Starting phenix.real_space_refine on Sun Mar 17 23:56:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgc_27421/03_2024/8dgc_27421_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgc_27421/03_2024/8dgc_27421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgc_27421/03_2024/8dgc_27421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgc_27421/03_2024/8dgc_27421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgc_27421/03_2024/8dgc_27421_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgc_27421/03_2024/8dgc_27421_updated.pdb" } resolution = 3.4 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= 0.002 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 P 24 5.49 5 Mg 8 5.21 5 S 302 5.16 5 C 51536 2.51 5 N 14302 2.21 5 O 15428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 55": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 806": "OE1" <-> "OE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "A TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "A GLU 1034": "OE1" <-> "OE2" Residue "A PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1062": "OE1" <-> "OE2" Residue "A ASP 1195": "OD1" <-> "OD2" Residue "A ASP 1308": "OD1" <-> "OD2" Residue "A PHE 1387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1497": "OD1" <-> "OD2" Residue "A GLU 1567": "OE1" <-> "OE2" Residue "A ASP 1763": "OD1" <-> "OD2" Residue "A PHE 1864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1902": "OE1" <-> "OE2" Residue "A PHE 1971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2042": "OD1" <-> "OD2" Residue "A PHE 2070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B ASP 245": "OD1" <-> "OD2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B ASP 588": "OD1" <-> "OD2" Residue "B ASP 605": "OD1" <-> "OD2" Residue "B GLU 652": "OE1" <-> "OE2" Residue "B ASP 660": "OD1" <-> "OD2" Residue "B GLU 764": "OE1" <-> "OE2" Residue "B GLU 914": "OE1" <-> "OE2" Residue "B TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 938": "OE1" <-> "OE2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B ASP 1124": "OD1" <-> "OD2" Residue "B PHE 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1153": "OD1" <-> "OD2" Residue "B GLU 1154": "OE1" <-> "OE2" Residue "B GLU 1323": "OE1" <-> "OE2" Residue "B PHE 1403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1629": "OD1" <-> "OD2" Residue "B GLU 1854": "OE1" <-> "OE2" Residue "B PHE 1864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1944": "OD1" <-> "OD2" Residue "B GLU 1947": "OE1" <-> "OE2" Residue "B TYR 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2012": "OE1" <-> "OE2" Residue "B GLU 2031": "OE1" <-> "OE2" Residue "B PHE 2070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 206": "OD1" <-> "OD2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C GLU 454": "OE1" <-> "OE2" Residue "C GLU 582": "OE1" <-> "OE2" Residue "C GLU 764": "OE1" <-> "OE2" Residue "C ASP 774": "OD1" <-> "OD2" Residue "C GLU 806": "OE1" <-> "OE2" Residue "C GLU 902": "OE1" <-> "OE2" Residue "C TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1023": "OE1" <-> "OE2" Residue "C GLU 1034": "OE1" <-> "OE2" Residue "C PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1062": "OE1" <-> "OE2" Residue "C ASP 1195": "OD1" <-> "OD2" Residue "C ASP 1308": "OD1" <-> "OD2" Residue "C GLU 1323": "OE1" <-> "OE2" Residue "C PHE 1387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1497": "OD1" <-> "OD2" Residue "C GLU 1567": "OE1" <-> "OE2" Residue "C ASP 1763": "OD1" <-> "OD2" Residue "C PHE 1864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1902": "OE1" <-> "OE2" Residue "C PHE 1971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2042": "OD1" <-> "OD2" Residue "C PHE 2070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D ASP 245": "OD1" <-> "OD2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D GLU 582": "OE1" <-> "OE2" Residue "D ASP 588": "OD1" <-> "OD2" Residue "D ASP 605": "OD1" <-> "OD2" Residue "D GLU 652": "OE1" <-> "OE2" Residue "D ASP 660": "OD1" <-> "OD2" Residue "D GLU 764": "OE1" <-> "OE2" Residue "D GLU 914": "OE1" <-> "OE2" Residue "D TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 938": "OE1" <-> "OE2" Residue "D GLU 1041": "OE1" <-> "OE2" Residue "D ASP 1124": "OD1" <-> "OD2" Residue "D PHE 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1153": "OD1" <-> "OD2" Residue "D GLU 1154": "OE1" <-> "OE2" Residue "D GLU 1211": "OE1" <-> "OE2" Residue "D GLU 1323": "OE1" <-> "OE2" Residue "D PHE 1403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1497": "OD1" <-> "OD2" Residue "D ASP 1629": "OD1" <-> "OD2" Residue "D GLU 1854": "OE1" <-> "OE2" Residue "D PHE 1864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1944": "OD1" <-> "OD2" Residue "D GLU 1947": "OE1" <-> "OE2" Residue "D TYR 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2012": "OE1" <-> "OE2" Residue "D GLU 2031": "OE1" <-> "OE2" Residue "D PHE 2070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "F PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 206": "OE1" <-> "OE2" Residue "F GLU 252": "OE1" <-> "OE2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 372": "OD1" <-> "OD2" Residue "F GLU 390": "OE1" <-> "OE2" Residue "F ASP 460": "OD1" <-> "OD2" Residue "G GLU 114": "OE1" <-> "OE2" Residue "G ASP 123": "OD1" <-> "OD2" Residue "G PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H ASP 123": "OD1" <-> "OD2" Residue "H PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H GLU 252": "OE1" <-> "OE2" Residue "H PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 390": "OE1" <-> "OE2" Residue "H ASP 460": "OD1" <-> "OD2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 81600 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 16152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2028, 16152 Classifications: {'peptide': 2028} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 1942} Chain breaks: 5 Chain: "B" Number of atoms: 15974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2004, 15974 Classifications: {'peptide': 2004} Link IDs: {'PCIS': 1, 'PTRANS': 83, 'TRANS': 1919} Chain breaks: 6 Chain: "C" Number of atoms: 16152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2028, 16152 Classifications: {'peptide': 2028} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 1942} Chain breaks: 5 Chain: "D" Number of atoms: 15974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2004, 15974 Classifications: {'peptide': 2004} Link IDs: {'PCIS': 1, 'PTRANS': 83, 'TRANS': 1919} Chain breaks: 6 Chain: "E" Number of atoms: 4273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4273 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 26, 'TRANS': 511} Chain: "F" Number of atoms: 4273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4273 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 26, 'TRANS': 511} Chain: "G" Number of atoms: 4273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4273 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 26, 'TRANS': 511} Chain: "H" Number of atoms: 4273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4273 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 26, 'TRANS': 511} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 33.40, per 1000 atoms: 0.41 Number of scatterers: 81600 At special positions: 0 Unit cell: (240.037, 239.168, 232.21, 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) S 302 16.00 P 24 15.00 Mg 8 11.99 O 15428 8.00 N 14302 7.00 C 51536 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: 26.20 Conformation dependent library (CDL) restraints added in 10.6 seconds 20312 Ramachandran restraints generated. 10156 Oldfield, 0 Emsley, 10156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 504 helices and 24 sheets defined 53.1% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 20.01 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 4.011A pdb=" N SER A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A 11 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ARG A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 96 through 116 removed outlier: 4.616A pdb=" N LYS A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 4.749A pdb=" N THR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.924A pdb=" N ILE A 175 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 removed outlier: 4.481A pdb=" N ASN A 194 " --> pdb=" O TRP A 190 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 removed outlier: 3.635A pdb=" N LYS A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.798A pdb=" N ALA A 269 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 272 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 274 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.676A pdb=" N THR A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLU A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N HIS A 303 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 331 through 344 removed outlier: 4.756A pdb=" N VAL A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 380 removed outlier: 3.567A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 372 " --> pdb=" O HIS A 368 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 402 removed outlier: 4.246A pdb=" N GLN A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.820A pdb=" N GLN A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 477 Processing helix chain 'A' and resid 482 through 491 removed outlier: 4.325A pdb=" N GLN A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 532 through 543 removed outlier: 4.051A pdb=" N ASP A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 589 through 598 Processing helix chain 'A' and resid 603 through 618 removed outlier: 3.860A pdb=" N HIS A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Proline residue: A 615 - end of helix removed outlier: 4.926A pdb=" N LYS A 618 " --> pdb=" O ARG A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 633 Proline residue: A 628 - end of helix removed outlier: 3.568A pdb=" N LEU A 632 " --> pdb=" O PRO A 628 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'A' and resid 655 through 676 removed outlier: 3.720A pdb=" N ASP A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 662 " --> pdb=" O ARG A 658 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 663 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 671 " --> pdb=" O GLN A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 713 removed outlier: 4.533A pdb=" N GLY A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 707 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 724 Processing helix chain 'A' and resid 736 through 747 removed outlier: 3.951A pdb=" N TYR A 741 " --> pdb=" O ASN A 738 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 744 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 745 " --> pdb=" O ALA A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 771 removed outlier: 3.592A pdb=" N SER A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TRP A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 779 removed outlier: 3.837A pdb=" N ARG A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 798 Processing helix chain 'A' and resid 800 through 809 removed outlier: 3.744A pdb=" N GLU A 806 " --> pdb=" O ALA A 802 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 807 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG A 809 " --> pdb=" O ARG A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 829 removed outlier: 3.803A pdb=" N ALA A 829 " --> pdb=" O MET A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 847 through 859 removed outlier: 3.576A pdb=" N LEU A 855 " --> pdb=" O MET A 851 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 876 Processing helix chain 'A' and resid 893 through 906 Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 929 through 932 removed outlier: 3.570A pdb=" N THR A 932 " --> pdb=" O TYR A 929 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 929 through 932' Processing helix chain 'A' and resid 939 through 952 Processing helix chain 'A' and resid 959 through 962 No H-bonds generated for 'chain 'A' and resid 959 through 962' Processing helix chain 'A' and resid 965 through 972 Processing helix chain 'A' and resid 981 through 989 Processing helix chain 'A' and resid 991 through 1004 Proline residue: A 995 - end of helix removed outlier: 4.016A pdb=" N ASN A 998 " --> pdb=" O PRO A 995 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TRP A1000 " --> pdb=" O TYR A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1028 removed outlier: 5.976A pdb=" N GLU A1014 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A1017 " --> pdb=" O GLU A1014 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A1018 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP A1019 " --> pdb=" O GLU A1016 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN A1021 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A1024 " --> pdb=" O GLN A1021 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A1026 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1053 removed outlier: 3.507A pdb=" N ASN A1044 " --> pdb=" O ASN A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1069 removed outlier: 3.578A pdb=" N ILE A1064 " --> pdb=" O ASP A1060 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A1069 " --> pdb=" O ILE A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1089 removed outlier: 3.601A pdb=" N ALA A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A1089 " --> pdb=" O SER A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1106 removed outlier: 3.957A pdb=" N TYR A1098 " --> pdb=" O GLY A1094 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A1101 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1129 removed outlier: 3.948A pdb=" N LEU A1129 " --> pdb=" O LEU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1149 removed outlier: 4.015A pdb=" N GLU A1139 " --> pdb=" O PRO A1135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A1140 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A1141 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR A1148 " --> pdb=" O ALA A1144 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN A1149 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1169 removed outlier: 3.564A pdb=" N TYR A1168 " --> pdb=" O ASP A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1193 removed outlier: 3.576A pdb=" N LEU A1183 " --> pdb=" O ILE A1179 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A1184 " --> pdb=" O SER A1180 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1199 No H-bonds generated for 'chain 'A' and resid 1197 through 1199' Processing helix chain 'A' and resid 1202 through 1212 Processing helix chain 'A' and resid 1214 through 1227 removed outlier: 3.745A pdb=" N SER A1222 " --> pdb=" O LEU A1218 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A1223 " --> pdb=" O ALA A1219 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A1225 " --> pdb=" O ILE A1221 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP A1226 " --> pdb=" O SER A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1245 Processing helix chain 'A' and resid 1251 through 1259 Proline residue: A1256 - end of helix removed outlier: 5.532A pdb=" N THR A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1274 Processing helix chain 'A' and resid 1280 through 1294 Processing helix chain 'A' and resid 1301 through 1314 removed outlier: 3.544A pdb=" N LYS A1306 " --> pdb=" O GLN A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1328 removed outlier: 4.028A pdb=" N LEU A1328 " --> pdb=" O ARG A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1356 Processing helix chain 'A' and resid 1365 through 1376 removed outlier: 3.728A pdb=" N SER A1369 " --> pdb=" O ILE A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1394 Processing helix chain 'A' and resid 1400 through 1410 Processing helix chain 'A' and resid 1417 through 1424 removed outlier: 3.739A pdb=" N LEU A1422 " --> pdb=" O LYS A1419 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1431 Processing helix chain 'A' and resid 1433 through 1449 removed outlier: 3.954A pdb=" N LYS A1444 " --> pdb=" O ALA A1440 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU A1445 " --> pdb=" O GLY A1441 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A1446 " --> pdb=" O LEU A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1472 Processing helix chain 'A' and resid 1476 through 1488 removed outlier: 3.599A pdb=" N GLY A1481 " --> pdb=" O LYS A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1501 removed outlier: 3.655A pdb=" N SER A1501 " --> pdb=" O ASP A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1508 removed outlier: 5.140A pdb=" N SER A1508 " --> pdb=" O GLY A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1526 removed outlier: 3.807A pdb=" N ASP A1517 " --> pdb=" O ASN A1513 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A1524 " --> pdb=" O SER A1520 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A1525 " --> pdb=" O TYR A1521 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE A1526 " --> pdb=" O ALA A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1543 No H-bonds generated for 'chain 'A' and resid 1541 through 1543' Processing helix chain 'A' and resid 1549 through 1561 Processing helix chain 'A' and resid 1566 through 1580 Processing helix chain 'A' and resid 1585 through 1597 Processing helix chain 'A' and resid 1601 through 1603 No H-bonds generated for 'chain 'A' and resid 1601 through 1603' Processing helix chain 'A' and resid 1612 through 1629 removed outlier: 3.565A pdb=" N ARG A1625 " --> pdb=" O ILE A1621 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A1628 " --> pdb=" O ALA A1624 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP A1629 " --> pdb=" O ARG A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1632 through 1644 Proline residue: A1636 - end of helix removed outlier: 5.496A pdb=" N GLY A1639 " --> pdb=" O PRO A1636 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A1642 " --> pdb=" O GLY A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1652 through 1667 Processing helix chain 'A' and resid 1675 through 1683 removed outlier: 3.555A pdb=" N ASN A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN A1683 " --> pdb=" O ASN A1679 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 4.486A pdb=" N LYS A1717 " --> pdb=" O PRO A1713 " (cutoff:3.500A) Proline residue: A1718 - end of helix removed outlier: 3.794A pdb=" N CYS A1722 " --> pdb=" O PRO A1718 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1727 through 1740 Proline residue: A1732 - end of helix Processing helix chain 'A' and resid 1750 through 1752 No H-bonds generated for 'chain 'A' and resid 1750 through 1752' Processing helix chain 'A' and resid 1754 through 1757 No H-bonds generated for 'chain 'A' and resid 1754 through 1757' Processing helix chain 'A' and resid 1779 through 1798 removed outlier: 3.723A pdb=" N PHE A1789 " --> pdb=" O TYR A1785 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A1793 " --> pdb=" O PHE A1789 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLN A1794 " --> pdb=" O MET A1790 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A1795 " --> pdb=" O THR A1791 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A1797 " --> pdb=" O GLY A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1820 removed outlier: 4.536A pdb=" N ARG A1819 " --> pdb=" O ASP A1815 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS A1820 " --> pdb=" O TRP A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1832 No H-bonds generated for 'chain 'A' and resid 1830 through 1832' Processing helix chain 'A' and resid 1842 through 1849 removed outlier: 4.727A pdb=" N SER A1849 " --> pdb=" O LEU A1845 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1857 removed outlier: 4.115A pdb=" N ALA A1857 " --> pdb=" O ASP A1853 " (cutoff:3.500A) Processing helix chain 'A' and resid 1861 through 1868 removed outlier: 3.855A pdb=" N LEU A1868 " --> pdb=" O ASN A1865 " (cutoff:3.500A) Processing helix chain 'A' and resid 1903 through 1912 removed outlier: 4.157A pdb=" N ARG A1909 " --> pdb=" O LEU A1905 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A1912 " --> pdb=" O LEU A1908 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1954 removed outlier: 3.922A pdb=" N PHE A1954 " --> pdb=" O ILE A1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1951 through 1954' Processing helix chain 'A' and resid 1970 through 1976 Processing helix chain 'A' and resid 2023 through 2033 Processing helix chain 'B' and resid 16 through 29 removed outlier: 3.684A pdb=" N ALA B 21 " --> pdb=" O HIS B 17 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG B 24 " --> pdb=" O TRP B 20 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 116 removed outlier: 4.130A pdb=" N LYS B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 4.363A pdb=" N THR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.979A pdb=" N ALA B 160 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS B 164 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.917A pdb=" N PHE B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 179 " --> pdb=" O ILE B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'B' and resid 206 through 209 Processing helix chain 'B' and resid 211 through 223 removed outlier: 3.671A pdb=" N LYS B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 242 Processing helix chain 'B' and resid 246 through 249 No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 268 through 277 removed outlier: 4.073A pdb=" N GLN B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 302 removed outlier: 5.062A pdb=" N GLU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU B 302 " --> pdb=" O THR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 331 through 344 removed outlier: 4.734A pdb=" N VAL B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 378 removed outlier: 3.661A pdb=" N ARG B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 403 removed outlier: 3.873A pdb=" N GLN B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 415 removed outlier: 4.714A pdb=" N ARG B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.705A pdb=" N ARG B 433 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU B 434 " --> pdb=" O TYR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 462 removed outlier: 3.926A pdb=" N GLN B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B 462 " --> pdb=" O HIS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 482 through 491 removed outlier: 4.523A pdb=" N GLN B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 502 removed outlier: 3.959A pdb=" N LEU B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 526 removed outlier: 3.801A pdb=" N LYS B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 544 removed outlier: 3.645A pdb=" N ALA B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 Processing helix chain 'B' and resid 563 through 573 Processing helix chain 'B' and resid 589 through 598 Processing helix chain 'B' and resid 603 through 618 Proline residue: B 615 - end of helix removed outlier: 5.077A pdb=" N LYS B 618 " --> pdb=" O ARG B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 634 Proline residue: B 628 - end of helix removed outlier: 3.605A pdb=" N GLU B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 645 Processing helix chain 'B' and resid 655 through 675 removed outlier: 4.095A pdb=" N ASP B 660 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS B 671 " --> pdb=" O GLN B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 704 removed outlier: 3.703A pdb=" N LYS B 684 " --> pdb=" O GLN B 680 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 713 removed outlier: 3.989A pdb=" N LYS B 712 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 725 Processing helix chain 'B' and resid 736 through 747 removed outlier: 3.762A pdb=" N TYR B 741 " --> pdb=" O ASN B 738 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 742 " --> pdb=" O ALA B 739 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 744 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 745 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 747 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 771 removed outlier: 3.803A pdb=" N SER B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TRP B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 779 removed outlier: 3.802A pdb=" N ARG B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 797 Processing helix chain 'B' and resid 800 through 809 removed outlier: 3.757A pdb=" N GLU B 806 " --> pdb=" O ALA B 802 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 807 " --> pdb=" O ALA B 803 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 808 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG B 809 " --> pdb=" O ARG B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 829 removed outlier: 3.844A pdb=" N ILE B 822 " --> pdb=" O ASP B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 843 Processing helix chain 'B' and resid 847 through 859 removed outlier: 3.808A pdb=" N LYS B 859 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 878 removed outlier: 4.689A pdb=" N SER B 878 " --> pdb=" O ARG B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 906 Processing helix chain 'B' and resid 912 through 922 removed outlier: 3.597A pdb=" N TYR B 922 " --> pdb=" O LEU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 932 Processing helix chain 'B' and resid 939 through 952 Processing helix chain 'B' and resid 959 through 962 No H-bonds generated for 'chain 'B' and resid 959 through 962' Processing helix chain 'B' and resid 965 through 971 Processing helix chain 'B' and resid 981 through 989 removed outlier: 4.001A pdb=" N LEU B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Proline residue: B 995 - end of helix removed outlier: 3.925A pdb=" N ASN B 998 " --> pdb=" O PRO B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1028 removed outlier: 6.134A pdb=" N GLU B1014 " --> pdb=" O ALA B1011 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER B1015 " --> pdb=" O ASP B1012 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B1018 " --> pdb=" O SER B1015 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B1021 " --> pdb=" O SER B1018 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B1024 " --> pdb=" O GLN B1021 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B1026 " --> pdb=" O GLU B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1053 removed outlier: 3.528A pdb=" N ASN B1044 " --> pdb=" O ASN B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1069 removed outlier: 3.595A pdb=" N ILE B1064 " --> pdb=" O ASP B1060 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B1069 " --> pdb=" O ILE B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1089 removed outlier: 3.673A pdb=" N ALA B1088 " --> pdb=" O SER B1084 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU B1089 " --> pdb=" O SER B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1106 removed outlier: 3.942A pdb=" N TYR B1098 " --> pdb=" O GLY B1094 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B1101 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1129 removed outlier: 3.603A pdb=" N GLY B1121 " --> pdb=" O ILE B1117 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR B1122 " --> pdb=" O LYS B1118 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B1123 " --> pdb=" O ALA B1119 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B1129 " --> pdb=" O LEU B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1149 removed outlier: 4.063A pdb=" N GLU B1139 " --> pdb=" O PRO B1135 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR B1140 " --> pdb=" O GLU B1136 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR B1148 " --> pdb=" O ALA B1144 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN B1149 " --> pdb=" O ILE B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1169 removed outlier: 3.560A pdb=" N TYR B1168 " --> pdb=" O ASP B1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1193 removed outlier: 3.559A pdb=" N ALA B1184 " --> pdb=" O SER B1180 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR B1193 " --> pdb=" O LEU B1189 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1199 No H-bonds generated for 'chain 'B' and resid 1197 through 1199' Processing helix chain 'B' and resid 1202 through 1212 Processing helix chain 'B' and resid 1214 through 1227 removed outlier: 3.726A pdb=" N ALA B1219 " --> pdb=" O SER B1215 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B1222 " --> pdb=" O LEU B1218 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B1226 " --> pdb=" O SER B1222 " (cutoff:3.500A) Processing helix chain 'B' and resid 1235 through 1245 Processing helix chain 'B' and resid 1251 through 1259 Proline residue: B1256 - end of helix removed outlier: 5.554A pdb=" N THR B1259 " --> pdb=" O LEU B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1266 through 1274 Processing helix chain 'B' and resid 1280 through 1294 removed outlier: 3.714A pdb=" N ILE B1284 " --> pdb=" O ASP B1280 " (cutoff:3.500A) Processing helix chain 'B' and resid 1301 through 1314 removed outlier: 3.649A pdb=" N LYS B1306 " --> pdb=" O GLN B1302 " (cutoff:3.500A) Processing helix chain 'B' and resid 1319 through 1328 removed outlier: 4.239A pdb=" N LEU B1328 " --> pdb=" O ARG B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1350 through 1356 Processing helix chain 'B' and resid 1365 through 1377 removed outlier: 3.665A pdb=" N SER B1369 " --> pdb=" O ILE B1365 " (cutoff:3.500A) Processing helix chain 'B' and resid 1384 through 1394 Processing helix chain 'B' and resid 1400 through 1410 Processing helix chain 'B' and resid 1417 through 1424 removed outlier: 3.784A pdb=" N LEU B1422 " --> pdb=" O LYS B1419 " (cutoff:3.500A) Processing helix chain 'B' and resid 1427 through 1431 Processing helix chain 'B' and resid 1433 through 1449 Processing helix chain 'B' and resid 1465 through 1472 Processing helix chain 'B' and resid 1476 through 1488 removed outlier: 3.687A pdb=" N GLY B1481 " --> pdb=" O LYS B1477 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B1486 " --> pdb=" O ILE B1482 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1501 removed outlier: 3.588A pdb=" N SER B1501 " --> pdb=" O ASP B1497 " (cutoff:3.500A) Processing helix chain 'B' and resid 1503 through 1508 removed outlier: 5.328A pdb=" N SER B1508 " --> pdb=" O GLY B1504 " (cutoff:3.500A) Processing helix chain 'B' and resid 1512 through 1526 removed outlier: 3.784A pdb=" N ASP B1524 " --> pdb=" O SER B1520 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU B1525 " --> pdb=" O TYR B1521 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B1526 " --> pdb=" O ALA B1522 " (cutoff:3.500A) Processing helix chain 'B' and resid 1541 through 1543 No H-bonds generated for 'chain 'B' and resid 1541 through 1543' Processing helix chain 'B' and resid 1549 through 1561 Processing helix chain 'B' and resid 1566 through 1580 Processing helix chain 'B' and resid 1585 through 1597 Processing helix chain 'B' and resid 1601 through 1603 No H-bonds generated for 'chain 'B' and resid 1601 through 1603' Processing helix chain 'B' and resid 1612 through 1629 removed outlier: 3.572A pdb=" N ARG B1625 " --> pdb=" O ILE B1621 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B1628 " --> pdb=" O ALA B1624 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP B1629 " --> pdb=" O ARG B1625 " (cutoff:3.500A) Processing helix chain 'B' and resid 1632 through 1644 Proline residue: B1636 - end of helix removed outlier: 5.529A pdb=" N GLY B1639 " --> pdb=" O PRO B1636 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR B1642 " --> pdb=" O GLY B1639 " (cutoff:3.500A) Processing helix chain 'B' and resid 1652 through 1667 Processing helix chain 'B' and resid 1675 through 1683 removed outlier: 3.662A pdb=" N ASN B1683 " --> pdb=" O ASN B1679 " (cutoff:3.500A) Processing helix chain 'B' and resid 1688 through 1691 Proline residue: B1691 - end of helix No H-bonds generated for 'chain 'B' and resid 1688 through 1691' Processing helix chain 'B' and resid 1711 through 1722 removed outlier: 4.458A pdb=" N LYS B1717 " --> pdb=" O PRO B1713 " (cutoff:3.500A) Proline residue: B1718 - end of helix removed outlier: 3.756A pdb=" N CYS B1722 " --> pdb=" O PRO B1718 " (cutoff:3.500A) Processing helix chain 'B' and resid 1727 through 1740 Proline residue: B1732 - end of helix Processing helix chain 'B' and resid 1750 through 1752 No H-bonds generated for 'chain 'B' and resid 1750 through 1752' Processing helix chain 'B' and resid 1754 through 1757 No H-bonds generated for 'chain 'B' and resid 1754 through 1757' Processing helix chain 'B' and resid 1779 through 1796 removed outlier: 3.645A pdb=" N PHE B1789 " --> pdb=" O TYR B1785 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY B1793 " --> pdb=" O PHE B1789 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN B1794 " --> pdb=" O MET B1790 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B1795 " --> pdb=" O THR B1791 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B1796 " --> pdb=" O ALA B1792 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1820 removed outlier: 4.485A pdb=" N ARG B1819 " --> pdb=" O ASP B1815 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS B1820 " --> pdb=" O TRP B1816 " (cutoff:3.500A) Processing helix chain 'B' and resid 1830 through 1832 No H-bonds generated for 'chain 'B' and resid 1830 through 1832' Processing helix chain 'B' and resid 1842 through 1849 removed outlier: 4.710A pdb=" N SER B1849 " --> pdb=" O LEU B1845 " (cutoff:3.500A) Processing helix chain 'B' and resid 1852 through 1855 No H-bonds generated for 'chain 'B' and resid 1852 through 1855' Processing helix chain 'B' and resid 1862 through 1868 Processing helix chain 'B' and resid 1903 through 1912 removed outlier: 4.069A pdb=" N ARG B1909 " --> pdb=" O LEU B1905 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B1912 " --> pdb=" O LEU B1908 " (cutoff:3.500A) Processing helix chain 'B' and resid 1951 through 1954 removed outlier: 3.877A pdb=" N PHE B1954 " --> pdb=" O ILE B1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1951 through 1954' Processing helix chain 'B' and resid 1970 through 1976 Processing helix chain 'B' and resid 2023 through 2033 Processing helix chain 'C' and resid 4 through 29 removed outlier: 4.013A pdb=" N SER C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY C 13 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ARG C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'C' and resid 96 through 116 removed outlier: 4.612A pdb=" N LYS C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 removed outlier: 4.758A pdb=" N THR C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 156 through 166 Processing helix chain 'C' and resid 170 through 179 removed outlier: 3.923A pdb=" N ILE C 175 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 202 removed outlier: 4.480A pdb=" N ASN C 194 " --> pdb=" O TRP C 190 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 196 " --> pdb=" O GLN C 192 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.641A pdb=" N LYS C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 242 Processing helix chain 'C' and resid 246 through 249 No H-bonds generated for 'chain 'C' and resid 246 through 249' Processing helix chain 'C' and resid 266 through 278 removed outlier: 3.795A pdb=" N ALA C 269 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 272 " --> pdb=" O ALA C 269 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 274 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU C 277 " --> pdb=" O ARG C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 removed outlier: 3.679A pdb=" N THR C 298 " --> pdb=" O SER C 294 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N HIS C 303 " --> pdb=" O HIS C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 331 through 344 removed outlier: 4.754A pdb=" N VAL C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 380 removed outlier: 3.569A pdb=" N ARG C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 372 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER C 380 " --> pdb=" O ILE C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 removed outlier: 4.248A pdb=" N GLN C 397 " --> pdb=" O ALA C 393 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C 398 " --> pdb=" O ASP C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'C' and resid 433 through 435 No H-bonds generated for 'chain 'C' and resid 433 through 435' Processing helix chain 'C' and resid 452 through 461 removed outlier: 3.832A pdb=" N GLN C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 477 Processing helix chain 'C' and resid 482 through 491 removed outlier: 4.334A pdb=" N GLN C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'C' and resid 515 through 526 Processing helix chain 'C' and resid 532 through 543 removed outlier: 4.051A pdb=" N ASP C 537 " --> pdb=" O ARG C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 559 Processing helix chain 'C' and resid 563 through 573 Processing helix chain 'C' and resid 589 through 598 Processing helix chain 'C' and resid 603 through 618 removed outlier: 3.860A pdb=" N HIS C 607 " --> pdb=" O ALA C 603 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Proline residue: C 615 - end of helix removed outlier: 4.931A pdb=" N LYS C 618 " --> pdb=" O ARG C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 633 Proline residue: C 628 - end of helix removed outlier: 3.571A pdb=" N LEU C 632 " --> pdb=" O PRO C 628 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU C 633 " --> pdb=" O ALA C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 645 Processing helix chain 'C' and resid 655 through 676 removed outlier: 3.720A pdb=" N ASP C 660 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 662 " --> pdb=" O ARG C 658 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 663 " --> pdb=" O ARG C 659 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 671 " --> pdb=" O GLN C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 713 removed outlier: 4.532A pdb=" N GLY C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL C 701 " --> pdb=" O ASN C 697 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 706 " --> pdb=" O LEU C 702 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE C 707 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU C 709 " --> pdb=" O ASP C 705 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS C 712 " --> pdb=" O ASP C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 724 Processing helix chain 'C' and resid 736 through 747 removed outlier: 3.950A pdb=" N TYR C 741 " --> pdb=" O ASN C 738 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 744 " --> pdb=" O TYR C 741 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU C 745 " --> pdb=" O ALA C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 771 removed outlier: 3.592A pdb=" N SER C 757 " --> pdb=" O GLY C 753 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 762 " --> pdb=" O ARG C 758 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU C 764 " --> pdb=" O ARG C 760 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TRP C 765 " --> pdb=" O LEU C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 779 removed outlier: 3.845A pdb=" N ARG C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 798 Processing helix chain 'C' and resid 800 through 809 removed outlier: 3.583A pdb=" N GLU C 806 " --> pdb=" O ALA C 802 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 807 " --> pdb=" O ALA C 803 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG C 808 " --> pdb=" O ALA C 804 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG C 809 " --> pdb=" O ARG C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 829 removed outlier: 3.771A pdb=" N ASP C 818 " --> pdb=" O LYS C 814 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 829 " --> pdb=" O MET C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 842 Processing helix chain 'C' and resid 847 through 859 removed outlier: 3.573A pdb=" N LEU C 855 " --> pdb=" O MET C 851 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 856 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS C 859 " --> pdb=" O LEU C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 876 Processing helix chain 'C' and resid 893 through 906 Processing helix chain 'C' and resid 912 through 922 removed outlier: 3.629A pdb=" N TYR C 922 " --> pdb=" O LEU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 932 removed outlier: 3.565A pdb=" N THR C 932 " --> pdb=" O TYR C 929 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 929 through 932' Processing helix chain 'C' and resid 939 through 952 Processing helix chain 'C' and resid 959 through 962 No H-bonds generated for 'chain 'C' and resid 959 through 962' Processing helix chain 'C' and resid 965 through 972 Processing helix chain 'C' and resid 981 through 989 Processing helix chain 'C' and resid 991 through 1004 Proline residue: C 995 - end of helix removed outlier: 4.015A pdb=" N ASN C 998 " --> pdb=" O PRO C 995 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP C1000 " --> pdb=" O TYR C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1028 removed outlier: 5.974A pdb=" N GLU C1014 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C1017 " --> pdb=" O GLU C1014 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C1018 " --> pdb=" O SER C1015 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C1019 " --> pdb=" O GLU C1016 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN C1021 " --> pdb=" O SER C1018 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER C1024 " --> pdb=" O GLN C1021 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C1026 " --> pdb=" O GLU C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1053 removed outlier: 3.503A pdb=" N ASN C1044 " --> pdb=" O ASN C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1069 removed outlier: 3.574A pdb=" N ILE C1064 " --> pdb=" O ASP C1060 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C1069 " --> pdb=" O ILE C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1089 removed outlier: 3.597A pdb=" N ALA C1088 " --> pdb=" O SER C1084 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU C1089 " --> pdb=" O SER C1085 " (cutoff:3.500A) Processing helix chain 'C' and resid 1094 through 1106 removed outlier: 3.959A pdb=" N TYR C1098 " --> pdb=" O GLY C1094 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C1101 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1129 removed outlier: 3.948A pdb=" N LEU C1129 " --> pdb=" O LEU C1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1149 removed outlier: 4.007A pdb=" N GLU C1139 " --> pdb=" O PRO C1135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR C1140 " --> pdb=" O GLU C1136 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C1141 " --> pdb=" O ALA C1137 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR C1148 " --> pdb=" O ALA C1144 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASN C1149 " --> pdb=" O ILE C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1158 through 1169 removed outlier: 3.565A pdb=" N TYR C1168 " --> pdb=" O ASP C1164 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1193 removed outlier: 3.576A pdb=" N LEU C1183 " --> pdb=" O ILE C1179 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C1184 " --> pdb=" O SER C1180 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU C1192 " --> pdb=" O GLU C1188 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR C1193 " --> pdb=" O LEU C1189 " (cutoff:3.500A) Processing helix chain 'C' and resid 1197 through 1199 No H-bonds generated for 'chain 'C' and resid 1197 through 1199' Processing helix chain 'C' and resid 1202 through 1212 Processing helix chain 'C' and resid 1214 through 1227 removed outlier: 3.743A pdb=" N SER C1222 " --> pdb=" O LEU C1218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C1223 " --> pdb=" O ALA C1219 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C1225 " --> pdb=" O ILE C1221 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C1226 " --> pdb=" O SER C1222 " (cutoff:3.500A) Processing helix chain 'C' and resid 1235 through 1245 Processing helix chain 'C' and resid 1251 through 1259 Proline residue: C1256 - end of helix removed outlier: 5.526A pdb=" N THR C1259 " --> pdb=" O LEU C1255 " (cutoff:3.500A) Processing helix chain 'C' and resid 1266 through 1274 Processing helix chain 'C' and resid 1280 through 1294 Processing helix chain 'C' and resid 1301 through 1314 removed outlier: 3.539A pdb=" N LYS C1306 " --> pdb=" O GLN C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1319 through 1328 removed outlier: 4.010A pdb=" N LEU C1328 " --> pdb=" O ARG C1324 " (cutoff:3.500A) Processing helix chain 'C' and resid 1350 through 1356 Processing helix chain 'C' and resid 1365 through 1376 removed outlier: 3.715A pdb=" N SER C1369 " --> pdb=" O ILE C1365 " (cutoff:3.500A) Processing helix chain 'C' and resid 1384 through 1394 Processing helix chain 'C' and resid 1400 through 1410 Processing helix chain 'C' and resid 1417 through 1424 removed outlier: 3.740A pdb=" N LEU C1422 " --> pdb=" O LYS C1419 " (cutoff:3.500A) Processing helix chain 'C' and resid 1428 through 1431 Processing helix chain 'C' and resid 1433 through 1449 removed outlier: 3.954A pdb=" N LYS C1444 " --> pdb=" O ALA C1440 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU C1445 " --> pdb=" O GLY C1441 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C1446 " --> pdb=" O LEU C1442 " (cutoff:3.500A) Processing helix chain 'C' and resid 1465 through 1472 Processing helix chain 'C' and resid 1476 through 1488 removed outlier: 3.591A pdb=" N GLY C1481 " --> pdb=" O LYS C1477 " (cutoff:3.500A) Processing helix chain 'C' and resid 1496 through 1501 removed outlier: 3.645A pdb=" N SER C1501 " --> pdb=" O ASP C1497 " (cutoff:3.500A) Processing helix chain 'C' and resid 1503 through 1508 removed outlier: 5.139A pdb=" N SER C1508 " --> pdb=" O GLY C1504 " (cutoff:3.500A) Processing helix chain 'C' and resid 1512 through 1526 removed outlier: 3.805A pdb=" N ASP C1517 " --> pdb=" O ASN C1513 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP C1524 " --> pdb=" O SER C1520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C1525 " --> pdb=" O TYR C1521 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE C1526 " --> pdb=" O ALA C1522 " (cutoff:3.500A) Processing helix chain 'C' and resid 1541 through 1543 No H-bonds generated for 'chain 'C' and resid 1541 through 1543' Processing helix chain 'C' and resid 1549 through 1561 Processing helix chain 'C' and resid 1566 through 1580 Processing helix chain 'C' and resid 1585 through 1597 Processing helix chain 'C' and resid 1601 through 1603 No H-bonds generated for 'chain 'C' and resid 1601 through 1603' Processing helix chain 'C' and resid 1612 through 1629 removed outlier: 3.565A pdb=" N ARG C1625 " --> pdb=" O ILE C1621 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU C1628 " --> pdb=" O ALA C1624 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP C1629 " --> pdb=" O ARG C1625 " (cutoff:3.500A) Processing helix chain 'C' and resid 1632 through 1644 Proline residue: C1636 - end of helix removed outlier: 5.498A pdb=" N GLY C1639 " --> pdb=" O PRO C1636 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR C1642 " --> pdb=" O GLY C1639 " (cutoff:3.500A) Processing helix chain 'C' and resid 1652 through 1667 Processing helix chain 'C' and resid 1675 through 1683 removed outlier: 3.522A pdb=" N ASN C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C1683 " --> pdb=" O ASN C1679 " (cutoff:3.500A) Processing helix chain 'C' and resid 1711 through 1722 removed outlier: 4.468A pdb=" N LYS C1717 " --> pdb=" O PRO C1713 " (cutoff:3.500A) Proline residue: C1718 - end of helix removed outlier: 3.780A pdb=" N CYS C1722 " --> pdb=" O PRO C1718 " (cutoff:3.500A) Processing helix chain 'C' and resid 1727 through 1740 Proline residue: C1732 - end of helix Processing helix chain 'C' and resid 1750 through 1752 No H-bonds generated for 'chain 'C' and resid 1750 through 1752' Processing helix chain 'C' and resid 1754 through 1757 No H-bonds generated for 'chain 'C' and resid 1754 through 1757' Processing helix chain 'C' and resid 1779 through 1798 removed outlier: 3.723A pdb=" N PHE C1789 " --> pdb=" O TYR C1785 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C1793 " --> pdb=" O PHE C1789 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN C1794 " --> pdb=" O MET C1790 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C1795 " --> pdb=" O THR C1791 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C1797 " --> pdb=" O GLY C1793 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1820 removed outlier: 4.533A pdb=" N ARG C1819 " --> pdb=" O ASP C1815 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS C1820 " --> pdb=" O TRP C1816 " (cutoff:3.500A) Processing helix chain 'C' and resid 1830 through 1832 No H-bonds generated for 'chain 'C' and resid 1830 through 1832' Processing helix chain 'C' and resid 1842 through 1849 removed outlier: 4.730A pdb=" N SER C1849 " --> pdb=" O LEU C1845 " (cutoff:3.500A) Processing helix chain 'C' and resid 1852 through 1857 removed outlier: 4.117A pdb=" N ALA C1857 " --> pdb=" O ASP C1853 " (cutoff:3.500A) Processing helix chain 'C' and resid 1861 through 1868 removed outlier: 3.854A pdb=" N LEU C1868 " --> pdb=" O ASN C1865 " (cutoff:3.500A) Processing helix chain 'C' and resid 1903 through 1912 removed outlier: 4.160A pdb=" N ARG C1909 " --> pdb=" O LEU C1905 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN C1912 " --> pdb=" O LEU C1908 " (cutoff:3.500A) Processing helix chain 'C' and resid 1951 through 1954 removed outlier: 3.921A pdb=" N PHE C1954 " --> pdb=" O ILE C1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1951 through 1954' Processing helix chain 'C' and resid 1970 through 1976 Processing helix chain 'C' and resid 2023 through 2033 Processing helix chain 'D' and resid 16 through 29 removed outlier: 3.683A pdb=" N ALA D 21 " --> pdb=" O HIS D 17 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU D 28 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 116 removed outlier: 4.620A pdb=" N LYS D 101 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU D 104 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE D 106 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR D 108 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS D 111 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE D 114 " --> pdb=" O LYS D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 removed outlier: 4.385A pdb=" N THR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 156 through 165 removed outlier: 3.973A pdb=" N ALA D 160 " --> pdb=" O HIS D 157 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 164 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 179 removed outlier: 3.919A pdb=" N PHE D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU D 179 " --> pdb=" O ILE D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 194 Processing helix chain 'D' and resid 206 through 209 Processing helix chain 'D' and resid 211 through 223 removed outlier: 3.669A pdb=" N LYS D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 242 Processing helix chain 'D' and resid 246 through 249 No H-bonds generated for 'chain 'D' and resid 246 through 249' Processing helix chain 'D' and resid 268 through 277 removed outlier: 4.072A pdb=" N GLN D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 302 removed outlier: 5.062A pdb=" N GLU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 331 through 344 removed outlier: 4.738A pdb=" N VAL D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 378 removed outlier: 3.662A pdb=" N ARG D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D 375 " --> pdb=" O SER D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.868A pdb=" N GLN D 397 " --> pdb=" O ALA D 393 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 415 removed outlier: 4.708A pdb=" N ARG D 415 " --> pdb=" O LYS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.706A pdb=" N ARG D 433 " --> pdb=" O PRO D 430 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU D 434 " --> pdb=" O TYR D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 462 removed outlier: 3.936A pdb=" N GLN D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS D 462 " --> pdb=" O HIS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 476 Processing helix chain 'D' and resid 482 through 491 removed outlier: 4.519A pdb=" N GLN D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 502 removed outlier: 3.960A pdb=" N LEU D 502 " --> pdb=" O THR D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 526 removed outlier: 3.784A pdb=" N LYS D 519 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 544 removed outlier: 3.642A pdb=" N ALA D 544 " --> pdb=" O CYS D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 559 Processing helix chain 'D' and resid 563 through 573 Processing helix chain 'D' and resid 589 through 598 Processing helix chain 'D' and resid 603 through 618 Proline residue: D 615 - end of helix removed outlier: 5.082A pdb=" N LYS D 618 " --> pdb=" O ARG D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 634 Proline residue: D 628 - end of helix removed outlier: 3.601A pdb=" N GLU D 633 " --> pdb=" O ALA D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 645 Processing helix chain 'D' and resid 655 through 675 removed outlier: 4.104A pdb=" N ASP D 660 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 704 removed outlier: 4.473A pdb=" N GLY D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 701 " --> pdb=" O ASN D 697 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 713 removed outlier: 3.989A pdb=" N LYS D 712 " --> pdb=" O ASP D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 724 Processing helix chain 'D' and resid 736 through 747 removed outlier: 3.756A pdb=" N TYR D 741 " --> pdb=" O ASN D 738 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D 742 " --> pdb=" O ALA D 739 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE D 744 " --> pdb=" O TYR D 741 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 745 " --> pdb=" O ALA D 742 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 747 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 771 removed outlier: 3.802A pdb=" N SER D 757 " --> pdb=" O GLY D 753 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU D 764 " --> pdb=" O ARG D 760 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TRP D 765 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 779 removed outlier: 3.806A pdb=" N ARG D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 797 Processing helix chain 'D' and resid 800 through 809 removed outlier: 3.777A pdb=" N GLU D 806 " --> pdb=" O ALA D 802 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D 807 " --> pdb=" O ALA D 803 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 808 " --> pdb=" O ALA D 804 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG D 809 " --> pdb=" O ARG D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 829 removed outlier: 3.844A pdb=" N ILE D 822 " --> pdb=" O ASP D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 843 Processing helix chain 'D' and resid 847 through 859 removed outlier: 3.811A pdb=" N LYS D 859 " --> pdb=" O LEU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 878 removed outlier: 4.622A pdb=" N SER D 878 " --> pdb=" O ARG D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 893 through 906 Processing helix chain 'D' and resid 912 through 922 removed outlier: 3.599A pdb=" N TYR D 922 " --> pdb=" O LEU D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 932 Processing helix chain 'D' and resid 939 through 952 Processing helix chain 'D' and resid 959 through 962 No H-bonds generated for 'chain 'D' and resid 959 through 962' Processing helix chain 'D' and resid 965 through 972 Processing helix chain 'D' and resid 981 through 989 removed outlier: 3.997A pdb=" N LEU D 986 " --> pdb=" O ASP D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 1004 Proline residue: D 995 - end of helix removed outlier: 3.936A pdb=" N ASN D 998 " --> pdb=" O PRO D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1028 removed outlier: 6.132A pdb=" N GLU D1014 " --> pdb=" O ALA D1011 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER D1015 " --> pdb=" O ASP D1012 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER D1018 " --> pdb=" O SER D1015 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN D1021 " --> pdb=" O SER D1018 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER D1024 " --> pdb=" O GLN D1021 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA D1026 " --> pdb=" O GLU D1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1053 removed outlier: 3.520A pdb=" N ASN D1044 " --> pdb=" O ASN D1040 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1069 removed outlier: 3.596A pdb=" N ILE D1064 " --> pdb=" O ASP D1060 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN D1069 " --> pdb=" O ILE D1065 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1089 removed outlier: 3.674A pdb=" N ALA D1088 " --> pdb=" O SER D1084 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU D1089 " --> pdb=" O SER D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1106 removed outlier: 3.943A pdb=" N TYR D1098 " --> pdb=" O GLY D1094 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA D1101 " --> pdb=" O SER D1097 " (cutoff:3.500A) Processing helix chain 'D' and resid 1115 through 1129 removed outlier: 3.606A pdb=" N GLY D1121 " --> pdb=" O ILE D1117 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR D1122 " --> pdb=" O LYS D1118 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE D1123 " --> pdb=" O ALA D1119 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D1129 " --> pdb=" O LEU D1125 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1149 removed outlier: 4.058A pdb=" N GLU D1139 " --> pdb=" O PRO D1135 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR D1140 " --> pdb=" O GLU D1136 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR D1148 " --> pdb=" O ALA D1144 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN D1149 " --> pdb=" O ILE D1145 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1169 removed outlier: 3.544A pdb=" N TYR D1168 " --> pdb=" O ASP D1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1193 removed outlier: 3.558A pdb=" N ALA D1184 " --> pdb=" O SER D1180 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU D1192 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR D1193 " --> pdb=" O LEU D1189 " (cutoff:3.500A) Processing helix chain 'D' and resid 1197 through 1199 No H-bonds generated for 'chain 'D' and resid 1197 through 1199' Processing helix chain 'D' and resid 1202 through 1212 Processing helix chain 'D' and resid 1214 through 1227 removed outlier: 3.727A pdb=" N ALA D1219 " --> pdb=" O SER D1215 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D1222 " --> pdb=" O LEU D1218 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP D1226 " --> pdb=" O SER D1222 " (cutoff:3.500A) Processing helix chain 'D' and resid 1235 through 1245 Processing helix chain 'D' and resid 1251 through 1259 Proline residue: D1256 - end of helix removed outlier: 5.555A pdb=" N THR D1259 " --> pdb=" O LEU D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1266 through 1274 Processing helix chain 'D' and resid 1280 through 1294 removed outlier: 3.712A pdb=" N ILE D1284 " --> pdb=" O ASP D1280 " (cutoff:3.500A) Processing helix chain 'D' and resid 1301 through 1314 removed outlier: 3.662A pdb=" N LYS D1306 " --> pdb=" O GLN D1302 " (cutoff:3.500A) Processing helix chain 'D' and resid 1319 through 1328 removed outlier: 4.219A pdb=" N LEU D1328 " --> pdb=" O ARG D1324 " (cutoff:3.500A) Processing helix chain 'D' and resid 1350 through 1356 Processing helix chain 'D' and resid 1365 through 1377 removed outlier: 3.658A pdb=" N SER D1369 " --> pdb=" O ILE D1365 " (cutoff:3.500A) Processing helix chain 'D' and resid 1384 through 1394 Processing helix chain 'D' and resid 1400 through 1410 Processing helix chain 'D' and resid 1417 through 1424 removed outlier: 3.783A pdb=" N LEU D1422 " --> pdb=" O LYS D1419 " (cutoff:3.500A) Processing helix chain 'D' and resid 1427 through 1431 Processing helix chain 'D' and resid 1433 through 1449 Processing helix chain 'D' and resid 1465 through 1472 Processing helix chain 'D' and resid 1476 through 1489 removed outlier: 3.676A pdb=" N GLY D1481 " --> pdb=" O LYS D1477 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1501 removed outlier: 3.603A pdb=" N SER D1501 " --> pdb=" O ASP D1497 " (cutoff:3.500A) Processing helix chain 'D' and resid 1503 through 1508 removed outlier: 5.331A pdb=" N SER D1508 " --> pdb=" O GLY D1504 " (cutoff:3.500A) Processing helix chain 'D' and resid 1512 through 1526 removed outlier: 3.571A pdb=" N ASP D1517 " --> pdb=" O ASN D1513 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP D1524 " --> pdb=" O SER D1520 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU D1525 " --> pdb=" O TYR D1521 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE D1526 " --> pdb=" O ALA D1522 " (cutoff:3.500A) Processing helix chain 'D' and resid 1541 through 1543 No H-bonds generated for 'chain 'D' and resid 1541 through 1543' Processing helix chain 'D' and resid 1549 through 1561 Processing helix chain 'D' and resid 1566 through 1580 Processing helix chain 'D' and resid 1585 through 1597 Processing helix chain 'D' and resid 1601 through 1603 No H-bonds generated for 'chain 'D' and resid 1601 through 1603' Processing helix chain 'D' and resid 1612 through 1629 removed outlier: 3.572A pdb=" N ARG D1625 " --> pdb=" O ILE D1621 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU D1628 " --> pdb=" O ALA D1624 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP D1629 " --> pdb=" O ARG D1625 " (cutoff:3.500A) Processing helix chain 'D' and resid 1632 through 1644 Proline residue: D1636 - end of helix removed outlier: 5.529A pdb=" N GLY D1639 " --> pdb=" O PRO D1636 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR D1642 " --> pdb=" O GLY D1639 " (cutoff:3.500A) Processing helix chain 'D' and resid 1652 through 1667 Processing helix chain 'D' and resid 1675 through 1683 removed outlier: 3.637A pdb=" N ASN D1683 " --> pdb=" O ASN D1679 " (cutoff:3.500A) Processing helix chain 'D' and resid 1688 through 1691 Proline residue: D1691 - end of helix No H-bonds generated for 'chain 'D' and resid 1688 through 1691' Processing helix chain 'D' and resid 1711 through 1722 removed outlier: 4.464A pdb=" N LYS D1717 " --> pdb=" O PRO D1713 " (cutoff:3.500A) Proline residue: D1718 - end of helix removed outlier: 3.759A pdb=" N CYS D1722 " --> pdb=" O PRO D1718 " (cutoff:3.500A) Processing helix chain 'D' and resid 1727 through 1740 Proline residue: D1732 - end of helix Processing helix chain 'D' and resid 1750 through 1752 No H-bonds generated for 'chain 'D' and resid 1750 through 1752' Processing helix chain 'D' and resid 1754 through 1757 No H-bonds generated for 'chain 'D' and resid 1754 through 1757' Processing helix chain 'D' and resid 1779 through 1796 removed outlier: 3.647A pdb=" N PHE D1789 " --> pdb=" O TYR D1785 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY D1793 " --> pdb=" O PHE D1789 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN D1794 " --> pdb=" O MET D1790 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D1795 " --> pdb=" O THR D1791 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D1796 " --> pdb=" O ALA D1792 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1820 removed outlier: 4.502A pdb=" N ARG D1819 " --> pdb=" O ASP D1815 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N HIS D1820 " --> pdb=" O TRP D1816 " (cutoff:3.500A) Processing helix chain 'D' and resid 1830 through 1832 No H-bonds generated for 'chain 'D' and resid 1830 through 1832' Processing helix chain 'D' and resid 1842 through 1849 removed outlier: 4.715A pdb=" N SER D1849 " --> pdb=" O LEU D1845 " (cutoff:3.500A) Processing helix chain 'D' and resid 1852 through 1855 No H-bonds generated for 'chain 'D' and resid 1852 through 1855' Processing helix chain 'D' and resid 1862 through 1868 Processing helix chain 'D' and resid 1903 through 1912 removed outlier: 4.068A pdb=" N ARG D1909 " --> pdb=" O LEU D1905 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN D1912 " --> pdb=" O LEU D1908 " (cutoff:3.500A) Processing helix chain 'D' and resid 1951 through 1954 removed outlier: 3.903A pdb=" N PHE D1954 " --> pdb=" O ILE D1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1951 through 1954' Processing helix chain 'D' and resid 1970 through 1976 Processing helix chain 'D' and resid 2023 through 2033 Processing helix chain 'E' and resid 3 through 15 removed outlier: 3.772A pdb=" N ALA E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 30 Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 65 through 79 Processing helix chain 'E' and resid 92 through 108 removed outlier: 3.744A pdb=" N ILE E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS E 103 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 172 through 187 removed outlier: 3.669A pdb=" N PHE E 185 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ALA E 187 " --> pdb=" O THR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 215 removed outlier: 4.152A pdb=" N GLU E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.721A pdb=" N TYR E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 250 Processing helix chain 'E' and resid 269 through 278 removed outlier: 3.581A pdb=" N ARG E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 400 through 412 Processing helix chain 'E' and resid 429 through 437 Proline residue: E 435 - end of helix Processing helix chain 'E' and resid 454 through 467 removed outlier: 3.764A pdb=" N CYS E 459 " --> pdb=" O GLU E 455 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.642A pdb=" N GLU E 480 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP E 481 " --> pdb=" O ILE E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 496 No H-bonds generated for 'chain 'E' and resid 494 through 496' Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 516 through 530 removed outlier: 3.963A pdb=" N ALA E 520 " --> pdb=" O ASP E 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 18 removed outlier: 3.739A pdb=" N LYS F 17 " --> pdb=" O ILE F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 30 Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 65 through 79 Processing helix chain 'F' and resid 92 through 108 Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 172 through 188 removed outlier: 3.579A pdb=" N PHE F 185 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA F 186 " --> pdb=" O VAL F 182 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA F 187 " --> pdb=" O THR F 183 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 215 removed outlier: 4.069A pdb=" N GLU F 214 " --> pdb=" O TYR F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 237 removed outlier: 3.707A pdb=" N TYR F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 269 through 278 removed outlier: 3.716A pdb=" N GLU F 274 " --> pdb=" O ASP F 270 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 287 Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 400 through 412 Processing helix chain 'F' and resid 429 through 439 Proline residue: F 435 - end of helix removed outlier: 4.325A pdb=" N LYS F 439 " --> pdb=" O PRO F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 467 Proline residue: F 464 - end of helix Processing helix chain 'F' and resid 475 through 484 removed outlier: 4.216A pdb=" N ARG F 479 " --> pdb=" O ASP F 475 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR F 482 " --> pdb=" O ILE F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 496 No H-bonds generated for 'chain 'F' and resid 494 through 496' Processing helix chain 'F' and resid 498 through 503 Processing helix chain 'F' and resid 516 through 530 removed outlier: 3.966A pdb=" N ALA F 520 " --> pdb=" O ASP F 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 removed outlier: 3.858A pdb=" N ALA G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 30 Processing helix chain 'G' and resid 38 through 48 Processing helix chain 'G' and resid 65 through 79 Processing helix chain 'G' and resid 92 through 108 removed outlier: 3.742A pdb=" N ILE G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 172 through 187 removed outlier: 3.680A pdb=" N PHE G 185 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA G 187 " --> pdb=" O THR G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 215 removed outlier: 4.159A pdb=" N GLU G 214 " --> pdb=" O TYR G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 237 removed outlier: 3.725A pdb=" N TYR G 237 " --> pdb=" O ALA G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 250 Processing helix chain 'G' and resid 269 through 278 removed outlier: 3.581A pdb=" N ARG G 275 " --> pdb=" O ASP G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 287 Processing helix chain 'G' and resid 304 through 306 No H-bonds generated for 'chain 'G' and resid 304 through 306' Processing helix chain 'G' and resid 400 through 412 Processing helix chain 'G' and resid 429 through 437 Proline residue: G 435 - end of helix Processing helix chain 'G' and resid 454 through 467 removed outlier: 3.764A pdb=" N CYS G 459 " --> pdb=" O GLU G 455 " (cutoff:3.500A) Proline residue: G 464 - end of helix Processing helix chain 'G' and resid 475 through 483 removed outlier: 4.191A pdb=" N ARG G 479 " --> pdb=" O ASP G 475 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR G 482 " --> pdb=" O ILE G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 496 No H-bonds generated for 'chain 'G' and resid 494 through 496' Processing helix chain 'G' and resid 498 through 503 Processing helix chain 'G' and resid 516 through 530 removed outlier: 3.863A pdb=" N ALA G 520 " --> pdb=" O ASP G 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 18 removed outlier: 3.761A pdb=" N LYS H 17 " --> pdb=" O ILE H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 30 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 65 through 79 Processing helix chain 'H' and resid 92 through 108 Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 172 through 188 removed outlier: 3.577A pdb=" N PHE H 185 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA H 186 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA H 187 " --> pdb=" O THR H 183 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU H 188 " --> pdb=" O GLU H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 215 removed outlier: 4.057A pdb=" N GLU H 214 " --> pdb=" O TYR H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 237 removed outlier: 3.763A pdb=" N TYR H 237 " --> pdb=" O ALA H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 250 Processing helix chain 'H' and resid 269 through 278 removed outlier: 3.575A pdb=" N GLU H 274 " --> pdb=" O ASP H 270 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG H 275 " --> pdb=" O ASP H 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU H 276 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 287 Processing helix chain 'H' and resid 304 through 306 No H-bonds generated for 'chain 'H' and resid 304 through 306' Processing helix chain 'H' and resid 400 through 412 Processing helix chain 'H' and resid 429 through 439 Proline residue: H 435 - end of helix removed outlier: 4.423A pdb=" N LYS H 439 " --> pdb=" O PRO H 435 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 467 Proline residue: H 464 - end of helix Processing helix chain 'H' and resid 475 through 484 removed outlier: 4.218A pdb=" N ARG H 479 " --> pdb=" O ASP H 475 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR H 482 " --> pdb=" O ILE H 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 496 No H-bonds generated for 'chain 'H' and resid 494 through 496' Processing helix chain 'H' and resid 498 through 503 Processing helix chain 'H' and resid 516 through 530 removed outlier: 3.953A pdb=" N ALA H 520 " --> pdb=" O ASP H 516 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 180 through 183 removed outlier: 8.156A pdb=" N HIS A 181 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 128 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLU A 183 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE A 130 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 78 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TRP A 129 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR A 80 " --> pdb=" O TRP A 129 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL A 131 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN A 82 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 443 through 446 removed outlier: 6.664A pdb=" N LEU A 386 " --> pdb=" O CYS A 423 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A 425 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE A 388 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N LEU A 427 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ILE A 390 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 309 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE A 389 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 311 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP A 391 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR A 313 " --> pdb=" O ASP A 391 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 577 through 580 Processing sheet with id= D, first strand: chain 'A' and resid 2084 through 2086 removed outlier: 3.676A pdb=" N GLY A1879 " --> pdb=" O VAL A1894 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER A1896 " --> pdb=" O LEU A1877 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N LEU A1877 " --> pdb=" O SER A1896 " (cutoff:3.500A) removed outlier: 14.192A pdb=" N LEU A1898 " --> pdb=" O LEU A1875 " (cutoff:3.500A) removed outlier: 18.510A pdb=" N LEU A1875 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A2019 " --> pdb=" O LEU A1877 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLY A1879 " --> pdb=" O TYR A2017 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR A2017 " --> pdb=" O GLY A1879 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP A1881 " --> pdb=" O HIS A2015 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N HIS A2015 " --> pdb=" O TRP A1881 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 180 through 182 removed outlier: 8.463A pdb=" N HIS B 181 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE B 128 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 78 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N TRP B 129 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR B 80 " --> pdb=" O TRP B 129 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL B 131 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B 82 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR B 77 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 37 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 443 through 446 removed outlier: 6.628A pdb=" N LEU B 386 " --> pdb=" O CYS B 423 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL B 425 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 388 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N LEU B 427 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE B 390 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 309 " --> pdb=" O CYS B 387 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE B 389 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 311 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP B 391 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR B 313 " --> pdb=" O ASP B 391 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 577 through 580 Processing sheet with id= H, first strand: chain 'B' and resid 2084 through 2086 removed outlier: 3.644A pdb=" N GLY B1879 " --> pdb=" O VAL B1894 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER B1896 " --> pdb=" O LEU B1877 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N LEU B1877 " --> pdb=" O SER B1896 " (cutoff:3.500A) removed outlier: 14.338A pdb=" N LEU B1898 " --> pdb=" O LEU B1875 " (cutoff:3.500A) removed outlier: 18.509A pdb=" N LEU B1875 " --> pdb=" O LEU B1898 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU B2019 " --> pdb=" O LEU B1877 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLY B1879 " --> pdb=" O TYR B2017 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TYR B2017 " --> pdb=" O GLY B1879 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRP B1881 " --> pdb=" O HIS B2015 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N HIS B2015 " --> pdb=" O TRP B1881 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 180 through 183 removed outlier: 8.169A pdb=" N HIS C 181 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE C 128 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLU C 183 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE C 130 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 78 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TRP C 129 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR C 80 " --> pdb=" O TRP C 129 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL C 131 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN C 82 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 443 through 446 removed outlier: 6.666A pdb=" N LEU C 386 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VAL C 425 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE C 388 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU C 427 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE C 390 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 309 " --> pdb=" O CYS C 387 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE C 389 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 311 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP C 391 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR C 313 " --> pdb=" O ASP C 391 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 577 through 580 Processing sheet with id= L, first strand: chain 'C' and resid 2084 through 2086 removed outlier: 3.682A pdb=" N GLY C1879 " --> pdb=" O VAL C1894 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C1896 " --> pdb=" O LEU C1877 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N LEU C1877 " --> pdb=" O SER C1896 " (cutoff:3.500A) removed outlier: 14.194A pdb=" N LEU C1898 " --> pdb=" O LEU C1875 " (cutoff:3.500A) removed outlier: 18.507A pdb=" N LEU C1875 " --> pdb=" O LEU C1898 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU C2019 " --> pdb=" O LEU C1877 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY C1879 " --> pdb=" O TYR C2017 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR C2017 " --> pdb=" O GLY C1879 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TRP C1881 " --> pdb=" O HIS C2015 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N HIS C2015 " --> pdb=" O TRP C1881 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 180 through 182 removed outlier: 8.470A pdb=" N HIS D 181 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE D 128 " --> pdb=" O HIS D 181 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL D 78 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N TRP D 129 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR D 80 " --> pdb=" O TRP D 129 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL D 131 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN D 82 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D 77 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA D 37 " --> pdb=" O TYR D 66 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 443 through 446 removed outlier: 6.627A pdb=" N LEU D 386 " --> pdb=" O CYS D 423 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL D 425 " --> pdb=" O LEU D 386 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE D 388 " --> pdb=" O VAL D 425 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N LEU D 427 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE D 390 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL D 309 " --> pdb=" O CYS D 387 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE D 389 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 311 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASP D 391 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR D 313 " --> pdb=" O ASP D 391 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 577 through 580 Processing sheet with id= P, first strand: chain 'D' and resid 2084 through 2086 removed outlier: 3.584A pdb=" N THR D2077 " --> pdb=" O ARG D2073 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY D1879 " --> pdb=" O VAL D1894 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER D1896 " --> pdb=" O LEU D1877 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N LEU D1877 " --> pdb=" O SER D1896 " (cutoff:3.500A) removed outlier: 14.330A pdb=" N LEU D1898 " --> pdb=" O LEU D1875 " (cutoff:3.500A) removed outlier: 18.509A pdb=" N LEU D1875 " --> pdb=" O LEU D1898 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU D2019 " --> pdb=" O LEU D1877 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLY D1879 " --> pdb=" O TYR D2017 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TYR D2017 " --> pdb=" O GLY D1879 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP D1881 " --> pdb=" O HIS D2015 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N HIS D2015 " --> pdb=" O TRP D1881 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 220 through 224 removed outlier: 6.738A pdb=" N VAL E 197 " --> pdb=" O PHE E 55 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU E 57 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR E 199 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ALA E 59 " --> pdb=" O TYR E 199 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY E 201 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 308 through 310 removed outlier: 6.306A pdb=" N ILE E 386 " --> pdb=" O VAL E 472 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG E 474 " --> pdb=" O ILE E 386 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU E 388 " --> pdb=" O ARG E 474 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL E 378 " --> pdb=" O MET E 389 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL E 391 " --> pdb=" O TYR E 376 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR E 376 " --> pdb=" O VAL E 391 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY E 393 " --> pdb=" O THR E 374 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR E 374 " --> pdb=" O GLY E 393 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER E 359 " --> pdb=" O SER E 381 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR E 417 " --> pdb=" O LEU E 362 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE E 364 " --> pdb=" O THR E 417 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL E 419 " --> pdb=" O ILE E 364 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA E 444 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N HIS E 420 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU E 446 " --> pdb=" O HIS E 420 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 220 through 224 removed outlier: 6.714A pdb=" N VAL F 197 " --> pdb=" O PHE F 55 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU F 57 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR F 199 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA F 59 " --> pdb=" O TYR F 199 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY F 201 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 308 through 310 removed outlier: 6.254A pdb=" N ILE F 386 " --> pdb=" O VAL F 472 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ARG F 474 " --> pdb=" O ILE F 386 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU F 388 " --> pdb=" O ARG F 474 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL F 378 " --> pdb=" O MET F 389 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL F 391 " --> pdb=" O TYR F 376 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR F 376 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY F 393 " --> pdb=" O THR F 374 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR F 374 " --> pdb=" O GLY F 393 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER F 359 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR F 417 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE F 364 " --> pdb=" O THR F 417 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 419 " --> pdb=" O ILE F 364 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA F 444 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N HIS F 420 " --> pdb=" O ALA F 444 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU F 446 " --> pdb=" O HIS F 420 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 220 through 224 removed outlier: 6.736A pdb=" N VAL G 197 " --> pdb=" O PHE G 55 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU G 57 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR G 199 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA G 59 " --> pdb=" O TYR G 199 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY G 201 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 308 through 310 removed outlier: 6.306A pdb=" N ILE G 386 " --> pdb=" O VAL G 472 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG G 474 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU G 388 " --> pdb=" O ARG G 474 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL G 378 " --> pdb=" O MET G 389 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL G 391 " --> pdb=" O TYR G 376 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR G 376 " --> pdb=" O VAL G 391 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY G 393 " --> pdb=" O THR G 374 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR G 374 " --> pdb=" O GLY G 393 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER G 359 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR G 417 " --> pdb=" O LEU G 362 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE G 364 " --> pdb=" O THR G 417 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL G 419 " --> pdb=" O ILE G 364 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA G 444 " --> pdb=" O VAL G 418 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N HIS G 420 " --> pdb=" O ALA G 444 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU G 446 " --> pdb=" O HIS G 420 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 220 through 224 removed outlier: 6.720A pdb=" N VAL H 197 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU H 57 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR H 199 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ALA H 59 " --> pdb=" O TYR H 199 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY H 201 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 308 through 310 removed outlier: 6.288A pdb=" N ILE H 386 " --> pdb=" O VAL H 472 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ARG H 474 " --> pdb=" O ILE H 386 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU H 388 " --> pdb=" O ARG H 474 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL H 378 " --> pdb=" O MET H 389 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL H 391 " --> pdb=" O TYR H 376 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR H 376 " --> pdb=" O VAL H 391 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY H 393 " --> pdb=" O THR H 374 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR H 374 " --> pdb=" O GLY H 393 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER H 359 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR H 417 " --> pdb=" O LEU H 362 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE H 364 " --> pdb=" O THR H 417 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL H 419 " --> pdb=" O ILE H 364 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA H 444 " --> pdb=" O VAL H 418 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N HIS H 420 " --> pdb=" O ALA H 444 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU H 446 " --> pdb=" O HIS H 420 " (cutoff:3.500A) 3168 hydrogen bonds defined for protein. 8808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 37.39 Time building geometry restraints manager: 28.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 27034 1.34 - 1.46: 18237 1.46 - 1.58: 37597 1.58 - 1.71: 20 1.71 - 1.83: 464 Bond restraints: 83352 Sorted by residual: bond pdb=" CG PRO C 96 " pdb=" CD PRO C 96 " ideal model delta sigma weight residual 1.503 1.358 0.145 3.40e-02 8.65e+02 1.83e+01 bond pdb=" CG PRO A 96 " pdb=" CD PRO A 96 " ideal model delta sigma weight residual 1.503 1.359 0.144 3.40e-02 8.65e+02 1.80e+01 bond pdb=" C LEU C 546 " pdb=" N ARG C 547 " ideal model delta sigma weight residual 1.331 1.446 -0.115 2.83e-02 1.25e+03 1.65e+01 bond pdb=" C LEU A 546 " pdb=" N ARG A 547 " ideal model delta sigma weight residual 1.331 1.445 -0.114 2.83e-02 1.25e+03 1.63e+01 bond pdb=" CB PRO B1923 " pdb=" CG PRO B1923 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 ... (remaining 83347 not shown) Histogram of bond angle deviations from ideal: 89.15 - 99.29: 28 99.29 - 109.44: 8865 109.44 - 119.58: 64240 119.58 - 129.72: 39103 129.72 - 139.87: 760 Bond angle restraints: 112996 Sorted by residual: angle pdb=" CA PRO D1923 " pdb=" N PRO D1923 " pdb=" CD PRO D1923 " ideal model delta sigma weight residual 112.00 94.87 17.13 1.40e+00 5.10e-01 1.50e+02 angle pdb=" CA PRO B1923 " pdb=" N PRO B1923 " pdb=" CD PRO B1923 " ideal model delta sigma weight residual 112.00 94.90 17.10 1.40e+00 5.10e-01 1.49e+02 angle pdb=" CA PRO F 191 " pdb=" N PRO F 191 " pdb=" CD PRO F 191 " ideal model delta sigma weight residual 112.00 99.89 12.11 1.40e+00 5.10e-01 7.48e+01 angle pdb=" CA PRO H 191 " pdb=" N PRO H 191 " pdb=" CD PRO H 191 " ideal model delta sigma weight residual 112.00 99.93 12.07 1.40e+00 5.10e-01 7.44e+01 angle pdb=" CA PRO G 191 " pdb=" N PRO G 191 " pdb=" CD PRO G 191 " ideal model delta sigma weight residual 112.00 99.94 12.06 1.40e+00 5.10e-01 7.42e+01 ... (remaining 112991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.19: 46609 18.19 - 36.39: 3026 36.39 - 54.58: 684 54.58 - 72.78: 233 72.78 - 90.97: 68 Dihedral angle restraints: 50620 sinusoidal: 20722 harmonic: 29898 Sorted by residual: dihedral pdb=" CA PRO B 548 " pdb=" C PRO B 548 " pdb=" N LEU B 549 " pdb=" CA LEU B 549 " ideal model delta harmonic sigma weight residual 180.00 135.88 44.12 0 5.00e+00 4.00e-02 7.79e+01 dihedral pdb=" CA PRO D 548 " pdb=" C PRO D 548 " pdb=" N LEU D 549 " pdb=" CA LEU D 549 " ideal model delta harmonic sigma weight residual 180.00 135.96 44.04 0 5.00e+00 4.00e-02 7.76e+01 dihedral pdb=" CA PRO A 548 " pdb=" C PRO A 548 " pdb=" N LEU A 549 " pdb=" CA LEU A 549 " ideal model delta harmonic sigma weight residual 180.00 143.13 36.87 0 5.00e+00 4.00e-02 5.44e+01 ... (remaining 50617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 9387 0.057 - 0.114: 2502 0.114 - 0.171: 557 0.171 - 0.228: 68 0.228 - 0.284: 6 Chirality restraints: 12520 Sorted by residual: chirality pdb=" CB ILE A 744 " pdb=" CA ILE A 744 " pdb=" CG1 ILE A 744 " pdb=" CG2 ILE A 744 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ASP G 162 " pdb=" N ASP G 162 " pdb=" C ASP G 162 " pdb=" CB ASP G 162 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ASP E 162 " pdb=" N ASP E 162 " pdb=" C ASP E 162 " pdb=" CB ASP E 162 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 12517 not shown) Planarity restraints: 14580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B1922 " -0.090 5.00e-02 4.00e+02 1.21e-01 2.36e+01 pdb=" N PRO B1923 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO B1923 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B1923 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D1922 " 0.089 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO D1923 " -0.208 5.00e-02 4.00e+02 pdb=" CA PRO D1923 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D1923 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1429 " -0.034 2.00e-02 2.50e+03 2.43e-02 1.47e+01 pdb=" CG TRP C1429 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP C1429 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C1429 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C1429 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C1429 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C1429 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1429 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1429 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C1429 " -0.007 2.00e-02 2.50e+03 ... (remaining 14577 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 260 2.57 - 3.16: 64629 3.16 - 3.74: 117968 3.74 - 4.32: 160901 4.32 - 4.90: 271344 Nonbonded interactions: 615102 Sorted by model distance: nonbonded pdb=" O2G ATP F 601 " pdb="MG MG F 602 " model vdw 1.993 2.170 nonbonded pdb=" O2G ATP G 601 " pdb="MG MG G 602 " model vdw 1.995 2.170 nonbonded pdb=" O2G ATP H 601 " pdb="MG MG H 602 " model vdw 1.998 2.170 nonbonded pdb=" O2G ATP E 601 " pdb="MG MG E 602 " model vdw 1.999 2.170 nonbonded pdb=" O2B ATP F 601 " pdb="MG MG F 602 " model vdw 2.013 2.170 ... (remaining 615097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 44 or resid 56 through 2087 or resid 2101 throu \ gh 2102)) selection = chain 'B' selection = (chain 'C' and (resid 15 through 44 or resid 56 through 2087 or resid 2101 throu \ gh 2102)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 12.770 Check model and map are aligned: 0.900 Set scattering table: 0.550 Process input model: 175.080 Find NCS groups from input model: 5.090 Set up NCS constraints: 0.430 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: 0.020 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 199.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5145 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 : 0.006 0.162 83352 Z= 0.366 Angle : 0.956 17.128 112996 Z= 0.524 Chirality : 0.054 0.284 12520 Planarity : 0.007 0.121 14580 Dihedral : 13.971 90.972 31236 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.14 % Allowed : 5.90 % Favored : 93.97 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.08), residues: 10156 helix: -0.26 (0.07), residues: 5352 sheet: 1.90 (0.18), residues: 778 loop : -0.39 (0.10), residues: 4026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP C1429 HIS 0.013 0.002 HIS A1070 PHE 0.048 0.003 PHE A1971 TYR 0.039 0.002 TYR D 929 ARG 0.016 0.001 ARG B 874 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20312 Ramachandran restraints generated. 10156 Oldfield, 0 Emsley, 10156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20312 Ramachandran restraints generated. 10156 Oldfield, 0 Emsley, 10156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1691 residues out of total 8804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1679 time to evaluate : 6.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ASP cc_start: 0.8398 (m-30) cc_final: 0.8179 (m-30) REVERT: A 549 LEU cc_start: 0.6696 (tp) cc_final: 0.5911 (tt) REVERT: A 851 MET cc_start: 0.5518 (mtp) cc_final: 0.5154 (ptp) REVERT: A 1110 ASP cc_start: 0.5697 (m-30) cc_final: 0.4557 (p0) REVERT: A 1350 ASP cc_start: 0.4145 (m-30) cc_final: 0.3682 (p0) REVERT: A 1366 ASP cc_start: 0.5562 (m-30) cc_final: 0.5077 (t0) REVERT: A 1470 ARG cc_start: 0.6077 (ttp-110) cc_final: 0.5657 (mtm-85) REVERT: A 1534 ASP cc_start: 0.3848 (m-30) cc_final: 0.3080 (m-30) REVERT: A 1539 TRP cc_start: 0.3693 (t-100) cc_final: 0.3381 (t-100) REVERT: A 2035 MET cc_start: 0.1219 (mmt) cc_final: 0.0703 (mmm) REVERT: B 134 ARG cc_start: 0.5325 (mtp85) cc_final: 0.4977 (mtt-85) REVERT: B 155 HIS cc_start: 0.6125 (m-70) cc_final: 0.5644 (m-70) REVERT: B 523 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7313 (ttp80) REVERT: B 549 LEU cc_start: 0.7160 (tp) cc_final: 0.6732 (tp) REVERT: B 666 LEU cc_start: 0.7506 (mt) cc_final: 0.7298 (mm) REVERT: B 784 ASP cc_start: 0.5576 (p0) cc_final: 0.4556 (t70) REVERT: B 809 ARG cc_start: 0.6225 (mtp180) cc_final: 0.5718 (mmt180) REVERT: B 1017 LEU cc_start: 0.6570 (mt) cc_final: 0.6264 (tt) REVERT: B 1280 ASP cc_start: 0.5538 (t0) cc_final: 0.5057 (m-30) REVERT: B 1404 ILE cc_start: 0.6899 (mt) cc_final: 0.6543 (tp) REVERT: B 1427 ASP cc_start: 0.4331 (p0) cc_final: 0.3460 (t0) REVERT: B 1821 ASP cc_start: 0.3139 (t0) cc_final: 0.2618 (m-30) REVERT: B 1976 MET cc_start: 0.1127 (mmt) cc_final: 0.0205 (tpt) REVERT: C 549 LEU cc_start: 0.6709 (tp) cc_final: 0.5952 (tt) REVERT: C 851 MET cc_start: 0.5568 (mtp) cc_final: 0.5161 (ptp) REVERT: C 1110 ASP cc_start: 0.5687 (m-30) cc_final: 0.4533 (p0) REVERT: C 1350 ASP cc_start: 0.4195 (m-30) cc_final: 0.3704 (p0) REVERT: C 1366 ASP cc_start: 0.5548 (m-30) cc_final: 0.5059 (t0) REVERT: C 1470 ARG cc_start: 0.6078 (ttp-110) cc_final: 0.5666 (mtm-85) REVERT: C 1534 ASP cc_start: 0.3808 (m-30) cc_final: 0.3060 (m-30) REVERT: C 1539 TRP cc_start: 0.3737 (t-100) cc_final: 0.3468 (t-100) REVERT: C 2035 MET cc_start: 0.1244 (mmt) cc_final: 0.0539 (mmm) REVERT: D 134 ARG cc_start: 0.5356 (mtp85) cc_final: 0.4998 (mtt-85) REVERT: D 155 HIS cc_start: 0.6049 (m-70) cc_final: 0.5594 (m-70) REVERT: D 164 LYS cc_start: 0.6672 (tttt) cc_final: 0.6447 (tptt) REVERT: D 549 LEU cc_start: 0.7137 (tp) cc_final: 0.6611 (tp) REVERT: D 784 ASP cc_start: 0.5558 (p0) cc_final: 0.4529 (t70) REVERT: D 809 ARG cc_start: 0.5973 (mtp180) cc_final: 0.5488 (mmt180) REVERT: D 886 ARG cc_start: 0.4727 (tpm170) cc_final: 0.4423 (tpp-160) REVERT: D 1017 LEU cc_start: 0.6574 (mt) cc_final: 0.6264 (tt) REVERT: D 1280 ASP cc_start: 0.5584 (t0) cc_final: 0.5081 (m-30) REVERT: D 1404 ILE cc_start: 0.6842 (mt) cc_final: 0.6470 (tp) REVERT: D 1427 ASP cc_start: 0.4224 (p0) cc_final: 0.3366 (t0) REVERT: D 1821 ASP cc_start: 0.3103 (t0) cc_final: 0.2586 (m-30) REVERT: D 1976 MET cc_start: 0.1107 (mmt) cc_final: 0.0192 (tpt) REVERT: E 35 LYS cc_start: 0.3454 (mttt) cc_final: 0.3208 (mmtt) REVERT: E 207 MET cc_start: 0.2648 (tmm) cc_final: 0.1811 (ttm) REVERT: E 224 TRP cc_start: 0.3483 (m-90) cc_final: 0.3282 (m-90) REVERT: E 289 MET cc_start: 0.2866 (mmm) cc_final: 0.2535 (tpp) REVERT: E 343 ASP cc_start: 0.3016 (m-30) cc_final: 0.2549 (m-30) REVERT: E 484 THR cc_start: 0.4688 (p) cc_final: 0.4312 (t) REVERT: F 20 PHE cc_start: 0.0854 (t80) cc_final: 0.0345 (t80) REVERT: F 227 GLN cc_start: 0.4245 (pt0) cc_final: 0.3982 (pt0) REVERT: F 424 PHE cc_start: 0.2562 (m-80) cc_final: 0.2181 (m-10) REVERT: F 453 MET cc_start: 0.3533 (ttt) cc_final: 0.3160 (mmt) REVERT: G 35 LYS cc_start: 0.3578 (mttt) cc_final: 0.3311 (mmtt) REVERT: G 207 MET cc_start: 0.2500 (tmm) cc_final: 0.1708 (ttm) REVERT: G 224 TRP cc_start: 0.3451 (m-90) cc_final: 0.3247 (m-90) REVERT: G 289 MET cc_start: 0.2821 (mmm) cc_final: 0.2542 (tpp) REVERT: G 343 ASP cc_start: 0.3004 (m-30) cc_final: 0.2546 (m-30) REVERT: G 484 THR cc_start: 0.4830 (p) cc_final: 0.4452 (t) REVERT: G 532 MET cc_start: -0.0341 (mtm) cc_final: -0.0630 (mtp) REVERT: H 20 PHE cc_start: 0.0835 (t80) cc_final: 0.0381 (t80) REVERT: H 227 GLN cc_start: 0.4143 (pt0) cc_final: 0.3833 (pt0) REVERT: H 424 PHE cc_start: 0.2534 (m-80) cc_final: 0.1944 (m-10) REVERT: H 453 MET cc_start: 0.3561 (ttt) cc_final: 0.3216 (mmt) outliers start: 12 outliers final: 0 residues processed: 1686 average time/residue: 0.8182 time to fit residues: 2283.3367 Evaluate side-chains 815 residues out of total 8804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 815 time to evaluate : 6.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 857 optimal weight: 6.9990 chunk 770 optimal weight: 5.9990 chunk 427 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 519 optimal weight: 9.9990 chunk 411 optimal weight: 7.9990 chunk 796 optimal weight: 0.0970 chunk 308 optimal weight: 0.5980 chunk 484 optimal weight: 0.8980 chunk 592 optimal weight: 7.9990 chunk 922 optimal weight: 6.9990 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 585 GLN A 798 HIS A 956 GLN ** A1574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 607 HIS B1030 HIS B1081 HIS B1099 HIS B1149 ASN ** B1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1865 ASN C 181 HIS C 585 GLN C 798 HIS C 956 GLN ** C1574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN D 607 HIS D1081 HIS D1099 HIS D1149 ASN D1199 HIS ** D1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1865 ASN E 104 ASN E 231 ASN F 58 GLN F 231 ASN F 423 ASN F 492 HIS G 104 ASN G 231 ASN H 58 GLN H 492 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 83352 Z= 0.194 Angle : 0.614 15.459 112996 Z= 0.319 Chirality : 0.042 0.167 12520 Planarity : 0.005 0.068 14580 Dihedral : 7.294 89.370 11478 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.72 % Allowed : 9.73 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.08), residues: 10156 helix: 0.45 (0.07), residues: 5314 sheet: 1.58 (0.18), residues: 828 loop : -0.45 (0.10), residues: 4014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 733 HIS 0.010 0.001 HIS C1656 PHE 0.020 0.002 PHE A 165 TYR 0.023 0.002 TYR H 380 ARG 0.014 0.001 ARG A1834 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20312 Ramachandran restraints generated. 10156 Oldfield, 0 Emsley, 10156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20312 Ramachandran restraints generated. 10156 Oldfield, 0 Emsley, 10156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 8804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 892 time to evaluate : 6.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 GLU cc_start: 0.8682 (tp30) cc_final: 0.8024 (tm-30) REVERT: A 597 ARG cc_start: 0.8103 (ptm160) cc_final: 0.7788 (ttp80) REVERT: A 851 MET cc_start: 0.5885 (OUTLIER) cc_final: 0.5267 (ptp) REVERT: A 853 ILE cc_start: 0.4837 (mt) cc_final: 0.4565 (mt) REVERT: A 953 MET cc_start: 0.5995 (mmm) cc_final: 0.5646 (mmp) REVERT: A 1110 ASP cc_start: 0.5485 (m-30) cc_final: 0.5015 (p0) REVERT: A 1366 ASP cc_start: 0.5641 (m-30) cc_final: 0.5095 (t0) REVERT: A 1470 ARG cc_start: 0.6073 (ttp-110) cc_final: 0.5472 (ttm-80) REVERT: A 1534 ASP cc_start: 0.3087 (m-30) cc_final: 0.2580 (t70) REVERT: A 2035 MET cc_start: 0.1323 (mmt) cc_final: 0.0947 (mpp) REVERT: B 134 ARG cc_start: 0.5319 (mtp85) cc_final: 0.4977 (mtt-85) REVERT: B 523 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7246 (ttp80) REVERT: B 549 LEU cc_start: 0.7149 (tp) cc_final: 0.6791 (tp) REVERT: B 809 ARG cc_start: 0.6099 (mtp180) cc_final: 0.5678 (mmt180) REVERT: B 1280 ASP cc_start: 0.5283 (t0) cc_final: 0.5033 (m-30) REVERT: B 1305 LYS cc_start: 0.4515 (pttt) cc_final: 0.3688 (mtpt) REVERT: B 1404 ILE cc_start: 0.7040 (mt) cc_final: 0.6606 (tp) REVERT: B 1539 TRP cc_start: 0.5514 (t60) cc_final: 0.4794 (t60) REVERT: B 1589 GLN cc_start: 0.4654 (tm-30) cc_final: 0.3349 (pt0) REVERT: B 1821 ASP cc_start: 0.2919 (t0) cc_final: 0.2485 (m-30) REVERT: B 1976 MET cc_start: 0.0845 (mmt) cc_final: 0.0157 (tpt) REVERT: C 518 GLU cc_start: 0.8677 (tp30) cc_final: 0.8021 (tm-30) REVERT: C 750 GLU cc_start: 0.6443 (mm-30) cc_final: 0.6203 (mp0) REVERT: C 851 MET cc_start: 0.5875 (OUTLIER) cc_final: 0.5253 (ptp) REVERT: C 853 ILE cc_start: 0.4831 (mt) cc_final: 0.4568 (mt) REVERT: C 953 MET cc_start: 0.6017 (mmm) cc_final: 0.5684 (mmp) REVERT: C 1110 ASP cc_start: 0.5461 (m-30) cc_final: 0.4975 (p0) REVERT: C 1366 ASP cc_start: 0.5705 (m-30) cc_final: 0.5164 (t0) REVERT: C 1384 LYS cc_start: 0.6119 (mmmt) cc_final: 0.5525 (tppt) REVERT: C 1470 ARG cc_start: 0.6082 (ttp-110) cc_final: 0.5482 (ttm-80) REVERT: C 1534 ASP cc_start: 0.3092 (m-30) cc_final: 0.2589 (t70) REVERT: C 2035 MET cc_start: 0.1352 (mmt) cc_final: 0.0931 (mpp) REVERT: D 102 THR cc_start: 0.4519 (OUTLIER) cc_final: 0.4296 (p) REVERT: D 134 ARG cc_start: 0.5322 (mtp85) cc_final: 0.4974 (mtt-85) REVERT: D 155 HIS cc_start: 0.6023 (m-70) cc_final: 0.5636 (m-70) REVERT: D 164 LYS cc_start: 0.6766 (tttt) cc_final: 0.6481 (tptt) REVERT: D 784 ASP cc_start: 0.5532 (p0) cc_final: 0.4862 (t70) REVERT: D 809 ARG cc_start: 0.6050 (mtp180) cc_final: 0.5583 (mmt180) REVERT: D 900 MET cc_start: 0.6268 (mmm) cc_final: 0.4328 (ptm) REVERT: D 1280 ASP cc_start: 0.5245 (t0) cc_final: 0.4962 (m-30) REVERT: D 1305 LYS cc_start: 0.4445 (pttt) cc_final: 0.3618 (mtpt) REVERT: D 1404 ILE cc_start: 0.7065 (mt) cc_final: 0.6639 (tp) REVERT: D 1539 TRP cc_start: 0.5483 (t60) cc_final: 0.4780 (t60) REVERT: D 1589 GLN cc_start: 0.4623 (tm-30) cc_final: 0.3371 (pt0) REVERT: D 1821 ASP cc_start: 0.2771 (t0) cc_final: 0.2397 (m-30) REVERT: D 1976 MET cc_start: 0.0834 (mmt) cc_final: 0.0153 (tpt) REVERT: E 35 LYS cc_start: 0.3516 (mttt) cc_final: 0.3282 (mptt) REVERT: E 224 TRP cc_start: 0.3475 (m-90) cc_final: 0.3190 (m-90) REVERT: E 306 ASP cc_start: 0.3308 (OUTLIER) cc_final: 0.3108 (m-30) REVERT: E 484 THR cc_start: 0.4891 (p) cc_final: 0.4509 (t) REVERT: E 527 TYR cc_start: 0.2980 (t80) cc_final: 0.2698 (t80) REVERT: F 17 LYS cc_start: 0.4238 (mtmt) cc_final: 0.3934 (tppt) REVERT: F 20 PHE cc_start: 0.1061 (t80) cc_final: 0.0437 (t80) REVERT: F 121 GLN cc_start: -0.1583 (mp10) cc_final: -0.1787 (mp10) REVERT: F 245 MET cc_start: -0.0242 (ptt) cc_final: -0.1004 (tmm) REVERT: F 373 GLU cc_start: 0.4535 (tt0) cc_final: 0.3352 (mp0) REVERT: F 446 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6773 (mt-10) REVERT: F 453 MET cc_start: 0.3148 (ttt) cc_final: 0.2793 (mmm) REVERT: F 532 MET cc_start: 0.3461 (tmm) cc_final: 0.2697 (tmm) REVERT: G 35 LYS cc_start: 0.3498 (mttt) cc_final: 0.3262 (mptt) REVERT: G 289 MET cc_start: 0.2671 (mmm) cc_final: 0.2440 (tpp) REVERT: G 306 ASP cc_start: 0.3312 (OUTLIER) cc_final: 0.3103 (m-30) REVERT: G 379 LEU cc_start: 0.4620 (mp) cc_final: 0.4131 (mt) REVERT: G 484 THR cc_start: 0.4921 (p) cc_final: 0.4530 (t) REVERT: G 527 TYR cc_start: 0.3070 (t80) cc_final: 0.2842 (t80) REVERT: H 17 LYS cc_start: 0.4227 (mtmt) cc_final: 0.3969 (tppt) REVERT: H 20 PHE cc_start: 0.1007 (t80) cc_final: 0.0415 (t80) REVERT: H 121 GLN cc_start: -0.1541 (mp10) cc_final: -0.1788 (mp10) REVERT: H 245 MET cc_start: -0.0357 (ptt) cc_final: -0.0970 (tmm) REVERT: H 453 MET cc_start: 0.3218 (ttt) cc_final: 0.2841 (mmm) REVERT: H 532 MET cc_start: 0.3180 (tmm) cc_final: 0.2827 (tmm) outliers start: 151 outliers final: 76 residues processed: 1010 average time/residue: 0.8225 time to fit residues: 1427.3537 Evaluate side-chains 787 residues out of total 8804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 705 time to evaluate : 6.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1085 SER Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1180 SER Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1268 ASP Chi-restraints excluded: chain B residue 1389 LYS Chi-restraints excluded: chain B residue 1397 THR Chi-restraints excluded: chain B residue 1489 GLU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 585 GLN Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1148 THR Chi-restraints excluded: chain C residue 1149 ASN Chi-restraints excluded: chain C residue 1747 SER Chi-restraints excluded: chain C residue 1961 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 607 HIS Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 893 THR Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain D residue 1079 THR Chi-restraints excluded: chain D residue 1085 SER Chi-restraints excluded: chain D residue 1151 LEU Chi-restraints excluded: chain D residue 1180 SER Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1216 SER Chi-restraints excluded: chain D residue 1235 ILE Chi-restraints excluded: chain D residue 1268 ASP Chi-restraints excluded: chain D residue 1397 THR Chi-restraints excluded: chain D residue 1558 TRP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 306 ASP Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 306 ASP Chi-restraints excluded: chain G residue 391 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 285 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 512 optimal weight: 20.0000 chunk 286 optimal weight: 4.9990 chunk 767 optimal weight: 4.9990 chunk 628 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 924 optimal weight: 30.0000 chunk 998 optimal weight: 20.0000 chunk 823 optimal weight: 7.9990 chunk 916 optimal weight: 40.0000 chunk 315 optimal weight: 10.0000 chunk 741 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN A 608 GLN A 771 GLN A 780 GLN A 826 GLN A 887 ASN A1081 HIS A1571 GLN A1597 ASN A1656 HIS B 155 HIS B 349 HIS ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 GLN B1030 HIS B1199 HIS ** B1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1351 GLN B1614 HIS B1651 HIS B1984 HIS C 505 ASN C 608 GLN ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 HIS C1571 GLN C1597 ASN C1656 HIS ** C1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS D 879 GLN D 985 GLN ** D1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1351 GLN D1614 HIS D1651 HIS D1984 HIS E 492 HIS E 514 HIS F 49 ASN F 52 HIS F 227 GLN G 58 GLN G 492 HIS G 514 HIS H 49 ASN H 52 HIS H 227 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5579 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 83352 Z= 0.268 Angle : 0.634 12.843 112996 Z= 0.329 Chirality : 0.043 0.265 12520 Planarity : 0.005 0.061 14580 Dihedral : 6.964 89.425 11478 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.51 % Allowed : 10.85 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.08), residues: 10156 helix: 0.43 (0.07), residues: 5368 sheet: 1.25 (0.18), residues: 834 loop : -0.48 (0.10), residues: 3954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D1264 HIS 0.048 0.002 HIS D 607 PHE 0.043 0.002 PHE C1141 TYR 0.018 0.002 TYR D 741 ARG 0.023 0.001 ARG B1758 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20312 Ramachandran restraints generated. 10156 Oldfield, 0 Emsley, 10156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20312 Ramachandran restraints generated. 10156 Oldfield, 0 Emsley, 10156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 8804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 797 time to evaluate : 6.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.4610 (mm-40) cc_final: 0.4363 (tt0) REVERT: A 452 ARG cc_start: 0.8434 (ptm-80) cc_final: 0.8062 (ptm160) REVERT: A 465 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.6524 (p0) REVERT: A 549 LEU cc_start: 0.7117 (tp) cc_final: 0.6638 (tp) REVERT: A 809 ARG cc_start: 0.5409 (mmp-170) cc_final: 0.4466 (mmt90) REVERT: A 851 MET cc_start: 0.5688 (mtp) cc_final: 0.5103 (ptp) REVERT: A 1110 ASP cc_start: 0.5491 (m-30) cc_final: 0.5013 (p0) REVERT: A 1366 ASP cc_start: 0.5903 (m-30) cc_final: 0.5213 (t0) REVERT: A 1656 HIS cc_start: 0.3386 (OUTLIER) cc_final: 0.2453 (t70) REVERT: A 2035 MET cc_start: 0.1344 (mmt) cc_final: 0.0975 (mpp) REVERT: B 134 ARG cc_start: 0.5511 (mtp85) cc_final: 0.5074 (mtt-85) REVERT: B 237 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7270 (t0) REVERT: B 300 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8762 (tt) REVERT: B 301 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: B 523 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7304 (ttp80) REVERT: B 549 LEU cc_start: 0.7418 (tp) cc_final: 0.6965 (tp) REVERT: B 648 GLN cc_start: 0.4984 (mp10) cc_final: 0.4563 (mm-40) REVERT: B 659 ARG cc_start: 0.6597 (tpp80) cc_final: 0.6138 (mmt-90) REVERT: B 809 ARG cc_start: 0.6535 (mtp180) cc_final: 0.5854 (mmt180) REVERT: B 1280 ASP cc_start: 0.5374 (t0) cc_final: 0.5073 (m-30) REVERT: B 1305 LYS cc_start: 0.4527 (pttt) cc_final: 0.3589 (mtpt) REVERT: B 1404 ILE cc_start: 0.6988 (mt) cc_final: 0.6470 (tp) REVERT: B 1427 ASP cc_start: 0.3873 (p0) cc_final: 0.3048 (t0) REVERT: B 1821 ASP cc_start: 0.3190 (t0) cc_final: 0.2614 (m-30) REVERT: B 1976 MET cc_start: 0.1004 (mmt) cc_final: -0.0078 (tpt) REVERT: C 51 GLN cc_start: 0.4601 (mm-40) cc_final: 0.4300 (tm-30) REVERT: C 452 ARG cc_start: 0.8439 (ptm-80) cc_final: 0.8084 (ptm160) REVERT: C 465 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6478 (p0) REVERT: C 549 LEU cc_start: 0.7085 (tp) cc_final: 0.6661 (tp) REVERT: C 851 MET cc_start: 0.5680 (mtp) cc_final: 0.5094 (ptp) REVERT: C 1110 ASP cc_start: 0.5487 (m-30) cc_final: 0.5004 (p0) REVERT: C 1366 ASP cc_start: 0.5907 (m-30) cc_final: 0.5213 (t0) REVERT: C 1656 HIS cc_start: 0.3377 (OUTLIER) cc_final: 0.2413 (t70) REVERT: C 2035 MET cc_start: 0.1180 (mmt) cc_final: 0.0856 (mpp) REVERT: C 2037 LEU cc_start: 0.4372 (OUTLIER) cc_final: 0.3737 (mt) REVERT: D 102 THR cc_start: 0.4850 (OUTLIER) cc_final: 0.4522 (p) REVERT: D 134 ARG cc_start: 0.5502 (OUTLIER) cc_final: 0.5059 (mtt-85) REVERT: D 155 HIS cc_start: 0.6119 (m-70) cc_final: 0.5786 (m-70) REVERT: D 164 LYS cc_start: 0.6776 (tttt) cc_final: 0.6472 (tptt) REVERT: D 300 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8760 (tt) REVERT: D 648 GLN cc_start: 0.4987 (mp10) cc_final: 0.4564 (mm-40) REVERT: D 659 ARG cc_start: 0.6655 (tpp80) cc_final: 0.6191 (mmt-90) REVERT: D 809 ARG cc_start: 0.6252 (mtp180) cc_final: 0.5893 (mmt180) REVERT: D 879 GLN cc_start: 0.4681 (OUTLIER) cc_final: 0.4274 (mm-40) REVERT: D 1280 ASP cc_start: 0.5377 (t0) cc_final: 0.5081 (m-30) REVERT: D 1305 LYS cc_start: 0.4502 (pttt) cc_final: 0.3554 (mtpt) REVERT: D 1404 ILE cc_start: 0.6975 (mt) cc_final: 0.6431 (tp) REVERT: D 1427 ASP cc_start: 0.3780 (p0) cc_final: 0.2995 (t0) REVERT: D 1817 LEU cc_start: 0.4606 (tp) cc_final: 0.4287 (mp) REVERT: D 1821 ASP cc_start: 0.2955 (t0) cc_final: 0.2502 (m-30) REVERT: D 1976 MET cc_start: 0.1062 (mmt) cc_final: 0.0001 (tpt) REVERT: D 2008 LYS cc_start: 0.2888 (OUTLIER) cc_final: 0.2055 (ttpt) REVERT: E 35 LYS cc_start: 0.3743 (mttt) cc_final: 0.3478 (mptt) REVERT: E 379 LEU cc_start: 0.4508 (mp) cc_final: 0.3918 (mt) REVERT: E 389 MET cc_start: 0.3981 (mpp) cc_final: 0.2912 (ptp) REVERT: E 486 ARG cc_start: 0.4789 (mmt-90) cc_final: 0.4294 (ttm-80) REVERT: E 527 TYR cc_start: 0.3226 (t80) cc_final: 0.2919 (t80) REVERT: F 17 LYS cc_start: 0.4500 (mtmt) cc_final: 0.4072 (tppt) REVERT: F 20 PHE cc_start: 0.1383 (t80) cc_final: 0.0671 (t80) REVERT: F 117 PRO cc_start: 0.2710 (Cg_endo) cc_final: 0.2229 (Cg_exo) REVERT: F 245 MET cc_start: -0.0383 (ptt) cc_final: -0.0993 (tmm) REVERT: F 446 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6832 (mt-10) REVERT: G 35 LYS cc_start: 0.3766 (mttt) cc_final: 0.3493 (mptt) REVERT: G 389 MET cc_start: 0.4046 (mpp) cc_final: 0.2951 (ptp) REVERT: G 486 ARG cc_start: 0.4637 (mmt-90) cc_final: 0.4164 (ttm-80) REVERT: G 527 TYR cc_start: 0.3147 (t80) cc_final: 0.2816 (t80) REVERT: H 17 LYS cc_start: 0.4431 (mtmt) cc_final: 0.4076 (tppt) REVERT: H 20 PHE cc_start: 0.1276 (t80) cc_final: 0.0643 (t80) REVERT: H 117 PRO cc_start: 0.2630 (Cg_endo) cc_final: 0.2136 (Cg_exo) REVERT: H 245 MET cc_start: -0.0447 (ptt) cc_final: -0.1058 (tmm) REVERT: H 306 ASP cc_start: 0.3903 (OUTLIER) cc_final: 0.3089 (t0) REVERT: H 389 MET cc_start: 0.5461 (ptp) cc_final: 0.5011 (ptp) REVERT: H 413 TRP cc_start: 0.5083 (m100) cc_final: 0.4418 (m100) REVERT: H 453 MET cc_start: 0.3280 (ttt) cc_final: 0.2947 (mmm) outliers start: 221 outliers final: 141 residues processed: 976 average time/residue: 0.7641 time to fit residues: 1278.3863 Evaluate side-chains 841 residues out of total 8804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 685 time to evaluate : 6.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1224 TRP Chi-restraints excluded: chain A residue 1421 ILE Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1462 ILE Chi-restraints excluded: chain A residue 1485 GLU Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1656 HIS Chi-restraints excluded: chain A residue 1679 ASN Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 587 PHE Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 893 THR Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1085 SER Chi-restraints excluded: chain B residue 1126 SER Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1169 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1268 ASP Chi-restraints excluded: chain B residue 1397 THR Chi-restraints excluded: chain B residue 1885 CYS Chi-restraints excluded: chain B residue 1988 TYR Chi-restraints excluded: chain B residue 2020 CYS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 838 GLN Chi-restraints excluded: chain C residue 1044 ASN Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain C residue 1148 THR Chi-restraints excluded: chain C residue 1149 ASN Chi-restraints excluded: chain C residue 1224 TRP Chi-restraints excluded: chain C residue 1421 ILE Chi-restraints excluded: chain C residue 1437 THR Chi-restraints excluded: chain C residue 1462 ILE Chi-restraints excluded: chain C residue 1485 GLU Chi-restraints excluded: chain C residue 1487 ILE Chi-restraints excluded: chain C residue 1547 THR Chi-restraints excluded: chain C residue 1568 MET Chi-restraints excluded: chain C residue 1656 HIS Chi-restraints excluded: chain C residue 1747 SER Chi-restraints excluded: chain C residue 1779 TYR Chi-restraints excluded: chain C residue 1961 VAL Chi-restraints excluded: chain C residue 2037 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 610 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 770 SER Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 879 GLN Chi-restraints excluded: chain D residue 893 THR Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain D residue 1079 THR Chi-restraints excluded: chain D residue 1085 SER Chi-restraints excluded: chain D residue 1126 SER Chi-restraints excluded: chain D residue 1151 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1216 SER Chi-restraints excluded: chain D residue 1235 ILE Chi-restraints excluded: chain D residue 1268 ASP Chi-restraints excluded: chain D residue 1397 THR Chi-restraints excluded: chain D residue 1558 TRP Chi-restraints excluded: chain D residue 1885 CYS Chi-restraints excluded: chain D residue 1988 TYR Chi-restraints excluded: chain D residue 2008 LYS Chi-restraints excluded: chain D residue 2020 CYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 306 ASP Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 306 ASP Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 391 VAL Chi-restraints excluded: chain G residue 479 ARG Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 386 ILE Chi-restraints excluded: chain H residue 406 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 913 optimal weight: 7.9990 chunk 694 optimal weight: 0.9990 chunk 479 optimal weight: 7.9990 chunk 102 optimal weight: 30.0000 chunk 441 optimal weight: 2.9990 chunk 620 optimal weight: 6.9990 chunk 927 optimal weight: 9.9990 chunk 982 optimal weight: 40.0000 chunk 484 optimal weight: 7.9990 chunk 879 optimal weight: 0.8980 chunk 264 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 ASN B 998 ASN B1030 HIS ** B1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN C 771 GLN ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 826 GLN ** C 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 ASN D 998 ASN ** D1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 104 ASN E 412 GLN E 469 HIS F 49 ASN F 227 GLN F 469 HIS G 104 ASN G 412 GLN G 469 HIS H 49 ASN H 469 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 83352 Z= 0.228 Angle : 0.582 14.767 112996 Z= 0.303 Chirality : 0.042 0.177 12520 Planarity : 0.005 0.061 14580 Dihedral : 6.581 85.990 11478 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.53 % Allowed : 12.46 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.08), residues: 10156 helix: 0.50 (0.07), residues: 5322 sheet: 1.08 (0.18), residues: 838 loop : -0.51 (0.10), residues: 3996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C1000 HIS 0.028 0.001 HIS C1656 PHE 0.035 0.002 PHE A1141 TYR 0.015 0.002 TYR F 500 ARG 0.009 0.001 ARG H 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20312 Ramachandran restraints generated. 10156 Oldfield, 0 Emsley, 10156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20312 Ramachandran restraints generated. 10156 Oldfield, 0 Emsley, 10156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 8804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 754 time to evaluate : 6.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.4698 (mm-40) cc_final: 0.4372 (tm-30) REVERT: A 549 LEU cc_start: 0.7177 (tp) cc_final: 0.6641 (tp) REVERT: A 809 ARG cc_start: 0.5445 (mmp-170) cc_final: 0.4654 (mmt90) REVERT: A 851 MET cc_start: 0.5873 (OUTLIER) cc_final: 0.5337 (ptp) REVERT: A 1110 ASP cc_start: 0.5405 (m-30) cc_final: 0.4922 (p0) REVERT: A 1366 ASP cc_start: 0.5919 (m-30) cc_final: 0.5165 (t0) REVERT: A 1487 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7342 (tt) REVERT: A 1829 TRP cc_start: 0.3055 (m100) cc_final: 0.2592 (m100) REVERT: A 2035 MET cc_start: 0.1198 (mmt) cc_final: 0.0928 (mpp) REVERT: B 134 ARG cc_start: 0.5580 (OUTLIER) cc_final: 0.4866 (mmt180) REVERT: B 237 ASP cc_start: 0.7670 (m-30) cc_final: 0.7289 (t0) REVERT: B 301 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8053 (tp30) REVERT: B 523 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7333 (ttp80) REVERT: B 549 LEU cc_start: 0.7435 (tp) cc_final: 0.6998 (tp) REVERT: B 648 GLN cc_start: 0.5036 (mp10) cc_final: 0.4710 (mm-40) REVERT: B 659 ARG cc_start: 0.6613 (tpp80) cc_final: 0.6180 (mmt-90) REVERT: B 809 ARG cc_start: 0.6369 (mtp180) cc_final: 0.5708 (mmt180) REVERT: B 997 TYR cc_start: 0.3068 (m-80) cc_final: 0.2820 (m-80) REVERT: B 1060 ASP cc_start: 0.5595 (OUTLIER) cc_final: 0.5245 (t0) REVERT: B 1280 ASP cc_start: 0.5256 (t0) cc_final: 0.5052 (m-30) REVERT: B 1404 ILE cc_start: 0.6906 (mt) cc_final: 0.6406 (tp) REVERT: B 1427 ASP cc_start: 0.4130 (p0) cc_final: 0.3389 (t0) REVERT: B 1582 MET cc_start: 0.1701 (OUTLIER) cc_final: 0.1107 (ttp) REVERT: B 1821 ASP cc_start: 0.3078 (t0) cc_final: 0.2478 (m-30) REVERT: B 1866 GLU cc_start: 0.3723 (OUTLIER) cc_final: 0.3229 (mt-10) REVERT: B 1976 MET cc_start: 0.1275 (mmt) cc_final: -0.0017 (tpt) REVERT: C 51 GLN cc_start: 0.4690 (mm-40) cc_final: 0.4385 (tm-30) REVERT: C 549 LEU cc_start: 0.7166 (tp) cc_final: 0.6784 (tp) REVERT: C 851 MET cc_start: 0.5865 (OUTLIER) cc_final: 0.5313 (ptp) REVERT: C 953 MET cc_start: 0.5873 (mmm) cc_final: 0.5543 (mmt) REVERT: C 966 GLU cc_start: 0.3617 (OUTLIER) cc_final: 0.3415 (pt0) REVERT: C 1110 ASP cc_start: 0.5409 (m-30) cc_final: 0.4909 (p0) REVERT: C 1366 ASP cc_start: 0.6003 (m-30) cc_final: 0.5197 (t0) REVERT: C 1487 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7329 (tt) REVERT: C 1829 TRP cc_start: 0.3083 (m100) cc_final: 0.2578 (m100) REVERT: C 2035 MET cc_start: 0.1106 (mmt) cc_final: 0.0843 (mpp) REVERT: D 102 THR cc_start: 0.4791 (OUTLIER) cc_final: 0.4433 (p) REVERT: D 134 ARG cc_start: 0.5484 (mtp85) cc_final: 0.5140 (mtt-85) REVERT: D 164 LYS cc_start: 0.6737 (tttt) cc_final: 0.6397 (tptt) REVERT: D 301 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: D 648 GLN cc_start: 0.5037 (mp10) cc_final: 0.4715 (mm-40) REVERT: D 659 ARG cc_start: 0.6664 (tpp80) cc_final: 0.6217 (mmt-90) REVERT: D 809 ARG cc_start: 0.6254 (mtp180) cc_final: 0.5804 (mmt180) REVERT: D 890 ASN cc_start: 0.4219 (t0) cc_final: 0.3960 (m-40) REVERT: D 900 MET cc_start: 0.7765 (tpp) cc_final: 0.6588 (mtp) REVERT: D 1060 ASP cc_start: 0.5572 (OUTLIER) cc_final: 0.5240 (t0) REVERT: D 1280 ASP cc_start: 0.5254 (t0) cc_final: 0.5034 (m-30) REVERT: D 1404 ILE cc_start: 0.6923 (mt) cc_final: 0.6428 (tp) REVERT: D 1427 ASP cc_start: 0.4133 (p0) cc_final: 0.3473 (t0) REVERT: D 1817 LEU cc_start: 0.4669 (tp) cc_final: 0.4335 (mp) REVERT: D 1821 ASP cc_start: 0.2797 (t0) cc_final: 0.2343 (m-30) REVERT: D 1866 GLU cc_start: 0.3855 (OUTLIER) cc_final: 0.3348 (mt-10) REVERT: D 1976 MET cc_start: 0.1165 (mmt) cc_final: -0.0137 (tpt) REVERT: D 2008 LYS cc_start: 0.2708 (OUTLIER) cc_final: 0.2203 (ttpt) REVERT: E 35 LYS cc_start: 0.4057 (mttt) cc_final: 0.3730 (mptt) REVERT: E 362 LEU cc_start: 0.2308 (pt) cc_final: 0.2031 (pp) REVERT: E 389 MET cc_start: 0.3747 (mpp) cc_final: 0.2840 (ptp) REVERT: E 486 ARG cc_start: 0.4709 (mmt-90) cc_final: 0.4377 (ttm-80) REVERT: E 517 ARG cc_start: 0.4661 (mtt90) cc_final: 0.4201 (mtt180) REVERT: F 17 LYS cc_start: 0.4585 (mtmt) cc_final: 0.4181 (tppt) REVERT: F 45 ARG cc_start: 0.5812 (mtm180) cc_final: 0.5509 (tpp-160) REVERT: F 121 GLN cc_start: -0.0820 (mp10) cc_final: -0.1186 (pm20) REVERT: F 207 MET cc_start: 0.2151 (tmm) cc_final: 0.1861 (mtp) REVERT: F 245 MET cc_start: -0.0490 (ptt) cc_final: -0.1076 (tmm) REVERT: F 289 MET cc_start: 0.2498 (mmp) cc_final: 0.2217 (mmt) REVERT: F 446 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: G 35 LYS cc_start: 0.4058 (mttt) cc_final: 0.3731 (mptt) REVERT: G 289 MET cc_start: 0.3055 (mmm) cc_final: 0.2099 (mmm) REVERT: G 389 MET cc_start: 0.3894 (mpp) cc_final: 0.2924 (ptp) REVERT: G 517 ARG cc_start: 0.4493 (mtt90) cc_final: 0.4103 (mtt180) REVERT: H 17 LYS cc_start: 0.4677 (mtmt) cc_final: 0.4298 (tppt) REVERT: H 245 MET cc_start: -0.0606 (ptt) cc_final: -0.1150 (tmm) REVERT: H 289 MET cc_start: 0.3552 (mmt) cc_final: 0.3084 (mmp) REVERT: H 389 MET cc_start: 0.5487 (ptp) cc_final: 0.5274 (ptp) REVERT: H 413 TRP cc_start: 0.4994 (m100) cc_final: 0.4264 (m100) outliers start: 223 outliers final: 159 residues processed: 935 average time/residue: 0.7626 time to fit residues: 1226.0590 Evaluate side-chains 827 residues out of total 8804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 652 time to evaluate : 6.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1149 ASN Chi-restraints excluded: chain A residue 1224 TRP Chi-restraints excluded: chain A residue 1421 ILE Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1462 ILE Chi-restraints excluded: chain A residue 1485 GLU Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1530 LEU Chi-restraints excluded: chain A residue 1543 LEU Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1614 HIS Chi-restraints excluded: chain A residue 1679 ASN Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1747 SER Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1921 LYS Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 587 PHE Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 893 THR Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1060 ASP Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1085 SER Chi-restraints excluded: chain B residue 1126 SER Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1169 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1236 LEU Chi-restraints excluded: chain B residue 1397 THR Chi-restraints excluded: chain B residue 1507 VAL Chi-restraints excluded: chain B residue 1582 MET Chi-restraints excluded: chain B residue 1734 MET Chi-restraints excluded: chain B residue 1866 GLU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 966 GLU Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain C residue 1148 THR Chi-restraints excluded: chain C residue 1149 ASN Chi-restraints excluded: chain C residue 1224 TRP Chi-restraints excluded: chain C residue 1421 ILE Chi-restraints excluded: chain C residue 1427 ASP Chi-restraints excluded: chain C residue 1430 THR Chi-restraints excluded: chain C residue 1437 THR Chi-restraints excluded: chain C residue 1462 ILE Chi-restraints excluded: chain C residue 1485 GLU Chi-restraints excluded: chain C residue 1487 ILE Chi-restraints excluded: chain C residue 1530 LEU Chi-restraints excluded: chain C residue 1543 LEU Chi-restraints excluded: chain C residue 1547 THR Chi-restraints excluded: chain C residue 1557 ILE Chi-restraints excluded: chain C residue 1614 HIS Chi-restraints excluded: chain C residue 1687 SER Chi-restraints excluded: chain C residue 1747 SER Chi-restraints excluded: chain C residue 1779 TYR Chi-restraints excluded: chain C residue 1942 ILE Chi-restraints excluded: chain C residue 1961 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 770 SER Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 893 THR Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain D residue 936 SER Chi-restraints excluded: chain D residue 982 ASP Chi-restraints excluded: chain D residue 1060 ASP Chi-restraints excluded: chain D residue 1079 THR Chi-restraints excluded: chain D residue 1085 SER Chi-restraints excluded: chain D residue 1126 SER Chi-restraints excluded: chain D residue 1151 LEU Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1216 SER Chi-restraints excluded: chain D residue 1235 ILE Chi-restraints excluded: chain D residue 1236 LEU Chi-restraints excluded: chain D residue 1397 THR Chi-restraints excluded: chain D residue 1507 VAL Chi-restraints excluded: chain D residue 1558 TRP Chi-restraints excluded: chain D residue 1734 MET Chi-restraints excluded: chain D residue 1866 GLU Chi-restraints excluded: chain D residue 2008 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 306 ASP Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 306 ASP Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 386 ILE Chi-restraints excluded: chain H residue 406 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 817 optimal weight: 20.0000 chunk 557 optimal weight: 50.0000 chunk 14 optimal weight: 10.0000 chunk 731 optimal weight: 0.3980 chunk 405 optimal weight: 4.9990 chunk 838 optimal weight: 50.0000 chunk 678 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 501 optimal weight: 3.9990 chunk 881 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 GLN A 830 HIS A 892 GLN ** A1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 GLN B 879 GLN B 917 GLN B1232 HIS ** B1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 826 GLN C 830 HIS ** C 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 892 GLN ** C1846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 917 GLN D1232 HIS F 82 GLN F 216 ASN F 227 GLN F 469 HIS G 82 GLN H 82 GLN H 216 ASN H 227 GLN H 469 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 83352 Z= 0.287 Angle : 0.656 12.419 112996 Z= 0.343 Chirality : 0.045 0.283 12520 Planarity : 0.006 0.077 14580 Dihedral : 6.472 85.629 11478 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.61 % Allowed : 13.32 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.08), residues: 10156 helix: 0.23 (0.07), residues: 5300 sheet: 0.75 (0.17), residues: 864 loop : -0.81 (0.10), residues: 3992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A1539 HIS 0.010 0.002 HIS A1656 PHE 0.036 0.002 PHE G 288 TYR 0.019 0.002 TYR B1293 ARG 0.028 0.001 ARG C 808 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20312 Ramachandran restraints generated. 10156 Oldfield, 0 Emsley, 10156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20312 Ramachandran restraints generated. 10156 Oldfield, 0 Emsley, 10156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 8804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 720 time to evaluate : 6.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.4915 (mm-40) cc_final: 0.4587 (tm-30) REVERT: A 549 LEU cc_start: 0.7497 (tp) cc_final: 0.7030 (tp) REVERT: A 717 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7719 (m-40) REVERT: A 808 ARG cc_start: 0.5058 (mtm-85) cc_final: 0.4096 (mmm160) REVERT: A 809 ARG cc_start: 0.5867 (mmp-170) cc_final: 0.5067 (mmt90) REVERT: A 825 MET cc_start: 0.5914 (OUTLIER) cc_final: 0.5617 (ttt) REVERT: A 851 MET cc_start: 0.5954 (mtp) cc_final: 0.5350 (ptp) REVERT: A 936 SER cc_start: 0.4905 (OUTLIER) cc_final: 0.4662 (t) REVERT: A 1000 TRP cc_start: 0.5214 (t60) cc_final: 0.4935 (t60) REVERT: A 1110 ASP cc_start: 0.5912 (m-30) cc_final: 0.5252 (p0) REVERT: A 1330 HIS cc_start: 0.3122 (OUTLIER) cc_final: 0.1595 (t70) REVERT: A 1366 ASP cc_start: 0.6158 (m-30) cc_final: 0.5269 (t0) REVERT: A 1461 GLU cc_start: 0.4203 (mt-10) cc_final: 0.3966 (tt0) REVERT: A 1745 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6178 (tppt) REVERT: A 1801 LEU cc_start: 0.3294 (OUTLIER) cc_final: 0.2714 (mp) REVERT: A 1829 TRP cc_start: 0.3189 (m100) cc_final: 0.2745 (m100) REVERT: A 2035 MET cc_start: 0.1367 (mmt) cc_final: 0.0945 (mpp) REVERT: B 32 GLN cc_start: 0.7091 (mt0) cc_final: 0.6819 (mp10) REVERT: B 301 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8093 (tp30) REVERT: B 523 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7312 (ttp80) REVERT: B 659 ARG cc_start: 0.6652 (tpp80) cc_final: 0.6253 (mmt-90) REVERT: B 667 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.6755 (mt0) REVERT: B 809 ARG cc_start: 0.6554 (mtp180) cc_final: 0.5861 (mmt180) REVERT: B 900 MET cc_start: 0.6412 (mmm) cc_final: 0.6090 (mtm) REVERT: B 997 TYR cc_start: 0.3043 (m-80) cc_final: 0.2769 (m-10) REVERT: B 1060 ASP cc_start: 0.5906 (OUTLIER) cc_final: 0.5480 (t0) REVERT: B 1280 ASP cc_start: 0.5542 (t0) cc_final: 0.5076 (m-30) REVERT: B 1427 ASP cc_start: 0.4345 (p0) cc_final: 0.3908 (t70) REVERT: B 1821 ASP cc_start: 0.3293 (t0) cc_final: 0.2518 (m-30) REVERT: B 1866 GLU cc_start: 0.3610 (OUTLIER) cc_final: 0.3049 (mt-10) REVERT: B 1976 MET cc_start: 0.1793 (mmt) cc_final: 0.0294 (tpt) REVERT: B 1988 TYR cc_start: 0.0783 (OUTLIER) cc_final: 0.0556 (t80) REVERT: C 51 GLN cc_start: 0.4881 (mm-40) cc_final: 0.4532 (tm-30) REVERT: C 549 LEU cc_start: 0.7460 (tp) cc_final: 0.6970 (tp) REVERT: C 717 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7672 (m-40) REVERT: C 809 ARG cc_start: 0.5541 (mmp-170) cc_final: 0.4780 (mmt90) REVERT: C 825 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.6007 (tmm) REVERT: C 851 MET cc_start: 0.6105 (OUTLIER) cc_final: 0.5489 (ptp) REVERT: C 903 MET cc_start: 0.3718 (OUTLIER) cc_final: 0.2601 (mmt) REVERT: C 936 SER cc_start: 0.4912 (OUTLIER) cc_final: 0.4685 (t) REVERT: C 953 MET cc_start: 0.6083 (mmm) cc_final: 0.5490 (mmt) REVERT: C 966 GLU cc_start: 0.4120 (OUTLIER) cc_final: 0.3849 (pt0) REVERT: C 1000 TRP cc_start: 0.5178 (t60) cc_final: 0.4881 (t60) REVERT: C 1110 ASP cc_start: 0.5854 (m-30) cc_final: 0.5221 (p0) REVERT: C 1149 ASN cc_start: 0.6376 (OUTLIER) cc_final: 0.6155 (m110) REVERT: C 1330 HIS cc_start: 0.2991 (OUTLIER) cc_final: 0.1540 (t70) REVERT: C 1366 ASP cc_start: 0.6173 (m-30) cc_final: 0.5285 (t0) REVERT: C 1399 LYS cc_start: 0.6986 (mttt) cc_final: 0.5769 (pptt) REVERT: C 1461 GLU cc_start: 0.3980 (mt-10) cc_final: 0.3333 (mp0) REVERT: C 1745 LYS cc_start: 0.5401 (tppt) cc_final: 0.4954 (tmtt) REVERT: C 1801 LEU cc_start: 0.3302 (OUTLIER) cc_final: 0.2808 (mp) REVERT: C 1829 TRP cc_start: 0.3187 (m100) cc_final: 0.2749 (m100) REVERT: C 2035 MET cc_start: 0.1199 (mmt) cc_final: 0.0891 (mpp) REVERT: D 102 THR cc_start: 0.4876 (OUTLIER) cc_final: 0.4495 (p) REVERT: D 164 LYS cc_start: 0.6719 (tttt) cc_final: 0.6335 (tptt) REVERT: D 301 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7733 (tp30) REVERT: D 587 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8662 (m-80) REVERT: D 659 ARG cc_start: 0.6691 (tpp80) cc_final: 0.6278 (mmt-90) REVERT: D 667 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6781 (mt0) REVERT: D 809 ARG cc_start: 0.6470 (mtp180) cc_final: 0.5949 (mmt180) REVERT: D 873 TRP cc_start: 0.5502 (t-100) cc_final: 0.4998 (m-90) REVERT: D 890 ASN cc_start: 0.4223 (t0) cc_final: 0.4002 (m-40) REVERT: D 900 MET cc_start: 0.7624 (tpp) cc_final: 0.6705 (mtp) REVERT: D 997 TYR cc_start: 0.3237 (m-80) cc_final: 0.3019 (m-80) REVERT: D 1060 ASP cc_start: 0.5837 (OUTLIER) cc_final: 0.5420 (t0) REVERT: D 1280 ASP cc_start: 0.5617 (t0) cc_final: 0.5098 (m-30) REVERT: D 1427 ASP cc_start: 0.4379 (p0) cc_final: 0.3936 (t70) REVERT: D 1817 LEU cc_start: 0.4835 (tp) cc_final: 0.4538 (mp) REVERT: D 1821 ASP cc_start: 0.3006 (t0) cc_final: 0.2200 (m-30) REVERT: D 1866 GLU cc_start: 0.3672 (OUTLIER) cc_final: 0.3101 (mt-10) REVERT: D 1976 MET cc_start: 0.1763 (mmt) cc_final: 0.0282 (tpt) REVERT: D 2008 LYS cc_start: 0.2938 (OUTLIER) cc_final: 0.2186 (ttpt) REVERT: E 35 LYS cc_start: 0.3996 (mttt) cc_final: 0.3773 (mptt) REVERT: E 362 LEU cc_start: 0.2850 (pt) cc_final: 0.2649 (pp) REVERT: E 517 ARG cc_start: 0.4611 (mtt90) cc_final: 0.4312 (mtt180) REVERT: F 45 ARG cc_start: 0.6045 (mtm180) cc_final: 0.5585 (tpp-160) REVERT: F 200 LEU cc_start: 0.0571 (OUTLIER) cc_final: 0.0356 (pp) REVERT: F 245 MET cc_start: -0.0639 (ptt) cc_final: -0.1173 (tmm) REVERT: F 289 MET cc_start: 0.2372 (mmp) cc_final: 0.2108 (tpp) REVERT: F 389 MET cc_start: 0.5246 (OUTLIER) cc_final: 0.4120 (ptp) REVERT: F 445 LEU cc_start: 0.3853 (mp) cc_final: 0.3647 (pp) REVERT: G 35 LYS cc_start: 0.4108 (mttt) cc_final: 0.3817 (mptt) REVERT: G 289 MET cc_start: 0.2880 (mmm) cc_final: 0.1654 (tpp) REVERT: G 517 ARG cc_start: 0.4411 (mtt90) cc_final: 0.4176 (mtt-85) REVERT: H 245 MET cc_start: -0.0136 (ptt) cc_final: -0.0821 (tmm) REVERT: H 389 MET cc_start: 0.5528 (ptp) cc_final: 0.5265 (ptp) REVERT: H 445 LEU cc_start: 0.4393 (mp) cc_final: 0.3994 (pp) outliers start: 318 outliers final: 187 residues processed: 979 average time/residue: 0.7482 time to fit residues: 1262.3014 Evaluate side-chains 841 residues out of total 8804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 625 time to evaluate : 6.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1224 TRP Chi-restraints excluded: chain A residue 1330 HIS Chi-restraints excluded: chain A residue 1421 ILE Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1462 ILE Chi-restraints excluded: chain A residue 1485 GLU Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1543 LEU Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1579 LEU Chi-restraints excluded: chain A residue 1614 HIS Chi-restraints excluded: chain A residue 1679 ASN Chi-restraints excluded: chain A residue 1745 LYS Chi-restraints excluded: chain A residue 1747 SER Chi-restraints excluded: chain A residue 1777 ASP Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1801 LEU Chi-restraints excluded: chain A residue 1921 LYS Chi-restraints excluded: chain A residue 1942 ILE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1992 ASP Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 587 PHE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 667 GLN Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 805 ARG Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 893 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1060 ASP Chi-restraints excluded: chain B residue 1067 TRP Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1085 SER Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1126 SER Chi-restraints excluded: chain B residue 1148 THR Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1169 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1397 THR Chi-restraints excluded: chain B residue 1507 VAL Chi-restraints excluded: chain B residue 1548 HIS Chi-restraints excluded: chain B residue 1582 MET Chi-restraints excluded: chain B residue 1734 MET Chi-restraints excluded: chain B residue 1866 GLU Chi-restraints excluded: chain B residue 1885 CYS Chi-restraints excluded: chain B residue 1988 TYR Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 825 MET Chi-restraints excluded: chain C residue 838 GLN Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 903 MET Chi-restraints excluded: chain C residue 926 VAL Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 966 GLU Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain C residue 1148 THR Chi-restraints excluded: chain C residue 1149 ASN Chi-restraints excluded: chain C residue 1224 TRP Chi-restraints excluded: chain C residue 1330 HIS Chi-restraints excluded: chain C residue 1421 ILE Chi-restraints excluded: chain C residue 1427 ASP Chi-restraints excluded: chain C residue 1430 THR Chi-restraints excluded: chain C residue 1437 THR Chi-restraints excluded: chain C residue 1462 ILE Chi-restraints excluded: chain C residue 1485 GLU Chi-restraints excluded: chain C residue 1487 ILE Chi-restraints excluded: chain C residue 1543 LEU Chi-restraints excluded: chain C residue 1568 MET Chi-restraints excluded: chain C residue 1579 LEU Chi-restraints excluded: chain C residue 1614 HIS Chi-restraints excluded: chain C residue 1679 ASN Chi-restraints excluded: chain C residue 1747 SER Chi-restraints excluded: chain C residue 1777 ASP Chi-restraints excluded: chain C residue 1779 TYR Chi-restraints excluded: chain C residue 1801 LEU Chi-restraints excluded: chain C residue 1942 ILE Chi-restraints excluded: chain C residue 1961 VAL Chi-restraints excluded: chain C residue 1992 ASP Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 667 GLN Chi-restraints excluded: chain D residue 705 ASP Chi-restraints excluded: chain D residue 736 SER Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 770 SER Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain D residue 893 THR Chi-restraints excluded: chain D residue 936 SER Chi-restraints excluded: chain D residue 1060 ASP Chi-restraints excluded: chain D residue 1067 TRP Chi-restraints excluded: chain D residue 1079 THR Chi-restraints excluded: chain D residue 1085 SER Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1126 SER Chi-restraints excluded: chain D residue 1148 THR Chi-restraints excluded: chain D residue 1151 LEU Chi-restraints excluded: chain D residue 1169 VAL Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1216 SER Chi-restraints excluded: chain D residue 1235 ILE Chi-restraints excluded: chain D residue 1285 MET Chi-restraints excluded: chain D residue 1397 THR Chi-restraints excluded: chain D residue 1507 VAL Chi-restraints excluded: chain D residue 1548 HIS Chi-restraints excluded: chain D residue 1558 TRP Chi-restraints excluded: chain D residue 1579 LEU Chi-restraints excluded: chain D residue 1734 MET Chi-restraints excluded: chain D residue 1866 GLU Chi-restraints excluded: chain D residue 1885 CYS Chi-restraints excluded: chain D residue 1988 TYR Chi-restraints excluded: chain D residue 2008 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 306 ASP Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 306 ASP Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 479 ARG Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 386 ILE Chi-restraints excluded: chain H residue 406 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4096 > 50: distance: 21 - 27: 24.714 distance: 27 - 28: 7.098 distance: 28 - 29: 24.291 distance: 28 - 31: 24.215 distance: 29 - 30: 27.706 distance: 29 - 38: 24.758 distance: 31 - 32: 50.536 distance: 32 - 33: 57.114 distance: 33 - 34: 26.879 distance: 34 - 35: 11.422 distance: 35 - 36: 12.229 distance: 35 - 37: 17.246 distance: 38 - 39: 12.236 distance: 38 - 44: 19.166 distance: 39 - 42: 18.581 distance: 40 - 41: 6.538 distance: 40 - 45: 23.745 distance: 43 - 44: 10.212 distance: 45 - 46: 24.531 distance: 46 - 47: 11.102 distance: 46 - 49: 31.168 distance: 47 - 48: 40.429 distance: 49 - 50: 6.741 distance: 50 - 51: 15.643 distance: 51 - 52: 14.612 distance: 53 - 55: 40.923 distance: 57 - 58: 40.031 distance: 58 - 59: 24.565 distance: 58 - 65: 22.418 distance: 60 - 61: 40.714 distance: 61 - 62: 39.674 distance: 62 - 63: 42.363 distance: 63 - 64: 24.009 distance: 65 - 66: 20.590 distance: 66 - 67: 45.941 distance: 66 - 69: 27.623 distance: 67 - 68: 27.911 distance: 67 - 73: 18.969 distance: 68 - 98: 34.875 distance: 69 - 70: 55.609 distance: 70 - 72: 23.542 distance: 73 - 74: 27.503 distance: 74 - 75: 15.125 distance: 74 - 77: 25.435 distance: 76 - 103: 5.058 distance: 77 - 78: 46.602 distance: 79 - 80: 8.173 distance: 80 - 81: 12.904 distance: 80 - 83: 42.496 distance: 81 - 82: 21.466 distance: 81 - 90: 18.300 distance: 82 - 107: 32.060 distance: 83 - 84: 20.426 distance: 84 - 85: 26.536 distance: 84 - 86: 26.922 distance: 85 - 87: 34.658 distance: 87 - 89: 29.978 distance: 88 - 89: 16.215 distance: 90 - 91: 17.979 distance: 91 - 92: 48.530 distance: 91 - 94: 19.135 distance: 92 - 93: 14.871 distance: 92 - 98: 33.189 distance: 93 - 116: 36.563 distance: 94 - 95: 24.880 distance: 95 - 96: 11.765 distance: 95 - 97: 33.748 distance: 98 - 99: 43.443 distance: 99 - 100: 6.332 distance: 99 - 102: 36.668 distance: 100 - 101: 8.558 distance: 100 - 103: 29.530 distance: 101 - 123: 35.880 distance: 103 - 104: 15.020 distance: 104 - 105: 11.849 distance: 105 - 106: 15.238 distance: 105 - 107: 21.856 distance: 106 - 130: 27.806