Starting phenix.real_space_refine on Fri Mar 22 12:19:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6t_35206/03_2024/8i6t_35206_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6t_35206/03_2024/8i6t_35206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6t_35206/03_2024/8i6t_35206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6t_35206/03_2024/8i6t_35206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6t_35206/03_2024/8i6t_35206_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6t_35206/03_2024/8i6t_35206_neut.pdb" } resolution = 3.7 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 210 5.16 5 C 20926 2.51 5 N 5658 2.21 5 O 6189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 98": "OE1" <-> "OE2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ARG 719": "NH1" <-> "NH2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 486": "OD1" <-> "OD2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 622": "NH1" <-> "NH2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B ARG 730": "NH1" <-> "NH2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C ASP 142": "OD1" <-> "OD2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C ASP 258": "OD1" <-> "OD2" Residue "C TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ASP 353": "OD1" <-> "OD2" Residue "C TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C ASP 394": "OD1" <-> "OD2" Residue "C PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 622": "NH1" <-> "NH2" Residue "C GLU 640": "OE1" <-> "OE2" Residue "C GLU 643": "OE1" <-> "OE2" Residue "C PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C GLU 716": "OE1" <-> "OE2" Residue "C ARG 719": "NH1" <-> "NH2" Residue "C TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ASP 137": "OD1" <-> "OD2" Residue "D ASP 150": "OD1" <-> "OD2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D ASP 192": "OD1" <-> "OD2" Residue "D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 525": "OE1" <-> "OE2" Residue "D TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 573": "OE1" <-> "OE2" Residue "D ARG 622": "NH1" <-> "NH2" Residue "D GLU 640": "OE1" <-> "OE2" Residue "D GLU 643": "OE1" <-> "OE2" Residue "D ASP 645": "OD1" <-> "OD2" Residue "D GLU 672": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D GLU 716": "OE1" <-> "OE2" Residue "D ARG 719": "NH1" <-> "NH2" Residue "D PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E ASP 105": "OD1" <-> "OD2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "E ASP 271": "OD1" <-> "OD2" Residue "E PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 295": "OE1" <-> "OE2" Residue "E PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 328": "NH1" <-> "NH2" Residue "E TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "E PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 478": "NH1" <-> "NH2" Residue "E TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 529": "OE1" <-> "OE2" Residue "E PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 690": "NH1" <-> "NH2" Residue "E GLU 705": "OE1" <-> "OE2" Residue "E TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F ASP 240": "OD1" <-> "OD2" Residue "F PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 341": "OD1" <-> "OD2" Residue "F TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "F PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 465": "OE1" <-> "OE2" Residue "F TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 585": "OD1" <-> "OD2" Residue "F ASP 614": "OD1" <-> "OD2" Residue "F ASP 615": "OD1" <-> "OD2" Residue "F ARG 622": "NH1" <-> "NH2" Residue "F ARG 690": "NH1" <-> "NH2" Residue "F GLU 716": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32983 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "B" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "C" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "D" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "E" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "F" Number of atoms: 5463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5463 Classifications: {'peptide': 682} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 657} Chain breaks: 1 Time building chain proxies: 16.81, per 1000 atoms: 0.51 Number of scatterers: 32983 At special positions: 0 Unit cell: (177.62, 176.55, 162.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 210 16.00 O 6189 8.00 N 5658 7.00 C 20926 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: 13.44 Conformation dependent library (CDL) restraints added in 6.9 seconds 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7708 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 8 sheets defined 61.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.572A pdb=" N ASP A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 removed outlier: 3.690A pdb=" N LEU A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 4.245A pdb=" N ILE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 163 removed outlier: 4.777A pdb=" N MET A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 162 " --> pdb=" O CYS A 158 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 removed outlier: 4.709A pdb=" N PHE A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.619A pdb=" N HIS A 188 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.641A pdb=" N HIS A 243 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.593A pdb=" N HIS A 251 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 288 removed outlier: 4.306A pdb=" N THR A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.982A pdb=" N TYR A 296 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU A 297 " --> pdb=" O CYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 removed outlier: 4.082A pdb=" N LEU A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 removed outlier: 4.020A pdb=" N HIS A 334 " --> pdb=" O ILE A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 334' Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.906A pdb=" N GLU A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 removed outlier: 3.724A pdb=" N GLY A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.937A pdb=" N VAL A 387 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 389 " --> pdb=" O CYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 419 removed outlier: 3.509A pdb=" N ARG A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 447 removed outlier: 3.512A pdb=" N SER A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 469 removed outlier: 3.864A pdb=" N VAL A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.722A pdb=" N LEU A 485 " --> pdb=" O ARG A 482 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 486 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN A 487 " --> pdb=" O TYR A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 487' Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 511 through 528 removed outlier: 4.433A pdb=" N ALA A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.941A pdb=" N TRP A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 563 removed outlier: 3.779A pdb=" N MET A 555 " --> pdb=" O GLN A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 570 Processing helix chain 'A' and resid 571 through 591 removed outlier: 4.044A pdb=" N LEU A 575 " --> pdb=" O ALA A 571 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 4.049A pdb=" N LEU A 610 " --> pdb=" O LEU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 618 Processing helix chain 'A' and resid 619 through 635 removed outlier: 3.600A pdb=" N GLU A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 659 removed outlier: 4.020A pdb=" N VAL A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 695 removed outlier: 4.250A pdb=" N LEU A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 675 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 679 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS A 685 " --> pdb=" O SER A 681 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG A 689 " --> pdb=" O CYS A 685 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 721 removed outlier: 4.836A pdb=" N GLN A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 710 " --> pdb=" O ILE A 706 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 712 " --> pdb=" O GLN A 708 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 714 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 717 " --> pdb=" O GLU A 713 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG A 719 " --> pdb=" O GLN A 715 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 747 removed outlier: 3.858A pdb=" N GLU A 734 " --> pdb=" O ARG A 730 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 740 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 747 " --> pdb=" O PHE A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 762 removed outlier: 4.522A pdb=" N SER A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS A 757 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.716A pdb=" N ALA B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 147 through 156 removed outlier: 4.099A pdb=" N MET B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.548A pdb=" N TRP B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.518A pdb=" N CYS B 172 " --> pdb=" O HIS B 168 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 176 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 206 removed outlier: 3.518A pdb=" N LEU B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 235 removed outlier: 4.226A pdb=" N ILE B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.519A pdb=" N HIS B 243 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 290 through 304 removed outlier: 3.848A pdb=" N GLU B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 300 " --> pdb=" O TYR B 296 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 329 removed outlier: 3.683A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.550A pdb=" N PHE B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 384 through 392 removed outlier: 3.791A pdb=" N VAL B 387 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 390 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 391 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 392 " --> pdb=" O LYS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 419 removed outlier: 3.933A pdb=" N THR B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR B 416 " --> pdb=" O MET B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 447 removed outlier: 3.867A pdb=" N VAL B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER B 439 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 446 " --> pdb=" O GLN B 442 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 468 removed outlier: 3.675A pdb=" N GLU B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.786A pdb=" N SER B 475 " --> pdb=" O TRP B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.636A pdb=" N LEU B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.853A pdb=" N TYR B 488 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 508 through 540 removed outlier: 3.924A pdb=" N LEU B 512 " --> pdb=" O ASN B 508 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN B 521 " --> pdb=" O ALA B 517 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 530 " --> pdb=" O CYS B 526 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 535 " --> pdb=" O ASN B 531 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP B 536 " --> pdb=" O GLY B 532 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 563 removed outlier: 4.030A pdb=" N LEU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.526A pdb=" N ALA B 578 " --> pdb=" O ARG B 574 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 581 " --> pdb=" O TRP B 577 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 595 removed outlier: 3.798A pdb=" N ARG B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG B 593 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 594 " --> pdb=" O HIS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.738A pdb=" N GLU B 606 " --> pdb=" O ASN B 603 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 607 " --> pdb=" O LEU B 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 603 through 607' Processing helix chain 'B' and resid 620 through 635 removed outlier: 4.253A pdb=" N ALA B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 631 " --> pdb=" O GLN B 627 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 657 removed outlier: 3.983A pdb=" N ALA B 647 " --> pdb=" O GLU B 643 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU B 655 " --> pdb=" O VAL B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 695 removed outlier: 3.698A pdb=" N LEU B 670 " --> pdb=" O GLN B 666 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 675 " --> pdb=" O TRP B 671 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 677 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 679 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 682 " --> pdb=" O GLN B 678 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS B 685 " --> pdb=" O SER B 681 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 690 " --> pdb=" O LYS B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 723 removed outlier: 4.002A pdb=" N GLU B 704 " --> pdb=" O THR B 700 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP B 707 " --> pdb=" O VAL B 703 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLN B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU B 712 " --> pdb=" O GLN B 708 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 722 " --> pdb=" O THR B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 749 removed outlier: 3.670A pdb=" N ARG B 733 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 734 " --> pdb=" O ARG B 730 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 740 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 747 " --> pdb=" O PHE B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 763 removed outlier: 4.099A pdb=" N ASP B 755 " --> pdb=" O PRO B 751 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 758 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.519A pdb=" N ILE C 87 " --> pdb=" O MET C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 removed outlier: 3.564A pdb=" N LEU C 108 " --> pdb=" O TYR C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 removed outlier: 3.796A pdb=" N VAL C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.506A pdb=" N ARG C 151 " --> pdb=" O MET C 147 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N MET C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 202 through 210 removed outlier: 3.524A pdb=" N ASP C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N MET C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 230 through 235 Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.505A pdb=" N LEU C 250 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 286 removed outlier: 4.386A pdb=" N ALA C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 304 removed outlier: 4.564A pdb=" N TYR C 296 " --> pdb=" O LYS C 292 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 297 " --> pdb=" O CYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 330 removed outlier: 3.610A pdb=" N LEU C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP C 321 " --> pdb=" O TYR C 317 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 325 " --> pdb=" O TRP C 321 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 334 removed outlier: 3.829A pdb=" N HIS C 334 " --> pdb=" O ILE C 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 331 through 334' Processing helix chain 'C' and resid 335 through 350 removed outlier: 4.455A pdb=" N GLU C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN C 349 " --> pdb=" O TYR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 380 removed outlier: 3.554A pdb=" N LEU C 375 " --> pdb=" O MET C 371 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 378 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR C 379 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 408 through 418 removed outlier: 4.034A pdb=" N MET C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN C 414 " --> pdb=" O THR C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 removed outlier: 3.884A pdb=" N GLU C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 435 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 438 " --> pdb=" O GLU C 434 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER C 439 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 460 through 470 removed outlier: 3.820A pdb=" N VAL C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP C 469 " --> pdb=" O GLU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 475 removed outlier: 3.631A pdb=" N SER C 475 " --> pdb=" O TRP C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 486 removed outlier: 3.763A pdb=" N LEU C 485 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 486 " --> pdb=" O ARG C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 538 removed outlier: 4.356A pdb=" N SER C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG C 535 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TRP C 536 " --> pdb=" O GLY C 532 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR C 537 " --> pdb=" O LEU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 removed outlier: 4.313A pdb=" N THR C 553 " --> pdb=" O ASP C 549 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 560 " --> pdb=" O THR C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 593 removed outlier: 3.626A pdb=" N VAL C 580 " --> pdb=" O GLY C 576 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 584 " --> pdb=" O VAL C 580 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP C 585 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA C 586 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL C 587 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 592 " --> pdb=" O SER C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 599 removed outlier: 4.328A pdb=" N LYS C 598 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN C 599 " --> pdb=" O GLY C 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 595 through 599' Processing helix chain 'C' and resid 606 through 611 removed outlier: 3.767A pdb=" N VAL C 611 " --> pdb=" O ILE C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 635 removed outlier: 3.741A pdb=" N ALA C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP C 625 " --> pdb=" O LEU C 621 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 630 " --> pdb=" O LYS C 626 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA C 631 " --> pdb=" O GLN C 627 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 658 removed outlier: 3.600A pdb=" N LEU C 649 " --> pdb=" O ASP C 645 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 650 " --> pdb=" O THR C 646 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU C 655 " --> pdb=" O VAL C 651 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE C 656 " --> pdb=" O ARG C 652 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 696 removed outlier: 3.650A pdb=" N SER C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 679 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS C 684 " --> pdb=" O THR C 680 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS C 685 " --> pdb=" O SER C 681 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C 686 " --> pdb=" O SER C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 711 through 723 removed outlier: 3.701A pdb=" N GLN C 715 " --> pdb=" O ASP C 711 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 717 " --> pdb=" O GLU C 713 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 718 " --> pdb=" O MET C 714 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C 720 " --> pdb=" O GLU C 716 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 721 " --> pdb=" O LEU C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 747 removed outlier: 4.225A pdb=" N THR C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 736 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 740 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 742 " --> pdb=" O HIS C 738 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 747 " --> pdb=" O PHE C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 762 removed outlier: 3.507A pdb=" N ILE C 762 " --> pdb=" O ILE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 92 removed outlier: 4.332A pdb=" N GLY D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 removed outlier: 4.332A pdb=" N LEU D 108 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 removed outlier: 3.566A pdb=" N ASP D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.588A pdb=" N ILE D 152 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 removed outlier: 3.934A pdb=" N GLY D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.821A pdb=" N LEU D 202 " --> pdb=" O PHE D 198 " (cutoff:3.500A) Proline residue: D 203 - end of helix Processing helix chain 'D' and resid 220 through 235 removed outlier: 3.812A pdb=" N ALA D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 235 " --> pdb=" O GLU D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 247 through 252 removed outlier: 3.871A pdb=" N LEU D 250 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS D 251 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER D 252 " --> pdb=" O LEU D 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 247 through 252' Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.639A pdb=" N LYS D 266 " --> pdb=" O LYS D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 288 removed outlier: 3.557A pdb=" N THR D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 3.719A pdb=" N GLU D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 296 " --> pdb=" O LYS D 292 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU D 297 " --> pdb=" O CYS D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 4.155A pdb=" N PHE D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 330 removed outlier: 3.608A pdb=" N LEU D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR D 327 " --> pdb=" O VAL D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 334 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 343 through 349 Processing helix chain 'D' and resid 365 through 375 removed outlier: 3.852A pdb=" N THR D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 380 Processing helix chain 'D' and resid 384 through 390 removed outlier: 4.288A pdb=" N VAL D 387 " --> pdb=" O ASP D 384 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 419 removed outlier: 3.601A pdb=" N ASN D 414 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR D 416 " --> pdb=" O MET D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 446 removed outlier: 4.343A pdb=" N GLY D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL D 435 " --> pdb=" O GLY D 431 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 436 " --> pdb=" O ARG D 432 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG D 438 " --> pdb=" O GLU D 434 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 4.009A pdb=" N TYR D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET D 468 " --> pdb=" O VAL D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 486 removed outlier: 3.753A pdb=" N THR D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 485 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP D 486 " --> pdb=" O ARG D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 540 removed outlier: 3.520A pdb=" N ALA D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA D 517 " --> pdb=" O LYS D 513 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP D 518 " --> pdb=" O ALA D 514 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 523 " --> pdb=" O PHE D 519 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 525 " --> pdb=" O ASN D 521 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG D 527 " --> pdb=" O GLN D 523 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG D 535 " --> pdb=" O ASN D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 565 removed outlier: 3.736A pdb=" N THR D 553 " --> pdb=" O ASP D 549 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 554 " --> pdb=" O PRO D 550 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 589 removed outlier: 3.663A pdb=" N ALA D 578 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 580 " --> pdb=" O GLY D 576 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP D 585 " --> pdb=" O ALA D 581 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 589 " --> pdb=" O ASP D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 595 removed outlier: 3.672A pdb=" N ILE D 594 " --> pdb=" O HIS D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 600 Processing helix chain 'D' and resid 603 through 611 removed outlier: 3.536A pdb=" N LEU D 607 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 608 " --> pdb=" O GLU D 605 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 611 " --> pdb=" O ILE D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 633 removed outlier: 3.887A pdb=" N MET D 630 " --> pdb=" O LYS D 626 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 631 " --> pdb=" O GLN D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 652 removed outlier: 3.682A pdb=" N VAL D 651 " --> pdb=" O ALA D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 696 removed outlier: 3.787A pdb=" N GLN D 675 " --> pdb=" O TRP D 671 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 678 " --> pdb=" O SER D 674 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 679 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS D 685 " --> pdb=" O SER D 681 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 686 " --> pdb=" O SER D 682 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 688 " --> pdb=" O CYS D 684 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 689 " --> pdb=" O CYS D 685 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 693 " --> pdb=" O ARG D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 722 Processing helix chain 'D' and resid 730 through 747 removed outlier: 4.007A pdb=" N GLU D 734 " --> pdb=" O ARG D 730 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR D 735 " --> pdb=" O LEU D 731 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE D 736 " --> pdb=" O THR D 732 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 742 " --> pdb=" O HIS D 738 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR D 745 " --> pdb=" O LYS D 741 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 747 " --> pdb=" O PHE D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 763 removed outlier: 4.574A pdb=" N SER D 756 " --> pdb=" O GLU D 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.796A pdb=" N ALA E 90 " --> pdb=" O GLY E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 124 through 131 Processing helix chain 'E' and resid 149 through 164 removed outlier: 3.566A pdb=" N MET E 153 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR E 155 " --> pdb=" O ARG E 151 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU E 156 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA E 157 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 162 " --> pdb=" O CYS E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 181 removed outlier: 3.568A pdb=" N PHE E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 210 removed outlier: 3.662A pdb=" N ASP E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 235 removed outlier: 3.528A pdb=" N LYS E 224 " --> pdb=" O GLU E 220 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU E 231 " --> pdb=" O TYR E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 245 removed outlier: 3.591A pdb=" N MET E 245 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 264 removed outlier: 3.662A pdb=" N LYS E 263 " --> pdb=" O ASP E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 288 removed outlier: 4.025A pdb=" N THR E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA E 282 " --> pdb=" O PRO E 278 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN E 287 " --> pdb=" O THR E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 303 removed outlier: 3.549A pdb=" N TYR E 296 " --> pdb=" O LYS E 292 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS E 303 " --> pdb=" O GLY E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 330 removed outlier: 3.879A pdb=" N ARG E 319 " --> pdb=" O ASP E 315 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 320 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 323 " --> pdb=" O ARG E 319 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASP E 324 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 325 " --> pdb=" O TRP E 321 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 326 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG E 328 " --> pdb=" O ASP E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 348 removed outlier: 3.849A pdb=" N ASP E 344 " --> pdb=" O GLU E 340 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N TYR E 345 " --> pdb=" O ASP E 341 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE E 346 " --> pdb=" O CYS E 342 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 347 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 375 removed outlier: 3.618A pdb=" N MET E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.885A pdb=" N LEU E 388 " --> pdb=" O PRO E 385 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS E 390 " --> pdb=" O VAL E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 417 removed outlier: 4.004A pdb=" N MET E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN E 414 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 445 removed outlier: 3.655A pdb=" N SER E 439 " --> pdb=" O VAL E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 468 removed outlier: 4.306A pdb=" N VAL E 464 " --> pdb=" O ILE E 460 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET E 468 " --> pdb=" O VAL E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 488 removed outlier: 3.920A pdb=" N LEU E 483 " --> pdb=" O ILE E 479 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 485 " --> pdb=" O THR E 481 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP E 486 " --> pdb=" O ARG E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 541 removed outlier: 3.923A pdb=" N ALA E 514 " --> pdb=" O LEU E 510 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 515 " --> pdb=" O TYR E 511 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS E 516 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA E 517 " --> pdb=" O LYS E 513 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER E 520 " --> pdb=" O LYS E 516 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU E 525 " --> pdb=" O ASN E 521 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU E 529 " --> pdb=" O GLU E 525 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 530 " --> pdb=" O CYS E 526 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN E 531 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY E 532 " --> pdb=" O VAL E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 546 removed outlier: 4.114A pdb=" N PHE E 545 " --> pdb=" O LEU E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 563 removed outlier: 3.832A pdb=" N THR E 553 " --> pdb=" O ASP E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 593 removed outlier: 4.540A pdb=" N ARG E 579 " --> pdb=" O LEU E 575 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU E 582 " --> pdb=" O ALA E 578 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL E 587 " --> pdb=" O LEU E 583 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG E 592 " --> pdb=" O SER E 588 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E 593 " --> pdb=" O SER E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 611 removed outlier: 4.061A pdb=" N GLU E 606 " --> pdb=" O ASN E 603 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU E 607 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE E 608 " --> pdb=" O GLU E 605 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 610 " --> pdb=" O LEU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 629 Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 642 through 658 removed outlier: 3.800A pdb=" N ALA E 647 " --> pdb=" O GLU E 643 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU E 649 " --> pdb=" O ASP E 645 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU E 650 " --> pdb=" O THR E 646 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG E 652 " --> pdb=" O ILE E 648 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 654 " --> pdb=" O LEU E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 666 through 685 removed outlier: 4.107A pdb=" N LEU E 670 " --> pdb=" O GLN E 666 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP E 671 " --> pdb=" O ARG E 667 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN E 675 " --> pdb=" O TRP E 671 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR E 680 " --> pdb=" O LEU E 676 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N CYS E 684 " --> pdb=" O THR E 680 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYS E 685 " --> pdb=" O SER E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 696 Processing helix chain 'E' and resid 699 through 706 removed outlier: 3.555A pdb=" N GLU E 704 " --> pdb=" O THR E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 723 removed outlier: 3.578A pdb=" N VAL E 710 " --> pdb=" O ILE E 706 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP E 711 " --> pdb=" O ASP E 707 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU E 712 " --> pdb=" O GLN E 708 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG E 719 " --> pdb=" O GLN E 715 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG E 720 " --> pdb=" O GLU E 716 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 723 " --> pdb=" O ARG E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 746 removed outlier: 3.762A pdb=" N LEU E 737 " --> pdb=" O ARG E 733 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 739 " --> pdb=" O THR E 735 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL E 740 " --> pdb=" O PHE E 736 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR E 745 " --> pdb=" O LYS E 741 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 746 " --> pdb=" O SER E 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 92 removed outlier: 3.913A pdb=" N GLY F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE F 87 " --> pdb=" O MET F 83 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 90 " --> pdb=" O GLY F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 110 Processing helix chain 'F' and resid 126 through 131 Processing helix chain 'F' and resid 150 through 163 removed outlier: 3.589A pdb=" N THR F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU F 156 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA F 157 " --> pdb=" O MET F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 183 removed outlier: 3.555A pdb=" N CYS F 172 " --> pdb=" O HIS F 168 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET F 183 " --> pdb=" O ILE F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 209 removed outlier: 3.565A pdb=" N ASP F 207 " --> pdb=" O PRO F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 225 Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 240 through 245 removed outlier: 3.917A pdb=" N MET F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 252 removed outlier: 4.127A pdb=" N LEU F 250 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS F 251 " --> pdb=" O THR F 248 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER F 252 " --> pdb=" O LEU F 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 247 through 252' Processing helix chain 'F' and resid 260 through 265 removed outlier: 3.872A pdb=" N LEU F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 268 No H-bonds generated for 'chain 'F' and resid 266 through 268' Processing helix chain 'F' and resid 281 through 286 removed outlier: 3.715A pdb=" N PHE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 281 through 286' Processing helix chain 'F' and resid 290 through 304 removed outlier: 3.768A pdb=" N PHE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 330 removed outlier: 3.831A pdb=" N VAL F 323 " --> pdb=" O ARG F 319 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG F 325 " --> pdb=" O TRP F 321 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 326 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG F 328 " --> pdb=" O ASP F 324 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 334 removed outlier: 3.925A pdb=" N HIS F 334 " --> pdb=" O ILE F 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 331 through 334' Processing helix chain 'F' and resid 335 through 349 removed outlier: 3.746A pdb=" N GLU F 340 " --> pdb=" O THR F 336 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP F 341 " --> pdb=" O SER F 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP F 344 " --> pdb=" O GLU F 340 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR F 345 " --> pdb=" O ASP F 341 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 377 removed outlier: 3.516A pdb=" N THR F 369 " --> pdb=" O ASP F 365 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET F 371 " --> pdb=" O ASP F 367 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU F 375 " --> pdb=" O MET F 371 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU F 376 " --> pdb=" O GLY F 372 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG F 377 " --> pdb=" O PHE F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 390 removed outlier: 3.807A pdb=" N LEU F 388 " --> pdb=" O PRO F 385 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 389 " --> pdb=" O CYS F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 419 removed outlier: 4.147A pdb=" N MET F 412 " --> pdb=" O SER F 408 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR F 416 " --> pdb=" O MET F 412 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG F 417 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER F 419 " --> pdb=" O THR F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 443 removed outlier: 3.797A pdb=" N VAL F 435 " --> pdb=" O GLY F 431 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG F 438 " --> pdb=" O GLU F 434 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER F 439 " --> pdb=" O VAL F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 468 removed outlier: 3.760A pdb=" N VAL F 464 " --> pdb=" O ILE F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 475 Processing helix chain 'F' and resid 477 through 485 removed outlier: 4.026A pdb=" N THR F 481 " --> pdb=" O PRO F 477 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG F 482 " --> pdb=" O ARG F 478 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 529 removed outlier: 3.775A pdb=" N LYS F 513 " --> pdb=" O ASP F 509 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG F 527 " --> pdb=" O GLN F 523 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F 529 " --> pdb=" O GLU F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 540 removed outlier: 4.143A pdb=" N LEU F 533 " --> pdb=" O GLU F 529 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU F 538 " --> pdb=" O ARG F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 562 removed outlier: 3.535A pdb=" N PHE F 559 " --> pdb=" O MET F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 569 No H-bonds generated for 'chain 'F' and resid 567 through 569' Processing helix chain 'F' and resid 570 through 595 removed outlier: 4.004A pdb=" N ARG F 574 " --> pdb=" O ARG F 570 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG F 579 " --> pdb=" O LEU F 575 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL F 580 " --> pdb=" O GLY F 576 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP F 585 " --> pdb=" O ALA F 581 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 586 " --> pdb=" O LEU F 582 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL F 587 " --> pdb=" O LEU F 583 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER F 588 " --> pdb=" O ALA F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 600 removed outlier: 4.082A pdb=" N ASN F 599 " --> pdb=" O GLY F 596 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER F 600 " --> pdb=" O PRO F 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 596 through 600' Processing helix chain 'F' and resid 606 through 610 removed outlier: 3.864A pdb=" N SER F 609 " --> pdb=" O GLU F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 618 removed outlier: 3.884A pdb=" N TYR F 617 " --> pdb=" O ASP F 614 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER F 618 " --> pdb=" O ASP F 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 614 through 618' Processing helix chain 'F' and resid 619 through 636 removed outlier: 3.795A pdb=" N ALA F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F 631 " --> pdb=" O GLN F 627 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP F 632 " --> pdb=" O TRP F 628 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 656 removed outlier: 4.022A pdb=" N THR F 646 " --> pdb=" O ILE F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 686 removed outlier: 4.185A pdb=" N LEU F 670 " --> pdb=" O GLN F 666 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU F 672 " --> pdb=" O PRO F 668 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN F 675 " --> pdb=" O TRP F 671 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR F 680 " --> pdb=" O LEU F 676 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER F 681 " --> pdb=" O GLU F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 692 removed outlier: 4.233A pdb=" N VAL F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 722 removed outlier: 3.681A pdb=" N VAL F 703 " --> pdb=" O SER F 699 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN F 709 " --> pdb=" O GLU F 705 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU F 713 " --> pdb=" O GLN F 709 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET F 714 " --> pdb=" O VAL F 710 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN F 715 " --> pdb=" O ASP F 711 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU F 716 " --> pdb=" O LEU F 712 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 722 " --> pdb=" O THR F 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 746 removed outlier: 3.854A pdb=" N LEU F 737 " --> pdb=" O ARG F 733 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS F 741 " --> pdb=" O LEU F 737 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER F 742 " --> pdb=" O HIS F 738 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL F 746 " --> pdb=" O SER F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 749 No H-bonds generated for 'chain 'F' and resid 747 through 749' Processing helix chain 'F' and resid 750 through 760 removed outlier: 3.721A pdb=" N ILE F 754 " --> pdb=" O SER F 750 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP F 755 " --> pdb=" O PRO F 751 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP F 759 " --> pdb=" O ASP F 755 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 455 through 456 removed outlier: 3.598A pdb=" N VAL A 494 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 455 through 456 removed outlier: 3.626A pdb=" N ILE B 456 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 494 " --> pdb=" O ILE B 456 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 455 through 456 Processing sheet with id=AA4, first strand: chain 'D' and resid 495 through 496 removed outlier: 4.191A pdb=" N HIS D 501 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 392 through 393 Processing sheet with id=AA6, first strand: chain 'E' and resid 455 through 456 removed outlier: 3.606A pdb=" N VAL E 494 " --> pdb=" O ILE E 456 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 392 through 393 Processing sheet with id=AA8, first strand: chain 'F' and resid 495 through 496 1139 hydrogen bonds defined for protein. 3243 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: 10.24 Time building geometry restraints manager: 14.41 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: 10765 1.34 - 1.46: 7678 1.46 - 1.58: 14962 1.58 - 1.70: 1 1.70 - 1.82: 312 Bond restraints: 33718 Sorted by residual: bond pdb=" C ILE D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.335 1.382 -0.047 9.40e-03 1.13e+04 2.50e+01 bond pdb=" C ARG D 667 " pdb=" N PRO D 668 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.19e-02 7.06e+03 1.64e+01 bond pdb=" C ARG A 667 " pdb=" N PRO A 668 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.08e-02 8.57e+03 1.58e+01 bond pdb=" C PHE A 423 " pdb=" N PRO A 424 " ideal model delta sigma weight residual 1.334 1.360 -0.026 8.40e-03 1.42e+04 9.71e+00 bond pdb=" CA MET B 412 " pdb=" C MET B 412 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.80e-02 3.09e+03 6.91e+00 ... (remaining 33713 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.16: 739 106.16 - 113.17: 17746 113.17 - 120.17: 13118 120.17 - 127.18: 13586 127.18 - 134.19: 439 Bond angle restraints: 45628 Sorted by residual: angle pdb=" N VAL B 323 " pdb=" CA VAL B 323 " pdb=" C VAL B 323 " ideal model delta sigma weight residual 113.71 106.50 7.21 9.50e-01 1.11e+00 5.77e+01 angle pdb=" N ILE A 706 " pdb=" CA ILE A 706 " pdb=" C ILE A 706 " ideal model delta sigma weight residual 113.47 106.97 6.50 1.01e+00 9.80e-01 4.15e+01 angle pdb=" CA PHE D 178 " pdb=" C PHE D 178 " pdb=" N ILE D 179 " ideal model delta sigma weight residual 118.06 111.26 6.80 1.26e+00 6.30e-01 2.92e+01 angle pdb=" C GLU A 716 " pdb=" N LEU A 717 " pdb=" CA LEU A 717 " ideal model delta sigma weight residual 120.38 127.54 -7.16 1.37e+00 5.33e-01 2.73e+01 angle pdb=" C LYS B 393 " pdb=" N ASP B 394 " pdb=" CA ASP B 394 " ideal model delta sigma weight residual 121.54 130.55 -9.01 1.91e+00 2.74e-01 2.23e+01 ... (remaining 45623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 17607 17.99 - 35.98: 2086 35.98 - 53.96: 370 53.96 - 71.95: 88 71.95 - 89.94: 40 Dihedral angle restraints: 20191 sinusoidal: 8236 harmonic: 11955 Sorted by residual: dihedral pdb=" CA MET B 183 " pdb=" C MET B 183 " pdb=" N TRP B 184 " pdb=" CA TRP B 184 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LEU B 212 " pdb=" C LEU B 212 " pdb=" N ASP B 213 " pdb=" CA ASP B 213 " ideal model delta harmonic sigma weight residual -180.00 -153.67 -26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER C 638 " pdb=" C SER C 638 " pdb=" N GLN C 639 " pdb=" CA GLN C 639 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 20188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4613 0.096 - 0.192: 336 0.192 - 0.288: 18 0.288 - 0.384: 1 0.384 - 0.480: 1 Chirality restraints: 4969 Sorted by residual: chirality pdb=" CB ILE C 642 " pdb=" CA ILE C 642 " pdb=" CG1 ILE C 642 " pdb=" CG2 ILE C 642 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CG LEU F 320 " pdb=" CB LEU F 320 " pdb=" CD1 LEU F 320 " pdb=" CD2 LEU F 320 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA THR C 410 " pdb=" N THR C 410 " pdb=" C THR C 410 " pdb=" CB THR C 410 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4966 not shown) Planarity restraints: 5870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 135 " -0.048 5.00e-02 4.00e+02 7.19e-02 8.26e+00 pdb=" N PRO C 136 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 136 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 136 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 611 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO E 612 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 612 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 612 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 460 " -0.046 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO B 461 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 461 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 461 " -0.039 5.00e-02 4.00e+02 ... (remaining 5867 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6965 2.77 - 3.30: 30930 3.30 - 3.83: 54232 3.83 - 4.37: 64031 4.37 - 4.90: 102175 Nonbonded interactions: 258333 Sorted by model distance: nonbonded pdb=" O ALA E 209 " pdb=" OH TYR E 218 " model vdw 2.235 2.440 nonbonded pdb=" O ILE B 642 " pdb=" OG1 THR B 646 " model vdw 2.243 2.440 nonbonded pdb=" O THR B 89 " pdb=" OG SER B 93 " model vdw 2.246 2.440 nonbonded pdb=" O GLU E 606 " pdb=" OG SER E 609 " model vdw 2.256 2.440 nonbonded pdb=" O PHE C 274 " pdb=" OG SER C 280 " model vdw 2.258 2.440 ... (remaining 258328 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 80 through 544 or resid 551 through 767)) selection = (chain 'B' and (resid 80 through 544 or resid 551 through 767)) selection = (chain 'C' and (resid 80 through 544 or resid 551 through 767)) selection = (chain 'D' and (resid 80 through 544 or resid 551 through 767)) selection = (chain 'E' and (resid 80 through 544 or resid 551 through 767)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.020 Extract box with map and model: 6.960 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 83.400 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 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 : 0.005 0.080 33718 Z= 0.322 Angle : 0.984 12.446 45628 Z= 0.566 Chirality : 0.053 0.480 4969 Planarity : 0.007 0.072 5870 Dihedral : 16.224 89.942 12483 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.59 % Allowed : 12.19 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.42 (0.09), residues: 4108 helix: -4.23 (0.06), residues: 2166 sheet: None (None), residues: 0 loop : -2.71 (0.11), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 261 HIS 0.009 0.002 HIS D 738 PHE 0.023 0.003 PHE F 397 TYR 0.029 0.003 TYR D 227 ARG 0.015 0.001 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 288 time to evaluate : 4.165 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: A 144 SER cc_start: 0.6430 (m) cc_final: 0.6184 (p) REVERT: A 148 MET cc_start: 0.7520 (ttp) cc_final: 0.7285 (ptm) REVERT: A 245 MET cc_start: 0.5601 (ptm) cc_final: 0.5191 (pmm) REVERT: A 412 MET cc_start: 0.7847 (mmt) cc_final: 0.7623 (mmm) REVERT: B 98 GLU cc_start: 0.6563 (mp0) cc_final: 0.6309 (mp0) REVERT: B 148 MET cc_start: 0.5994 (tpp) cc_final: 0.5708 (tmm) REVERT: B 183 MET cc_start: 0.7152 (mtm) cc_final: 0.6812 (mmm) REVERT: B 303 LYS cc_start: 0.7422 (ptpt) cc_final: 0.7121 (tttt) REVERT: B 304 PHE cc_start: 0.6853 (m-80) cc_final: 0.6636 (m-80) REVERT: B 488 TYR cc_start: 0.6312 (t80) cc_final: 0.5962 (t80) REVERT: C 303 LYS cc_start: 0.6816 (tmtt) cc_final: 0.6556 (tttp) REVERT: C 412 MET cc_start: 0.8529 (mmt) cc_final: 0.7903 (mmt) REVERT: C 473 LYS cc_start: 0.8289 (mtmm) cc_final: 0.8007 (tmmt) REVERT: C 677 GLU cc_start: 0.7489 (tt0) cc_final: 0.7117 (mt-10) REVERT: D 194 MET cc_start: 0.6456 (tpt) cc_final: 0.5706 (mmm) REVERT: D 232 ARG cc_start: 0.7790 (mtm180) cc_final: 0.7533 (mtt90) REVERT: D 338 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7058 (mt-10) REVERT: E 83 MET cc_start: 0.6480 (ptp) cc_final: 0.6160 (ptm) REVERT: E 148 MET cc_start: 0.5300 (tpt) cc_final: 0.4842 (tpp) REVERT: E 153 MET cc_start: 0.7792 (tpp) cc_final: 0.7467 (tpp) REVERT: E 208 MET cc_start: 0.5582 (ppp) cc_final: 0.5257 (mmp) REVERT: E 456 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.6068 (mt) REVERT: F 153 MET cc_start: 0.8232 (tpt) cc_final: 0.7950 (tmm) REVERT: F 614 ASP cc_start: 0.5261 (OUTLIER) cc_final: 0.4967 (p0) REVERT: F 714 MET cc_start: 0.8079 (tpp) cc_final: 0.7613 (tpp) outliers start: 21 outliers final: 7 residues processed: 309 average time/residue: 0.4880 time to fit residues: 236.4990 Evaluate side-chains 182 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 4.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 614 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 9.9990 chunk 309 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 319 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 370 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS A 401 HIS ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN A 590 HIS A 639 GLN ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN B 405 ASN B 414 ASN B 694 GLN B 709 GLN C 168 HIS ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN C 448 ASN ** C 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS C 666 GLN D 134 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS D 420 GLN D 487 GLN D 501 HIS D 541 ASN E 182 ASN E 251 HIS E 334 HIS E 357 HIS ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 GLN E 678 GLN E 715 GLN F 122 GLN F 180 GLN F 334 HIS ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 ASN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 694 GLN F 696 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33718 Z= 0.289 Angle : 0.743 8.105 45628 Z= 0.395 Chirality : 0.045 0.201 4969 Planarity : 0.007 0.069 5870 Dihedral : 6.679 52.597 4532 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.63 % Allowed : 17.36 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.11), residues: 4108 helix: -2.89 (0.08), residues: 2244 sheet: None (None), residues: 0 loop : -2.38 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 628 HIS 0.007 0.002 HIS D 188 PHE 0.026 0.002 PHE E 440 TYR 0.036 0.003 TYR D 227 ARG 0.008 0.001 ARG E 622 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 181 time to evaluate : 4.339 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 181 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6442 (pm20) REVERT: A 231 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7200 (pt0) REVERT: A 245 MET cc_start: 0.5748 (ptm) cc_final: 0.5209 (pmm) REVERT: A 318 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7811 (pt0) REVERT: A 360 ASN cc_start: 0.6435 (OUTLIER) cc_final: 0.5514 (t0) REVERT: A 714 MET cc_start: 0.8361 (tpt) cc_final: 0.8074 (tpt) REVERT: A 736 PHE cc_start: 0.8492 (m-10) cc_final: 0.8259 (m-80) REVERT: B 488 TYR cc_start: 0.6186 (t80) cc_final: 0.5918 (t80) REVERT: C 256 MET cc_start: 0.5035 (tpt) cc_final: 0.4628 (ppp) REVERT: C 303 LYS cc_start: 0.7073 (tmtt) cc_final: 0.6747 (tttp) REVERT: C 412 MET cc_start: 0.8482 (mmt) cc_final: 0.7979 (mmt) REVERT: C 450 MET cc_start: 0.4594 (pmm) cc_final: 0.4289 (pmm) REVERT: C 473 LYS cc_start: 0.8296 (mtmm) cc_final: 0.8086 (tmmt) REVERT: C 530 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8016 (tt) REVERT: D 84 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7703 (tp) REVERT: D 94 ILE cc_start: 0.5841 (mm) cc_final: 0.5145 (mp) REVERT: D 186 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7371 (tt) REVERT: D 232 ARG cc_start: 0.7918 (mtm180) cc_final: 0.7645 (mtt90) REVERT: D 412 MET cc_start: 0.7413 (tpp) cc_final: 0.7173 (tpp) REVERT: D 456 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6969 (tp) REVERT: D 522 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6175 (p90) REVERT: D 670 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8356 (tt) REVERT: E 83 MET cc_start: 0.6319 (ptp) cc_final: 0.5752 (ptp) REVERT: E 148 MET cc_start: 0.5149 (tpt) cc_final: 0.4266 (tpp) REVERT: E 153 MET cc_start: 0.8079 (tpp) cc_final: 0.7614 (tpp) REVERT: E 208 MET cc_start: 0.5439 (ppp) cc_final: 0.5092 (mmp) REVERT: E 411 PRO cc_start: 0.7579 (OUTLIER) cc_final: 0.7177 (Cg_endo) REVERT: E 412 MET cc_start: 0.7315 (mtm) cc_final: 0.7103 (mpp) REVERT: E 456 ILE cc_start: 0.6090 (OUTLIER) cc_final: 0.5847 (mt) REVERT: E 503 MET cc_start: 0.5959 (mmm) cc_final: 0.5718 (mmm) REVERT: F 346 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8102 (mt) REVERT: F 714 MET cc_start: 0.7934 (tpp) cc_final: 0.7410 (tpp) outliers start: 94 outliers final: 56 residues processed: 268 average time/residue: 0.4285 time to fit residues: 191.6397 Evaluate side-chains 231 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 164 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 411 PRO Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain F residue 122 GLN Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 509 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 308 optimal weight: 8.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 8.9990 chunk 330 optimal weight: 6.9990 chunk 368 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 ASN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33718 Z= 0.279 Angle : 0.723 9.331 45628 Z= 0.380 Chirality : 0.045 0.197 4969 Planarity : 0.006 0.060 5870 Dihedral : 6.501 53.598 4527 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.42 % Allowed : 19.56 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.11), residues: 4108 helix: -2.43 (0.09), residues: 2266 sheet: None (None), residues: 0 loop : -2.19 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 625 HIS 0.007 0.001 HIS D 738 PHE 0.023 0.002 PHE A 304 TYR 0.033 0.003 TYR D 227 ARG 0.006 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 174 time to evaluate : 3.796 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 137 ASP cc_start: 0.5288 (OUTLIER) cc_final: 0.5046 (p0) REVERT: A 245 MET cc_start: 0.5755 (ptm) cc_final: 0.5172 (pmm) REVERT: A 735 THR cc_start: 0.8236 (p) cc_final: 0.7857 (t) REVERT: B 488 TYR cc_start: 0.6097 (t80) cc_final: 0.5786 (t80) REVERT: B 503 MET cc_start: 0.5344 (mpp) cc_final: 0.4951 (mpp) REVERT: B 535 ARG cc_start: 0.8177 (tmm-80) cc_final: 0.7757 (tmm-80) REVERT: C 114 ARG cc_start: 0.6277 (ttt180) cc_final: 0.6069 (ttt180) REVERT: C 148 MET cc_start: 0.6924 (mtm) cc_final: 0.6413 (ttt) REVERT: C 303 LYS cc_start: 0.7061 (tmtt) cc_final: 0.6783 (tttp) REVERT: C 412 MET cc_start: 0.8526 (mmt) cc_final: 0.8139 (mmt) REVERT: C 473 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7977 (tmmt) REVERT: C 530 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8013 (tt) REVERT: D 84 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7806 (tp) REVERT: D 94 ILE cc_start: 0.5866 (mm) cc_final: 0.5610 (mm) REVERT: D 186 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7255 (tt) REVERT: D 205 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7590 (tp) REVERT: D 412 MET cc_start: 0.7462 (tpp) cc_final: 0.7217 (tpp) REVERT: D 522 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6222 (p90) REVERT: D 670 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8378 (tt) REVERT: E 83 MET cc_start: 0.6565 (ptp) cc_final: 0.5963 (ptp) REVERT: E 148 MET cc_start: 0.5257 (tpt) cc_final: 0.4614 (tpt) REVERT: E 153 MET cc_start: 0.8061 (tpp) cc_final: 0.7625 (tpp) REVERT: E 208 MET cc_start: 0.5470 (ppp) cc_final: 0.5101 (mmp) REVERT: F 83 MET cc_start: 0.7048 (mtm) cc_final: 0.6730 (mtp) REVERT: F 614 ASP cc_start: 0.4908 (OUTLIER) cc_final: 0.4688 (p0) REVERT: F 656 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6885 (mt) outliers start: 158 outliers final: 106 residues processed: 321 average time/residue: 0.3865 time to fit residues: 212.5227 Evaluate side-chains 275 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 160 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 594 ILE Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 691 VAL Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 735 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 509 ASP Chi-restraints excluded: chain F residue 587 VAL Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 676 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 8.9990 chunk 279 optimal weight: 30.0000 chunk 192 optimal weight: 0.0370 chunk 41 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 372 optimal weight: 3.9990 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 353 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 overall best weight: 1.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN D 243 HIS E 551 GLN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 ASN F 442 GLN F 603 ASN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33718 Z= 0.145 Angle : 0.565 8.364 45628 Z= 0.293 Chirality : 0.041 0.164 4969 Planarity : 0.004 0.059 5870 Dihedral : 5.594 43.530 4525 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.60 % Allowed : 21.86 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.12), residues: 4108 helix: -1.85 (0.10), residues: 2289 sheet: None (None), residues: 0 loop : -1.97 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 628 HIS 0.004 0.001 HIS E 757 PHE 0.021 0.001 PHE A 304 TYR 0.025 0.001 TYR D 227 ARG 0.003 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 190 time to evaluate : 3.694 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 245 MET cc_start: 0.5775 (ptm) cc_final: 0.5223 (pmm) REVERT: A 722 LEU cc_start: 0.7600 (tp) cc_final: 0.7208 (tt) REVERT: A 735 THR cc_start: 0.8245 (p) cc_final: 0.7848 (t) REVERT: A 736 PHE cc_start: 0.8506 (m-10) cc_final: 0.8182 (m-80) REVERT: B 303 LYS cc_start: 0.7511 (ptpt) cc_final: 0.7207 (ttpp) REVERT: B 488 TYR cc_start: 0.6126 (t80) cc_final: 0.5818 (t80) REVERT: B 535 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7645 (tmm-80) REVERT: C 148 MET cc_start: 0.7038 (mtm) cc_final: 0.6660 (ttt) REVERT: C 303 LYS cc_start: 0.7053 (tmtt) cc_final: 0.6713 (mmmm) REVERT: C 412 MET cc_start: 0.8571 (mmt) cc_final: 0.8202 (mmt) REVERT: C 465 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: C 473 LYS cc_start: 0.8265 (mtmm) cc_final: 0.8030 (tmmt) REVERT: D 94 ILE cc_start: 0.5793 (mm) cc_final: 0.5114 (mp) REVERT: D 174 ARG cc_start: 0.6710 (ttp80) cc_final: 0.6348 (ttp80) REVERT: D 186 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7249 (tt) REVERT: D 232 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7510 (mtt180) REVERT: D 412 MET cc_start: 0.7468 (tpp) cc_final: 0.7223 (tpp) REVERT: D 522 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.6051 (p90) REVERT: D 670 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8401 (tt) REVERT: E 83 MET cc_start: 0.6276 (ptp) cc_final: 0.5597 (ptp) REVERT: E 148 MET cc_start: 0.5392 (tpt) cc_final: 0.4732 (tpt) REVERT: E 153 MET cc_start: 0.8038 (tpp) cc_final: 0.7585 (tpp) REVERT: E 208 MET cc_start: 0.5750 (ppp) cc_final: 0.5322 (mmp) REVERT: F 208 MET cc_start: 0.5395 (ptm) cc_final: 0.4807 (mmt) REVERT: F 614 ASP cc_start: 0.5203 (OUTLIER) cc_final: 0.5001 (p0) REVERT: F 714 MET cc_start: 0.7769 (tpt) cc_final: 0.6905 (tpp) outliers start: 93 outliers final: 56 residues processed: 276 average time/residue: 0.4117 time to fit residues: 190.0531 Evaluate side-chains 222 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 161 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 655 GLU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 509 ASP Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 617 TYR Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 755 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 0.0670 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 0.0970 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 0.7980 chunk 272 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 2.9990 chunk 353 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 overall best weight: 0.9918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 HIS ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN E 132 GLN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 678 GLN ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33718 Z= 0.126 Angle : 0.530 11.075 45628 Z= 0.271 Chirality : 0.040 0.164 4969 Planarity : 0.004 0.056 5870 Dihedral : 4.994 42.370 4525 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.82 % Allowed : 22.36 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.12), residues: 4108 helix: -1.39 (0.10), residues: 2315 sheet: None (None), residues: 0 loop : -1.77 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 628 HIS 0.005 0.001 HIS E 757 PHE 0.011 0.001 PHE B 440 TYR 0.024 0.001 TYR D 227 ARG 0.004 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 183 time to evaluate : 3.727 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: A 245 MET cc_start: 0.5773 (ptm) cc_final: 0.5225 (pmm) REVERT: A 503 MET cc_start: 0.4837 (mpp) cc_final: 0.4510 (mpp) REVERT: A 722 LEU cc_start: 0.7785 (tp) cc_final: 0.7394 (tt) REVERT: A 735 THR cc_start: 0.8247 (p) cc_final: 0.7794 (t) REVERT: A 736 PHE cc_start: 0.8428 (m-10) cc_final: 0.8060 (m-80) REVERT: B 227 TYR cc_start: 0.6330 (OUTLIER) cc_final: 0.5958 (m-80) REVERT: B 488 TYR cc_start: 0.6105 (t80) cc_final: 0.5753 (t80) REVERT: C 148 MET cc_start: 0.6838 (mtm) cc_final: 0.6491 (ttt) REVERT: C 183 MET cc_start: 0.7469 (mmm) cc_final: 0.6701 (mmt) REVERT: C 303 LYS cc_start: 0.7070 (tmtt) cc_final: 0.6734 (mmmm) REVERT: C 412 MET cc_start: 0.8537 (mmt) cc_final: 0.8160 (mmt) REVERT: C 465 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: C 473 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7882 (tmmt) REVERT: D 94 ILE cc_start: 0.5774 (mm) cc_final: 0.5086 (mp) REVERT: D 174 ARG cc_start: 0.6523 (ttp80) cc_final: 0.6194 (ttp80) REVERT: D 232 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7535 (mtt180) REVERT: D 412 MET cc_start: 0.7534 (tpp) cc_final: 0.7269 (tpp) REVERT: D 522 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6034 (p90) REVERT: D 670 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8414 (tt) REVERT: E 83 MET cc_start: 0.6459 (ptp) cc_final: 0.5779 (ptp) REVERT: E 148 MET cc_start: 0.5348 (tpt) cc_final: 0.4670 (tpt) REVERT: E 153 MET cc_start: 0.7841 (tpp) cc_final: 0.7359 (tpp) REVERT: E 208 MET cc_start: 0.5536 (ppp) cc_final: 0.5064 (mmp) REVERT: F 208 MET cc_start: 0.5734 (ptm) cc_final: 0.5170 (mmt) REVERT: F 412 MET cc_start: 0.7859 (mmt) cc_final: 0.6470 (ptm) REVERT: F 569 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7493 (p0) REVERT: F 617 TYR cc_start: 0.5154 (OUTLIER) cc_final: 0.4914 (p90) REVERT: F 714 MET cc_start: 0.7877 (tpt) cc_final: 0.7005 (tpp) REVERT: F 718 THR cc_start: 0.8722 (m) cc_final: 0.8429 (p) outliers start: 101 outliers final: 60 residues processed: 275 average time/residue: 0.4310 time to fit residues: 200.4585 Evaluate side-chains 232 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 166 time to evaluate : 4.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 655 GLU Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 569 ASN Chi-restraints excluded: chain F residue 617 TYR Chi-restraints excluded: chain F residue 676 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.8980 chunk 355 optimal weight: 20.0000 chunk 77 optimal weight: 0.3980 chunk 231 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 32 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 overall best weight: 3.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 678 GLN ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33718 Z= 0.170 Angle : 0.579 9.797 45628 Z= 0.296 Chirality : 0.042 0.302 4969 Planarity : 0.004 0.056 5870 Dihedral : 5.177 45.956 4522 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.86 % Allowed : 21.91 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.13), residues: 4108 helix: -1.35 (0.10), residues: 2310 sheet: None (None), residues: 0 loop : -1.65 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 321 HIS 0.006 0.001 HIS B 590 PHE 0.015 0.001 PHE A 304 TYR 0.026 0.002 TYR D 227 ARG 0.004 0.000 ARG C 579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 164 time to evaluate : 3.635 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: A 245 MET cc_start: 0.5745 (ptm) cc_final: 0.5185 (pmm) REVERT: A 503 MET cc_start: 0.4684 (mpp) cc_final: 0.4362 (mpp) REVERT: A 722 LEU cc_start: 0.7725 (tp) cc_final: 0.7306 (tt) REVERT: A 735 THR cc_start: 0.8284 (p) cc_final: 0.7874 (t) REVERT: B 360 ASN cc_start: 0.5583 (OUTLIER) cc_final: 0.4940 (p0) REVERT: B 488 TYR cc_start: 0.6167 (t80) cc_final: 0.5811 (t80) REVERT: B 594 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7704 (tp) REVERT: C 148 MET cc_start: 0.6914 (mtm) cc_final: 0.6571 (ttt) REVERT: C 303 LYS cc_start: 0.7070 (tmtt) cc_final: 0.6729 (mmmm) REVERT: C 366 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7560 (pt) REVERT: C 412 MET cc_start: 0.8567 (mmt) cc_final: 0.8354 (mmt) REVERT: C 473 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7868 (tmmt) REVERT: C 530 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7919 (tt) REVERT: D 94 ILE cc_start: 0.5666 (mm) cc_final: 0.4951 (mp) REVERT: D 105 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7431 (t0) REVERT: D 412 MET cc_start: 0.7376 (tpp) cc_final: 0.7157 (tpp) REVERT: D 522 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6013 (p90) REVERT: D 670 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8384 (tt) REVERT: E 82 THR cc_start: 0.7296 (OUTLIER) cc_final: 0.7069 (t) REVERT: E 83 MET cc_start: 0.6296 (ptp) cc_final: 0.5613 (ptp) REVERT: E 148 MET cc_start: 0.5346 (tpt) cc_final: 0.4724 (tpt) REVERT: E 153 MET cc_start: 0.7906 (tpp) cc_final: 0.7460 (tpp) REVERT: E 208 MET cc_start: 0.5729 (ppp) cc_final: 0.5294 (mmp) REVERT: E 218 TYR cc_start: 0.5871 (OUTLIER) cc_final: 0.4761 (m-10) REVERT: F 147 MET cc_start: 0.4830 (tmm) cc_final: 0.4438 (tmm) REVERT: F 208 MET cc_start: 0.5635 (ptm) cc_final: 0.4968 (mmt) REVERT: F 315 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7155 (p0) REVERT: F 569 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7482 (p0) REVERT: F 714 MET cc_start: 0.7746 (tpt) cc_final: 0.6908 (tpp) REVERT: F 718 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8432 (p) outliers start: 138 outliers final: 95 residues processed: 295 average time/residue: 0.4001 time to fit residues: 200.8679 Evaluate side-chains 264 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 157 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 655 GLU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 218 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 767 ILE Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 569 ASN Chi-restraints excluded: chain F residue 617 TYR Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain F residue 728 ILE Chi-restraints excluded: chain F residue 755 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.4980 chunk 44 optimal weight: 8.9990 chunk 224 optimal weight: 20.0000 chunk 288 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 393 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 239 optimal weight: 0.0020 chunk 181 optimal weight: 0.0870 overall best weight: 1.3170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33718 Z= 0.126 Angle : 0.533 9.240 45628 Z= 0.269 Chirality : 0.040 0.165 4969 Planarity : 0.004 0.054 5870 Dihedral : 4.836 42.652 4522 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.02 % Allowed : 23.20 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 4108 helix: -1.05 (0.11), residues: 2307 sheet: None (None), residues: 0 loop : -1.68 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 140 HIS 0.003 0.000 HIS E 757 PHE 0.013 0.001 PHE A 304 TYR 0.025 0.001 TYR D 227 ARG 0.007 0.000 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 176 time to evaluate : 4.215 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 245 MET cc_start: 0.5741 (ptm) cc_final: 0.5196 (pmm) REVERT: A 722 LEU cc_start: 0.7772 (tp) cc_final: 0.7388 (tt) REVERT: A 735 THR cc_start: 0.8266 (p) cc_final: 0.7861 (t) REVERT: A 736 PHE cc_start: 0.8478 (m-10) cc_final: 0.8099 (m-80) REVERT: B 360 ASN cc_start: 0.5680 (OUTLIER) cc_final: 0.5022 (p0) REVERT: B 488 TYR cc_start: 0.6147 (t80) cc_final: 0.5817 (t80) REVERT: B 496 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6548 (tt) REVERT: C 148 MET cc_start: 0.6843 (mtm) cc_final: 0.6493 (ttt) REVERT: C 303 LYS cc_start: 0.7126 (tmtt) cc_final: 0.6812 (mmmm) REVERT: C 473 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7912 (tmmt) REVERT: C 503 MET cc_start: 0.5639 (mpp) cc_final: 0.5306 (mmm) REVERT: C 530 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7936 (tt) REVERT: C 538 LEU cc_start: 0.8564 (mp) cc_final: 0.8311 (tt) REVERT: D 94 ILE cc_start: 0.5807 (mm) cc_final: 0.5117 (mp) REVERT: D 105 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7380 (t0) REVERT: D 232 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7762 (ttp-110) REVERT: D 315 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6341 (p0) REVERT: D 412 MET cc_start: 0.7393 (tpp) cc_final: 0.7123 (tpp) REVERT: D 522 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.5980 (p90) REVERT: D 670 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8442 (tt) REVERT: E 82 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.7081 (t) REVERT: E 83 MET cc_start: 0.6455 (ptp) cc_final: 0.5769 (ptp) REVERT: E 148 MET cc_start: 0.5344 (tpt) cc_final: 0.4680 (tpt) REVERT: E 153 MET cc_start: 0.7920 (tpp) cc_final: 0.7451 (tpp) REVERT: E 208 MET cc_start: 0.5563 (ppp) cc_final: 0.5081 (mmp) REVERT: F 183 MET cc_start: 0.5350 (tmm) cc_final: 0.5116 (tmm) REVERT: F 208 MET cc_start: 0.5829 (ptm) cc_final: 0.5241 (mmt) REVERT: F 315 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7161 (p0) REVERT: F 412 MET cc_start: 0.7868 (mmt) cc_final: 0.6451 (ptm) REVERT: F 714 MET cc_start: 0.7799 (tpt) cc_final: 0.6945 (tpp) REVERT: F 718 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8447 (p) outliers start: 108 outliers final: 81 residues processed: 278 average time/residue: 0.3988 time to fit residues: 189.1334 Evaluate side-chains 257 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 166 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 655 GLU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 707 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 599 ASN Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain F residue 728 ILE Chi-restraints excluded: chain F residue 755 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 250 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 chunk 194 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 HIS ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 ASN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33718 Z= 0.178 Angle : 0.594 10.482 45628 Z= 0.300 Chirality : 0.042 0.162 4969 Planarity : 0.004 0.054 5870 Dihedral : 5.134 46.469 4522 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.69 % Allowed : 22.86 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.13), residues: 4108 helix: -1.11 (0.11), residues: 2305 sheet: None (None), residues: 0 loop : -1.61 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 321 HIS 0.004 0.001 HIS D 168 PHE 0.013 0.001 PHE F 398 TYR 0.027 0.002 TYR D 227 ARG 0.009 0.001 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 164 time to evaluate : 4.289 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: A 245 MET cc_start: 0.5729 (ptm) cc_final: 0.5184 (pmm) REVERT: A 360 ASN cc_start: 0.6145 (OUTLIER) cc_final: 0.5839 (p0) REVERT: A 722 LEU cc_start: 0.7690 (tp) cc_final: 0.7263 (tt) REVERT: A 735 THR cc_start: 0.8326 (p) cc_final: 0.7939 (t) REVERT: B 360 ASN cc_start: 0.5697 (OUTLIER) cc_final: 0.5092 (p0) REVERT: B 488 TYR cc_start: 0.6082 (t80) cc_final: 0.5831 (t80) REVERT: B 560 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7722 (tp) REVERT: B 594 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7704 (tp) REVERT: C 148 MET cc_start: 0.6971 (mtm) cc_final: 0.6579 (ttt) REVERT: C 303 LYS cc_start: 0.7055 (tmtt) cc_final: 0.6713 (mmmm) REVERT: C 366 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7571 (pt) REVERT: C 503 MET cc_start: 0.5668 (mpp) cc_final: 0.5306 (mmm) REVERT: C 530 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8023 (tt) REVERT: C 666 GLN cc_start: 0.7273 (mm110) cc_final: 0.6801 (tt0) REVERT: D 94 ILE cc_start: 0.5727 (mm) cc_final: 0.5513 (mm) REVERT: D 105 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7425 (t0) REVERT: D 232 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7654 (mtt180) REVERT: D 315 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6400 (p0) REVERT: D 412 MET cc_start: 0.7524 (tpp) cc_final: 0.7315 (tpp) REVERT: D 522 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.5968 (p90) REVERT: D 670 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8406 (tt) REVERT: E 82 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.7032 (t) REVERT: E 83 MET cc_start: 0.6313 (ptp) cc_final: 0.5628 (ptp) REVERT: E 148 MET cc_start: 0.5353 (tpt) cc_final: 0.4789 (tpt) REVERT: E 153 MET cc_start: 0.7937 (tpp) cc_final: 0.7500 (tpp) REVERT: E 208 MET cc_start: 0.5513 (ppp) cc_final: 0.5078 (mmp) REVERT: E 218 TYR cc_start: 0.5953 (OUTLIER) cc_final: 0.4731 (m-10) REVERT: E 599 ASN cc_start: 0.7156 (OUTLIER) cc_final: 0.6903 (m-40) REVERT: F 148 MET cc_start: 0.6320 (tmm) cc_final: 0.6073 (mtt) REVERT: F 208 MET cc_start: 0.5591 (ptm) cc_final: 0.5013 (mmt) REVERT: F 315 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7168 (p0) REVERT: F 398 PHE cc_start: 0.4920 (m-80) cc_final: 0.4430 (m-80) REVERT: F 714 MET cc_start: 0.7705 (tpt) cc_final: 0.6879 (tpp) REVERT: F 718 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8433 (p) outliers start: 132 outliers final: 104 residues processed: 289 average time/residue: 0.4153 time to fit residues: 206.9796 Evaluate side-chains 279 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 160 time to evaluate : 4.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 655 GLU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 218 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 599 ASN Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 735 THR Chi-restraints excluded: chain E residue 767 ILE Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain F residue 728 ILE Chi-restraints excluded: chain F residue 755 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.0030 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 8.9990 chunk 366 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 365 optimal weight: 5.9990 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33718 Z= 0.206 Angle : 0.628 10.891 45628 Z= 0.319 Chirality : 0.043 0.162 4969 Planarity : 0.005 0.054 5870 Dihedral : 5.366 47.142 4522 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.86 % Allowed : 23.14 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.13), residues: 4108 helix: -1.25 (0.10), residues: 2305 sheet: None (None), residues: 0 loop : -1.67 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 184 HIS 0.005 0.001 HIS D 168 PHE 0.013 0.002 PHE A 613 TYR 0.028 0.002 TYR D 227 ARG 0.008 0.001 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 165 time to evaluate : 4.078 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: A 245 MET cc_start: 0.5758 (ptm) cc_final: 0.5195 (pmm) REVERT: A 360 ASN cc_start: 0.5964 (OUTLIER) cc_final: 0.5632 (p0) REVERT: A 722 LEU cc_start: 0.7673 (tp) cc_final: 0.7241 (tt) REVERT: A 735 THR cc_start: 0.8346 (p) cc_final: 0.7975 (t) REVERT: B 360 ASN cc_start: 0.5913 (OUTLIER) cc_final: 0.5360 (p0) REVERT: B 560 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7633 (tp) REVERT: B 594 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7647 (tp) REVERT: C 148 MET cc_start: 0.6970 (mtm) cc_final: 0.6574 (ttt) REVERT: C 303 LYS cc_start: 0.7062 (tmtt) cc_final: 0.6724 (mmmm) REVERT: C 503 MET cc_start: 0.5454 (mpp) cc_final: 0.5077 (mmm) REVERT: C 530 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8040 (tt) REVERT: C 666 GLN cc_start: 0.7215 (mm110) cc_final: 0.6461 (mt0) REVERT: D 84 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7919 (tp) REVERT: D 94 ILE cc_start: 0.5791 (mm) cc_final: 0.5478 (mm) REVERT: D 105 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7419 (t0) REVERT: D 412 MET cc_start: 0.7423 (tpp) cc_final: 0.7191 (tpp) REVERT: D 522 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.6013 (p90) REVERT: D 670 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8384 (tt) REVERT: E 82 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.7053 (t) REVERT: E 83 MET cc_start: 0.6317 (ptp) cc_final: 0.5631 (ptp) REVERT: E 148 MET cc_start: 0.5339 (tpt) cc_final: 0.4858 (tpt) REVERT: E 153 MET cc_start: 0.7948 (tpp) cc_final: 0.7498 (tpp) REVERT: E 208 MET cc_start: 0.5384 (ppp) cc_final: 0.4911 (mmt) REVERT: E 218 TYR cc_start: 0.5880 (OUTLIER) cc_final: 0.4603 (m-10) REVERT: E 704 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: F 315 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7194 (p0) REVERT: F 714 MET cc_start: 0.7613 (tpt) cc_final: 0.6813 (tpp) REVERT: F 718 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8424 (p) outliers start: 138 outliers final: 110 residues processed: 295 average time/residue: 0.3819 time to fit residues: 195.4274 Evaluate side-chains 280 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 156 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 655 GLU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 218 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 704 GLU Chi-restraints excluded: chain E residue 735 THR Chi-restraints excluded: chain E residue 767 ILE Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 617 TYR Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain F residue 728 ILE Chi-restraints excluded: chain F residue 755 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 8.9990 chunk 387 optimal weight: 9.9990 chunk 236 optimal weight: 0.1980 chunk 183 optimal weight: 8.9990 chunk 269 optimal weight: 0.0050 chunk 406 optimal weight: 3.9990 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 250 optimal weight: 0.4980 chunk 198 optimal weight: 4.9990 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 ASN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33718 Z= 0.140 Angle : 0.567 11.297 45628 Z= 0.284 Chirality : 0.041 0.161 4969 Planarity : 0.004 0.055 5870 Dihedral : 5.009 42.996 4522 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.19 % Allowed : 23.73 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 4108 helix: -1.02 (0.11), residues: 2306 sheet: None (None), residues: 0 loop : -1.59 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP D 454 HIS 0.003 0.001 HIS E 757 PHE 0.013 0.001 PHE F 398 TYR 0.025 0.001 TYR D 227 ARG 0.006 0.000 ARG E 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 165 time to evaluate : 3.979 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: A 245 MET cc_start: 0.5749 (ptm) cc_final: 0.5207 (pmm) REVERT: A 360 ASN cc_start: 0.6055 (OUTLIER) cc_final: 0.5706 (p0) REVERT: A 722 LEU cc_start: 0.7676 (tp) cc_final: 0.7202 (tt) REVERT: A 735 THR cc_start: 0.8301 (p) cc_final: 0.7897 (t) REVERT: B 360 ASN cc_start: 0.5887 (OUTLIER) cc_final: 0.5311 (p0) REVERT: B 535 ARG cc_start: 0.8283 (tmm-80) cc_final: 0.7829 (tmm-80) REVERT: B 560 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7751 (tp) REVERT: C 148 MET cc_start: 0.6939 (mtm) cc_final: 0.6558 (ttt) REVERT: C 303 LYS cc_start: 0.6971 (tmtt) cc_final: 0.6659 (mmmm) REVERT: C 366 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7589 (pt) REVERT: C 503 MET cc_start: 0.5432 (mpp) cc_final: 0.5083 (mmm) REVERT: C 530 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8007 (tt) REVERT: C 538 LEU cc_start: 0.8584 (mp) cc_final: 0.8311 (tt) REVERT: C 663 LEU cc_start: 0.7247 (mt) cc_final: 0.6936 (tp) REVERT: C 666 GLN cc_start: 0.7347 (mm110) cc_final: 0.6445 (mt0) REVERT: D 84 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7871 (tp) REVERT: D 94 ILE cc_start: 0.5740 (mm) cc_final: 0.5532 (mm) REVERT: D 105 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7439 (t0) REVERT: D 232 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7755 (ttp-110) REVERT: D 315 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.6369 (p0) REVERT: D 412 MET cc_start: 0.7447 (tpp) cc_final: 0.7216 (tpp) REVERT: D 522 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.5973 (p90) REVERT: D 670 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8407 (tt) REVERT: E 82 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.6981 (t) REVERT: E 83 MET cc_start: 0.6299 (ptp) cc_final: 0.5617 (ptp) REVERT: E 148 MET cc_start: 0.5325 (tpt) cc_final: 0.4849 (tpt) REVERT: E 153 MET cc_start: 0.7914 (tpp) cc_final: 0.7471 (tpp) REVERT: E 208 MET cc_start: 0.5335 (ppp) cc_final: 0.4751 (mmt) REVERT: E 218 TYR cc_start: 0.5948 (OUTLIER) cc_final: 0.4582 (m-10) REVERT: E 704 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: F 208 MET cc_start: 0.5764 (ptm) cc_final: 0.5157 (mmt) REVERT: F 315 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7191 (p0) REVERT: F 714 MET cc_start: 0.7725 (tpt) cc_final: 0.6895 (tpp) REVERT: F 718 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8445 (p) outliers start: 114 outliers final: 96 residues processed: 274 average time/residue: 0.4250 time to fit residues: 202.5473 Evaluate side-chains 273 residues out of total 3578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 162 time to evaluate : 3.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 655 GLU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 218 TYR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 704 GLU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain F residue 728 ILE Chi-restraints excluded: chain F residue 755 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 332 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 HIS ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.034061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.025861 restraints weight = 375644.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.026689 restraints weight = 211813.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.027264 restraints weight = 142929.138| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33718 Z= 0.163 Angle : 0.589 11.212 45628 Z= 0.295 Chirality : 0.042 0.160 4969 Planarity : 0.004 0.055 5870 Dihedral : 5.100 44.718 4522 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.49 % Allowed : 23.64 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.13), residues: 4108 helix: -1.01 (0.11), residues: 2302 sheet: None (None), residues: 0 loop : -1.62 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 184 HIS 0.004 0.001 HIS D 168 PHE 0.011 0.001 PHE F 398 TYR 0.026 0.002 TYR D 227 ARG 0.006 0.000 ARG E 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5478.04 seconds wall clock time: 101 minutes 19.50 seconds (6079.50 seconds total)