.14 (0.11), residues: 2188 sheet: -1.08 (0.19), residues: 754 loop : -1.39 (0.11), residues: 3137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 700 time to evaluate : 4.317 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 714 average time/residue: 0.5443 time to fit residues: 647.0850 Evaluate side-chains 674 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 661 time to evaluate : 5.163 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3965 time to fit residues: 16.5036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 365 optimal weight: 5.9990 chunk 588 optimal weight: 0.7980 chunk 359 optimal weight: 0.0170 chunk 279 optimal weight: 0.8980 chunk 409 optimal weight: 0.0470 chunk 617 optimal weight: 3.9990 chunk 568 optimal weight: 0.4980 chunk 491 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 379 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 225 GLN S 454 GLN R 221 HIS I 91 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1447 GLN A1662 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 52873 Z= 0.146 Angle : 0.554 13.953 71860 Z= 0.288 Chirality : 0.042 0.177 8014 Planarity : 0.004 0.063 8879 Dihedral : 12.854 178.608 7662 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 6079 helix: 0.05 (0.11), residues: 2205 sheet: -1.06 (0.19), residues: 745 loop : -1.35 (0.11), residues: 3129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 731 time to evaluate : 4.759 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 735 average time/residue: 0.5265 time to fit residues: 645.8650 Evaluate side-chains 683 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 678 time to evaluate : 4.317 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4091 time to fit residues: 9.9367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 390 optimal weight: 2.9990 chunk 523 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 453 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 492 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 505 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 HIS ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 ASN M 89 GLN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1447 GLN B1038 HIS ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.192549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161372 restraints weight = 73490.649| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.25 r_work: 0.3623 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 52873 Z= 0.247 Angle : 0.603 13.574 71860 Z= 0.313 Chirality : 0.045 0.325 8014 Planarity : 0.004 0.051 8879 Dihedral : 12.913 179.861 7662 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.11), residues: 6079 helix: -0.05 (0.11), residues: 2206 sheet: -1.09 (0.19), residues: 757 loop : -1.38 (0.11), residues: 3116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13406.49 seconds wall clock time: 237 minutes 39.52 seconds (14259.52 seconds total)