Starting phenix.real_space_refine on Wed Jan 22 23:28:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yhx_39302/01_2025/8yhx_39302_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yhx_39302/01_2025/8yhx_39302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yhx_39302/01_2025/8yhx_39302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yhx_39302/01_2025/8yhx_39302.map" model { file = "/net/cci-nas-00/data/ceres_data/8yhx_39302/01_2025/8yhx_39302_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yhx_39302/01_2025/8yhx_39302_neut.cif" } resolution = 2.81 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= 0.001 sd= 0.015 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 184 5.16 5 C 44739 2.51 5 N 11398 2.21 5 O 13646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 508 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 69979 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4601 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 549} Chain: "B" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4601 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 549} Chain: "C" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4601 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 549} Chain: "D" Number of atoms: 4593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4593 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 549} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4601 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 549} Chain: "F" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4601 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 549} Chain: "G" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3392 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 6, 'TRANS': 401} Chain: "H" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3568 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 420} Chain breaks: 1 Chain: "I" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3579 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 420} Chain: "J" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3545 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 6, 'TRANS': 418} Chain: "K" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3579 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 420} Chain: "L" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3545 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 6, 'TRANS': 418} Chain: "M" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3579 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 421} Chain: "N" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3545 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 6, 'TRANS': 418} Chain: "O" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3579 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 420} Chain: "P" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3545 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 6, 'TRANS': 418} Chain: "Q" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3479 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3230 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 383} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'APR': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'APR': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'APR': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'APR': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'APR': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'APR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 30.39, per 1000 atoms: 0.43 Number of scatterers: 69979 At special positions: 0 Unit cell: (210.16, 217.26, 207.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 12 15.00 O 13646 8.00 N 11398 7.00 C 44739 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM69867 O4D APR L 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.20 Conformation dependent library (CDL) restraints added in 6.7 seconds 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16160 Finding SS restraints... Secondary structure from input PDB file: 362 helices and 54 sheets defined 45.8% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.71 Creating SS restraints... Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 246 removed outlier: 4.167A pdb=" N MET A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.952A pdb=" N SER A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.250A pdb=" N LYS A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 316 removed outlier: 3.869A pdb=" N GLU A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 336 through 354 Processing helix chain 'A' and resid 360 through 377 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 423 removed outlier: 3.642A pdb=" N GLU A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 454 through 468 removed outlier: 3.954A pdb=" N ARG A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ARG A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS A 466 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 229 through 246 removed outlier: 4.168A pdb=" N ILE B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 266 removed outlier: 4.005A pdb=" N TYR B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.779A pdb=" N LYS B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 313 removed outlier: 4.017A pdb=" N ILE B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 317 removed outlier: 3.541A pdb=" N GLY B 317 " --> pdb=" O VAL B 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 314 through 317' Processing helix chain 'B' and resid 322 through 329 Processing helix chain 'B' and resid 336 through 355 removed outlier: 3.994A pdb=" N LEU B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 377 removed outlier: 4.037A pdb=" N ILE B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS B 371 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 423 removed outlier: 3.741A pdb=" N LYS B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 468 removed outlier: 3.529A pdb=" N ARG B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARG B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.531A pdb=" N LEU B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS B 489 " --> pdb=" O VAL B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 508 Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 517 through 522 removed outlier: 4.082A pdb=" N PHE B 521 " --> pdb=" O GLN B 517 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 517 through 522' Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 66 through 70 removed outlier: 4.121A pdb=" N GLU C 70 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 121 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 161 through 174 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 230 through 246 removed outlier: 4.215A pdb=" N LEU C 234 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.813A pdb=" N CYS C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 260 " --> pdb=" O CYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'C' and resid 299 through 318 removed outlier: 3.903A pdb=" N GLU C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C 306 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 329 removed outlier: 3.994A pdb=" N VAL C 326 " --> pdb=" O THR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 354 Processing helix chain 'C' and resid 364 through 376 removed outlier: 3.681A pdb=" N ARG C 376 " --> pdb=" O ASN C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 423 removed outlier: 3.584A pdb=" N MET C 423 " --> pdb=" O LYS C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 442 removed outlier: 4.006A pdb=" N TYR C 441 " --> pdb=" O GLU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 462 removed outlier: 4.037A pdb=" N PHE C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 477 through 481 Processing helix chain 'C' and resid 500 through 508 Processing helix chain 'C' and resid 514 through 523 removed outlier: 3.727A pdb=" N ARG C 520 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE C 521 " --> pdb=" O GLN C 517 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 26 removed outlier: 3.518A pdb=" N LYS D 24 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN D 26 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 165 through 172 Processing helix chain 'D' and resid 215 through 223 removed outlier: 3.548A pdb=" N TRP D 219 " --> pdb=" O GLU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 241 removed outlier: 3.975A pdb=" N ILE D 233 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 245 Processing helix chain 'D' and resid 250 through 263 removed outlier: 4.086A pdb=" N LEU D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.533A pdb=" N THR D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 317 removed outlier: 4.333A pdb=" N ILE D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 330 removed outlier: 3.844A pdb=" N VAL D 326 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE D 327 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU D 328 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 354 removed outlier: 3.848A pdb=" N ASN D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR D 346 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 377 removed outlier: 3.801A pdb=" N ARG D 369 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE D 377 " --> pdb=" O VAL D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 423 Processing helix chain 'D' and resid 437 through 442 Processing helix chain 'D' and resid 454 through 462 removed outlier: 4.205A pdb=" N ILE D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 502 through 510 Processing helix chain 'D' and resid 514 through 523 removed outlier: 3.911A pdb=" N SER D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 523 " --> pdb=" O ASN D 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 26 removed outlier: 3.538A pdb=" N LYS E 24 " --> pdb=" O ASP E 21 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN E 26 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 121 Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'E' and resid 161 through 175 removed outlier: 3.683A pdb=" N ASN E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 removed outlier: 4.475A pdb=" N ASP E 194 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE E 195 " --> pdb=" O TYR E 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 195' Processing helix chain 'E' and resid 217 through 224 Processing helix chain 'E' and resid 229 through 246 removed outlier: 3.801A pdb=" N ILE E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE E 244 " --> pdb=" O TYR E 240 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN E 246 " --> pdb=" O ASN E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 265 Processing helix chain 'E' and resid 269 through 281 Processing helix chain 'E' and resid 288 through 292 removed outlier: 3.792A pdb=" N ASP E 292 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 315 removed outlier: 3.650A pdb=" N GLU E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL E 314 " --> pdb=" O LEU E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 355 removed outlier: 3.746A pdb=" N LEU E 340 " --> pdb=" O SER E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 382 removed outlier: 3.695A pdb=" N SER E 361 " --> pdb=" O ASN E 357 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR E 365 " --> pdb=" O SER E 361 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU E 366 " --> pdb=" O TYR E 362 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU E 380 " --> pdb=" O ARG E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 400 No H-bonds generated for 'chain 'E' and resid 398 through 400' Processing helix chain 'E' and resid 401 through 423 removed outlier: 3.833A pdb=" N LEU E 413 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS E 422 " --> pdb=" O GLU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 448 Processing helix chain 'E' and resid 454 through 463 Processing helix chain 'E' and resid 464 through 466 No H-bonds generated for 'chain 'E' and resid 464 through 466' Processing helix chain 'E' and resid 499 through 508 Processing helix chain 'E' and resid 517 through 523 removed outlier: 3.867A pdb=" N PHE E 521 " --> pdb=" O GLN E 517 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER E 522 " --> pdb=" O LEU E 518 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 517 through 523' Processing helix chain 'F' and resid 21 through 26 removed outlier: 3.594A pdb=" N ASN F 26 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 121 Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 161 through 176 removed outlier: 3.706A pdb=" N LEU F 176 " --> pdb=" O LYS F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 224 removed outlier: 3.515A pdb=" N ILE F 223 " --> pdb=" O TRP F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 247 removed outlier: 3.937A pdb=" N ILE F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET F 236 " --> pdb=" O PRO F 232 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS F 239 " --> pdb=" O GLN F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 removed outlier: 3.736A pdb=" N SER F 261 " --> pdb=" O TYR F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 276 through 281 Processing helix chain 'F' and resid 287 through 292 removed outlier: 4.126A pdb=" N LYS F 290 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP F 292 " --> pdb=" O GLU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 318 removed outlier: 4.352A pdb=" N GLU F 303 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY F 318 " --> pdb=" O VAL F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 330 removed outlier: 4.104A pdb=" N ALA F 330 " --> pdb=" O VAL F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 355 Processing helix chain 'F' and resid 364 through 377 removed outlier: 4.112A pdb=" N THR F 368 " --> pdb=" O ALA F 364 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL F 373 " --> pdb=" O ARG F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 381 Processing helix chain 'F' and resid 403 through 423 Processing helix chain 'F' and resid 438 through 441 Processing helix chain 'F' and resid 454 through 463 Processing helix chain 'F' and resid 482 through 488 Processing helix chain 'F' and resid 499 through 510 removed outlier: 3.878A pdb=" N ASN F 508 " --> pdb=" O GLU F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 522 removed outlier: 3.645A pdb=" N ARG F 520 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER F 522 " --> pdb=" O LEU F 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 24 Processing helix chain 'G' and resid 28 through 34 removed outlier: 3.648A pdb=" N SER G 34 " --> pdb=" O ASN G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 65 Processing helix chain 'G' and resid 66 through 78 Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.568A pdb=" N PHE G 84 " --> pdb=" O GLY G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 111 removed outlier: 4.141A pdb=" N ALA G 103 " --> pdb=" O LYS G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 130 removed outlier: 4.199A pdb=" N ASP G 130 " --> pdb=" O LEU G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 147 Processing helix chain 'G' and resid 150 through 160 removed outlier: 3.743A pdb=" N LEU G 154 " --> pdb=" O ASN G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 163 No H-bonds generated for 'chain 'G' and resid 161 through 163' Processing helix chain 'G' and resid 168 through 186 removed outlier: 3.508A pdb=" N LYS G 172 " --> pdb=" O ASN G 168 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR G 185 " --> pdb=" O GLU G 181 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE G 186 " --> pdb=" O PHE G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.608A pdb=" N TYR G 194 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR G 196 " --> pdb=" O GLU G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 211 Processing helix chain 'G' and resid 229 through 238 removed outlier: 3.509A pdb=" N ASN G 237 " --> pdb=" O TYR G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 259 Processing helix chain 'G' and resid 319 through 324 Processing helix chain 'G' and resid 327 through 340 removed outlier: 4.244A pdb=" N GLU G 331 " --> pdb=" O ALA G 327 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU G 340 " --> pdb=" O PHE G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 368 removed outlier: 3.813A pdb=" N ASN G 360 " --> pdb=" O ASP G 356 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN G 366 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS G 368 " --> pdb=" O ALA G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 392 Processing helix chain 'H' and resid 17 through 33 removed outlier: 4.351A pdb=" N GLN H 22 " --> pdb=" O SER H 18 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU H 23 " --> pdb=" O ASN H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 58 Processing helix chain 'H' and resid 59 through 64 removed outlier: 3.947A pdb=" N GLU H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 74 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 81 through 92 Processing helix chain 'H' and resid 97 through 112 removed outlier: 4.396A pdb=" N ILE H 107 " --> pdb=" O ALA H 103 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 128 removed outlier: 3.801A pdb=" N MET H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 148 removed outlier: 3.528A pdb=" N ASP H 142 " --> pdb=" O LEU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 Processing helix chain 'H' and resid 169 through 184 removed outlier: 3.662A pdb=" N ASP H 173 " --> pdb=" O GLY H 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS H 184 " --> pdb=" O SER H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.535A pdb=" N TYR H 194 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 210 removed outlier: 3.757A pdb=" N ARG H 207 " --> pdb=" O LYS H 203 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR H 208 " --> pdb=" O ASP H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 238 Processing helix chain 'H' and resid 255 through 259 Processing helix chain 'H' and resid 326 through 340 removed outlier: 3.809A pdb=" N LEU H 332 " --> pdb=" O PRO H 328 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU H 340 " --> pdb=" O PHE H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 366 removed outlier: 3.798A pdb=" N ASN H 360 " --> pdb=" O ASP H 356 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN H 366 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 369 No H-bonds generated for 'chain 'H' and resid 367 through 369' Processing helix chain 'H' and resid 382 through 392 Processing helix chain 'H' and resid 413 through 422 removed outlier: 3.549A pdb=" N LEU H 422 " --> pdb=" O VAL H 418 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 27 removed outlier: 3.694A pdb=" N GLN I 22 " --> pdb=" O SER I 18 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR I 27 " --> pdb=" O GLU I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 35 Processing helix chain 'I' and resid 53 through 65 Processing helix chain 'I' and resid 66 through 80 removed outlier: 4.084A pdb=" N GLY I 80 " --> pdb=" O LEU I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 92 removed outlier: 3.678A pdb=" N PHE I 84 " --> pdb=" O GLY I 80 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS I 86 " --> pdb=" O LYS I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 110 Processing helix chain 'I' and resid 118 through 130 Processing helix chain 'I' and resid 133 through 147 Processing helix chain 'I' and resid 150 through 160 removed outlier: 3.935A pdb=" N LEU I 154 " --> pdb=" O ASN I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 183 removed outlier: 3.936A pdb=" N LYS I 172 " --> pdb=" O ASN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 196 removed outlier: 3.570A pdb=" N TYR I 194 " --> pdb=" O ASP I 191 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR I 196 " --> pdb=" O GLU I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 214 removed outlier: 3.843A pdb=" N LYS I 212 " --> pdb=" O TYR I 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG I 213 " --> pdb=" O VAL I 209 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR I 214 " --> pdb=" O PHE I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 238 removed outlier: 3.798A pdb=" N ASN I 237 " --> pdb=" O TYR I 233 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN I 238 " --> pdb=" O ALA I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 259 Processing helix chain 'I' and resid 319 through 324 Processing helix chain 'I' and resid 328 through 340 removed outlier: 3.795A pdb=" N LEU I 332 " --> pdb=" O PRO I 328 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER I 337 " --> pdb=" O PHE I 333 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU I 340 " --> pdb=" O PHE I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 368 removed outlier: 3.673A pdb=" N ASN I 366 " --> pdb=" O ILE I 362 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS I 368 " --> pdb=" O ALA I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 391 removed outlier: 3.508A pdb=" N ASN I 391 " --> pdb=" O ASN I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 410 through 415 Processing helix chain 'J' and resid 11 through 16 removed outlier: 3.620A pdb=" N THR J 14 " --> pdb=" O ASP J 11 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP J 15 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU J 16 " --> pdb=" O LEU J 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 11 through 16' Processing helix chain 'J' and resid 17 through 33 removed outlier: 4.009A pdb=" N GLN J 22 " --> pdb=" O SER J 18 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU J 23 " --> pdb=" O ASN J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 58 Processing helix chain 'J' and resid 59 through 64 removed outlier: 3.833A pdb=" N GLU J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 74 removed outlier: 3.906A pdb=" N TYR J 71 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 78 Processing helix chain 'J' and resid 81 through 92 Processing helix chain 'J' and resid 97 through 114 removed outlier: 3.542A pdb=" N LEU J 111 " --> pdb=" O ILE J 107 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU J 112 " --> pdb=" O MET J 108 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA J 113 " --> pdb=" O ASP J 109 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 127 Processing helix chain 'J' and resid 134 through 148 Processing helix chain 'J' and resid 150 through 166 Processing helix chain 'J' and resid 169 through 185 Processing helix chain 'J' and resid 191 through 195 removed outlier: 3.704A pdb=" N TYR J 194 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 210 removed outlier: 3.769A pdb=" N ARG J 207 " --> pdb=" O LYS J 203 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR J 208 " --> pdb=" O ASP J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 213 No H-bonds generated for 'chain 'J' and resid 211 through 213' Processing helix chain 'J' and resid 229 through 238 Processing helix chain 'J' and resid 255 through 261 removed outlier: 3.746A pdb=" N TYR J 261 " --> pdb=" O GLN J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 340 removed outlier: 3.617A pdb=" N GLU J 331 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU J 332 " --> pdb=" O PRO J 328 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU J 340 " --> pdb=" O PHE J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 356 through 366 removed outlier: 4.223A pdb=" N ASN J 366 " --> pdb=" O ILE J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 392 Processing helix chain 'J' and resid 413 through 420 Processing helix chain 'K' and resid 18 through 27 removed outlier: 3.852A pdb=" N GLN K 22 " --> pdb=" O SER K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 34 removed outlier: 3.723A pdb=" N SER K 34 " --> pdb=" O ASN K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 48 removed outlier: 3.552A pdb=" N THR K 48 " --> pdb=" O GLY K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 65 Processing helix chain 'K' and resid 66 through 79 Processing helix chain 'K' and resid 80 through 90 removed outlier: 3.927A pdb=" N PHE K 84 " --> pdb=" O GLY K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 110 Processing helix chain 'K' and resid 118 through 130 removed outlier: 3.666A pdb=" N TYR K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 147 removed outlier: 3.573A pdb=" N ILE K 137 " --> pdb=" O TYR K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 160 removed outlier: 3.851A pdb=" N LEU K 154 " --> pdb=" O ASN K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 184 removed outlier: 4.304A pdb=" N LYS K 172 " --> pdb=" O ASN K 168 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 196 removed outlier: 3.641A pdb=" N TYR K 194 " --> pdb=" O ASP K 191 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR K 196 " --> pdb=" O GLU K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 214 removed outlier: 3.682A pdb=" N LYS K 212 " --> pdb=" O TYR K 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR K 214 " --> pdb=" O PHE K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 238 removed outlier: 3.807A pdb=" N ASN K 237 " --> pdb=" O TYR K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 261 removed outlier: 4.025A pdb=" N LYS K 260 " --> pdb=" O ILE K 256 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR K 261 " --> pdb=" O ASN K 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 256 through 261' Processing helix chain 'K' and resid 319 through 326 removed outlier: 3.745A pdb=" N ALA K 325 " --> pdb=" O HIS K 321 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN K 326 " --> pdb=" O LYS K 322 " (cutoff:3.500A) Processing helix chain 'K' and resid 328 through 341 removed outlier: 3.661A pdb=" N SER K 337 " --> pdb=" O PHE K 333 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU K 340 " --> pdb=" O PHE K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 356 through 366 removed outlier: 3.832A pdb=" N ASN K 360 " --> pdb=" O ASP K 356 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE K 362 " --> pdb=" O HIS K 358 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN K 366 " --> pdb=" O ILE K 362 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 392 Processing helix chain 'K' and resid 411 through 417 Processing helix chain 'L' and resid 19 through 33 removed outlier: 4.349A pdb=" N GLU L 23 " --> pdb=" O ASN L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 58 Processing helix chain 'L' and resid 59 through 63 removed outlier: 3.814A pdb=" N LEU L 62 " --> pdb=" O LYS L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 74 removed outlier: 3.505A pdb=" N TYR L 71 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 78 Processing helix chain 'L' and resid 81 through 92 removed outlier: 3.715A pdb=" N GLU L 90 " --> pdb=" O LYS L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 114 removed outlier: 3.946A pdb=" N GLU L 112 " --> pdb=" O MET L 108 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA L 113 " --> pdb=" O ASP L 109 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU L 114 " --> pdb=" O GLN L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 126 Processing helix chain 'L' and resid 134 through 147 Processing helix chain 'L' and resid 150 through 165 removed outlier: 3.592A pdb=" N LEU L 154 " --> pdb=" O ASN L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 184 Processing helix chain 'L' and resid 192 through 196 removed outlier: 3.555A pdb=" N THR L 196 " --> pdb=" O GLU L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 210 removed outlier: 3.737A pdb=" N TYR L 208 " --> pdb=" O ASP L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 213 No H-bonds generated for 'chain 'L' and resid 211 through 213' Processing helix chain 'L' and resid 229 through 238 Processing helix chain 'L' and resid 255 through 259 Processing helix chain 'L' and resid 326 through 340 removed outlier: 4.066A pdb=" N GLU L 331 " --> pdb=" O ALA L 327 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU L 332 " --> pdb=" O PRO L 328 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU L 340 " --> pdb=" O PHE L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 365 removed outlier: 3.696A pdb=" N ASN L 360 " --> pdb=" O ASP L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 392 Processing helix chain 'L' and resid 413 through 421 Processing helix chain 'M' and resid 19 through 27 removed outlier: 4.456A pdb=" N THR M 27 " --> pdb=" O GLU M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 34 Processing helix chain 'M' and resid 53 through 65 removed outlier: 3.837A pdb=" N GLU M 64 " --> pdb=" O ASN M 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN M 65 " --> pdb=" O ILE M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 80 removed outlier: 3.847A pdb=" N GLY M 80 " --> pdb=" O LEU M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 92 removed outlier: 3.940A pdb=" N PHE M 84 " --> pdb=" O GLY M 80 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS M 86 " --> pdb=" O LYS M 82 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU M 92 " --> pdb=" O VAL M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 110 Processing helix chain 'M' and resid 118 through 130 Processing helix chain 'M' and resid 133 through 147 removed outlier: 3.601A pdb=" N ILE M 137 " --> pdb=" O TYR M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 160 removed outlier: 3.780A pdb=" N LEU M 154 " --> pdb=" O ASN M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 185 removed outlier: 3.670A pdb=" N THR M 185 " --> pdb=" O GLU M 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 195 Processing helix chain 'M' and resid 196 through 214 removed outlier: 3.605A pdb=" N GLU M 200 " --> pdb=" O THR M 196 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE M 201 " --> pdb=" O GLU M 197 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR M 202 " --> pdb=" O THR M 198 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS M 212 " --> pdb=" O TYR M 208 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG M 213 " --> pdb=" O VAL M 209 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR M 214 " --> pdb=" O PHE M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 238 removed outlier: 3.641A pdb=" N ASN M 238 " --> pdb=" O ALA M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 260 removed outlier: 3.994A pdb=" N LYS M 260 " --> pdb=" O ILE M 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 256 through 260' Processing helix chain 'M' and resid 319 through 327 removed outlier: 4.669A pdb=" N ALA M 325 " --> pdb=" O HIS M 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 329 through 339 Processing helix chain 'M' and resid 340 through 342 No H-bonds generated for 'chain 'M' and resid 340 through 342' Processing helix chain 'M' and resid 356 through 368 removed outlier: 4.008A pdb=" N ASN M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE M 362 " --> pdb=" O HIS M 358 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN M 366 " --> pdb=" O ILE M 362 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS M 368 " --> pdb=" O ALA M 364 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 392 Processing helix chain 'M' and resid 410 through 415 removed outlier: 3.606A pdb=" N PHE M 414 " --> pdb=" O LYS M 410 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 33 removed outlier: 4.088A pdb=" N GLN N 22 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU N 23 " --> pdb=" O ASN N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 58 Processing helix chain 'N' and resid 59 through 63 Processing helix chain 'N' and resid 67 through 74 Processing helix chain 'N' and resid 75 through 77 No H-bonds generated for 'chain 'N' and resid 75 through 77' Processing helix chain 'N' and resid 80 through 92 removed outlier: 4.362A pdb=" N PHE N 84 " --> pdb=" O GLY N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 114 removed outlier: 4.082A pdb=" N GLU N 112 " --> pdb=" O MET N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 127 removed outlier: 4.026A pdb=" N ASP N 127 " --> pdb=" O SER N 123 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 147 removed outlier: 3.992A pdb=" N ILE N 137 " --> pdb=" O TYR N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 166 removed outlier: 3.564A pdb=" N LEU N 154 " --> pdb=" O ASN N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 185 removed outlier: 3.613A pdb=" N GLU N 181 " --> pdb=" O THR N 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 196 removed outlier: 3.594A pdb=" N TYR N 194 " --> pdb=" O ASP N 191 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR N 196 " --> pdb=" O GLU N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 210 removed outlier: 3.584A pdb=" N ARG N 207 " --> pdb=" O LYS N 203 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR N 208 " --> pdb=" O ASP N 204 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 238 Processing helix chain 'N' and resid 255 through 259 Processing helix chain 'N' and resid 326 through 340 removed outlier: 4.004A pdb=" N GLU N 331 " --> pdb=" O ALA N 327 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU N 332 " --> pdb=" O PRO N 328 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE N 333 " --> pdb=" O TYR N 329 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU N 340 " --> pdb=" O PHE N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 356 through 366 removed outlier: 4.240A pdb=" N ASN N 366 " --> pdb=" O ILE N 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 369 No H-bonds generated for 'chain 'N' and resid 367 through 369' Processing helix chain 'N' and resid 382 through 393 removed outlier: 4.425A pdb=" N PHE N 392 " --> pdb=" O PHE N 388 " (cutoff:3.500A) Processing helix chain 'N' and resid 413 through 420 Processing helix chain 'O' and resid 18 through 27 removed outlier: 4.094A pdb=" N GLN O 22 " --> pdb=" O SER O 18 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR O 27 " --> pdb=" O GLU O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 35 Processing helix chain 'O' and resid 44 through 48 removed outlier: 3.535A pdb=" N THR O 48 " --> pdb=" O GLY O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 65 Processing helix chain 'O' and resid 66 through 78 removed outlier: 3.531A pdb=" N SER O 78 " --> pdb=" O LYS O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 91 removed outlier: 3.845A pdb=" N PHE O 84 " --> pdb=" O GLY O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 111 removed outlier: 4.321A pdb=" N ILE O 107 " --> pdb=" O ALA O 103 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N MET O 108 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP O 109 " --> pdb=" O HIS O 105 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN O 110 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 130 removed outlier: 3.575A pdb=" N TYR O 122 " --> pdb=" O ASN O 118 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET O 128 " --> pdb=" O GLY O 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN O 129 " --> pdb=" O TRP O 125 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP O 130 " --> pdb=" O LEU O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 147 Processing helix chain 'O' and resid 150 through 165 removed outlier: 3.764A pdb=" N LEU O 154 " --> pdb=" O ASN O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 184 Processing helix chain 'O' and resid 191 through 196 removed outlier: 3.627A pdb=" N TYR O 194 " --> pdb=" O ASP O 191 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR O 196 " --> pdb=" O GLU O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 212 Processing helix chain 'O' and resid 229 through 238 removed outlier: 3.504A pdb=" N ASN O 238 " --> pdb=" O ALA O 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 255 through 259 Processing helix chain 'O' and resid 319 through 327 removed outlier: 4.169A pdb=" N ALA O 325 " --> pdb=" O HIS O 321 " (cutoff:3.500A) Processing helix chain 'O' and resid 329 through 339 Processing helix chain 'O' and resid 340 through 342 No H-bonds generated for 'chain 'O' and resid 340 through 342' Processing helix chain 'O' and resid 357 through 366 removed outlier: 3.561A pdb=" N ILE O 362 " --> pdb=" O HIS O 358 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN O 366 " --> pdb=" O ILE O 362 " (cutoff:3.500A) Processing helix chain 'O' and resid 382 through 392 Processing helix chain 'O' and resid 411 through 417 removed outlier: 3.855A pdb=" N GLN O 415 " --> pdb=" O HIS O 412 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 16 removed outlier: 3.607A pdb=" N THR P 14 " --> pdb=" O ASP P 11 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP P 15 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU P 16 " --> pdb=" O LEU P 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 11 through 16' Processing helix chain 'P' and resid 17 through 33 Processing helix chain 'P' and resid 53 through 58 Processing helix chain 'P' and resid 59 through 63 Processing helix chain 'P' and resid 67 through 74 Processing helix chain 'P' and resid 75 through 78 Processing helix chain 'P' and resid 81 through 92 Processing helix chain 'P' and resid 97 through 109 Processing helix chain 'P' and resid 118 through 127 removed outlier: 3.789A pdb=" N ASP P 127 " --> pdb=" O SER P 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 133 through 148 Processing helix chain 'P' and resid 150 through 163 Processing helix chain 'P' and resid 169 through 184 removed outlier: 3.543A pdb=" N ASP P 173 " --> pdb=" O GLY P 169 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS P 184 " --> pdb=" O SER P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 195 Processing helix chain 'P' and resid 196 through 210 removed outlier: 3.584A pdb=" N TYR P 202 " --> pdb=" O THR P 198 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG P 207 " --> pdb=" O LYS P 203 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 238 Processing helix chain 'P' and resid 255 through 259 Processing helix chain 'P' and resid 327 through 340 removed outlier: 3.554A pdb=" N LEU P 332 " --> pdb=" O PRO P 328 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE P 333 " --> pdb=" O TYR P 329 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU P 340 " --> pdb=" O PHE P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 356 through 366 removed outlier: 3.593A pdb=" N ASN P 360 " --> pdb=" O ASP P 356 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN P 366 " --> pdb=" O ILE P 362 " (cutoff:3.500A) Processing helix chain 'P' and resid 367 through 369 No H-bonds generated for 'chain 'P' and resid 367 through 369' Processing helix chain 'P' and resid 382 through 392 Processing helix chain 'P' and resid 413 through 419 Processing helix chain 'Q' and resid 18 through 28 removed outlier: 3.897A pdb=" N GLN Q 22 " --> pdb=" O SER Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 34 removed outlier: 3.649A pdb=" N HIS Q 32 " --> pdb=" O PHE Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 65 Processing helix chain 'Q' and resid 66 through 78 Processing helix chain 'Q' and resid 80 through 91 removed outlier: 3.641A pdb=" N PHE Q 84 " --> pdb=" O GLY Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 110 Processing helix chain 'Q' and resid 118 through 130 removed outlier: 3.566A pdb=" N TYR Q 122 " --> pdb=" O ASN Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 147 removed outlier: 3.545A pdb=" N PHE Q 140 " --> pdb=" O GLU Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 160 removed outlier: 3.951A pdb=" N LEU Q 154 " --> pdb=" O ASN Q 150 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 184 removed outlier: 4.008A pdb=" N LYS Q 172 " --> pdb=" O ASN Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 196 removed outlier: 3.614A pdb=" N TYR Q 194 " --> pdb=" O ASP Q 191 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR Q 196 " --> pdb=" O GLU Q 193 " (cutoff:3.500A) Processing helix chain 'Q' and resid 198 through 212 removed outlier: 3.596A pdb=" N LYS Q 212 " --> pdb=" O TYR Q 208 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 238 removed outlier: 3.695A pdb=" N ASN Q 237 " --> pdb=" O TYR Q 233 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN Q 238 " --> pdb=" O ALA Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 256 through 260 removed outlier: 3.978A pdb=" N LYS Q 260 " --> pdb=" O ILE Q 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 256 through 260' Processing helix chain 'Q' and resid 319 through 324 Processing helix chain 'Q' and resid 327 through 340 removed outlier: 4.050A pdb=" N GLU Q 331 " --> pdb=" O ALA Q 327 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU Q 340 " --> pdb=" O PHE Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 356 through 368 removed outlier: 4.241A pdb=" N ASN Q 360 " --> pdb=" O ASP Q 356 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN Q 366 " --> pdb=" O ILE Q 362 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS Q 368 " --> pdb=" O ALA Q 364 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 392 Processing helix chain 'Q' and resid 413 through 415 No H-bonds generated for 'chain 'Q' and resid 413 through 415' Processing helix chain 'Q' and resid 416 through 421 Processing helix chain 'R' and resid 17 through 34 removed outlier: 4.057A pdb=" N SER R 34 " --> pdb=" O ASN R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 63 removed outlier: 4.070A pdb=" N LYS R 59 " --> pdb=" O SER R 55 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN R 60 " --> pdb=" O THR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 74 Processing helix chain 'R' and resid 81 through 91 Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 150 through 165 Processing helix chain 'R' and resid 169 through 185 removed outlier: 3.555A pdb=" N THR R 185 " --> pdb=" O GLU R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 196 removed outlier: 3.670A pdb=" N TYR R 194 " --> pdb=" O ASP R 191 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR R 196 " --> pdb=" O GLU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 211 removed outlier: 3.785A pdb=" N ASP R 204 " --> pdb=" O GLU R 200 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG R 207 " --> pdb=" O LYS R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 238 Processing helix chain 'R' and resid 255 through 259 Processing helix chain 'R' and resid 326 through 340 removed outlier: 4.056A pdb=" N LEU R 332 " --> pdb=" O PRO R 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE R 333 " --> pdb=" O TYR R 329 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU R 340 " --> pdb=" O PHE R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 365 Processing helix chain 'R' and resid 366 through 369 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 413 through 420 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 removed outlier: 3.720A pdb=" N LYS A 6 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 16 " --> pdb=" O THR A 8 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 15 through 19 current: chain 'A' and resid 52 through 63 removed outlier: 6.513A pdb=" N LYS A 52 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET A 88 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 54 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU A 82 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 60 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG A 80 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP A 62 " --> pdb=" O HIS A 78 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N HIS A 78 " --> pdb=" O ASP A 62 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 93 through 95 current: chain 'B' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 15 through 19 current: chain 'B' and resid 52 through 63 removed outlier: 6.384A pdb=" N LYS B 52 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N MET B 88 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE B 54 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU B 82 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 60 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG B 80 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP B 62 " --> pdb=" O HIS B 78 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS B 78 " --> pdb=" O ASP B 62 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 93 through 95 current: chain 'C' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 15 through 19 current: chain 'C' and resid 52 through 63 removed outlier: 6.462A pdb=" N LYS C 52 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N MET C 88 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE C 54 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU C 82 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL C 60 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG C 80 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP C 62 " --> pdb=" O HIS C 78 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N HIS C 78 " --> pdb=" O ASP C 62 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 93 through 96 current: chain 'D' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 15 through 19 current: chain 'D' and resid 52 through 63 removed outlier: 6.457A pdb=" N LYS D 52 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET D 88 " --> pdb=" O LYS D 52 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE D 54 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU D 82 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL D 60 " --> pdb=" O ARG D 80 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG D 80 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP D 62 " --> pdb=" O HIS D 78 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N HIS D 78 " --> pdb=" O ASP D 62 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 93 through 95 current: chain 'E' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 15 through 19 current: chain 'E' and resid 52 through 63 removed outlier: 6.086A pdb=" N LYS E 52 " --> pdb=" O MET E 88 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET E 88 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE E 54 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU E 82 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL E 60 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG E 80 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASP E 62 " --> pdb=" O HIS E 78 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS E 78 " --> pdb=" O ASP E 62 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 93 through 95 current: chain 'F' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 15 through 19 current: chain 'F' and resid 52 through 63 removed outlier: 6.514A pdb=" N LYS F 52 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET F 88 " --> pdb=" O LYS F 52 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE F 54 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU F 82 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL F 60 " --> pdb=" O ARG F 80 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG F 80 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP F 62 " --> pdb=" O HIS F 78 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS F 78 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.883A pdb=" N ILE A 129 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 202 removed outlier: 3.705A pdb=" N VAL A 201 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 396 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE A 183 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N TYR A 395 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE A 185 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 152 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER A 475 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 154 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA A 153 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202 removed outlier: 3.683A pdb=" N SER B 396 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE B 183 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N TYR B 395 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 185 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR B 152 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N SER B 475 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE B 154 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 153 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 26 through 29 Processing sheet with id=AA8, first strand: chain 'C' and resid 129 through 134 removed outlier: 5.187A pdb=" N THR C 130 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE C 142 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLY C 132 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 140 " --> pdb=" O GLY C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 431 through 436 removed outlier: 6.230A pdb=" N ASN C 431 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N MET C 472 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE C 433 " --> pdb=" O MET C 472 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER C 474 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE C 435 " --> pdb=" O SER C 474 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 475 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA C 153 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS C 495 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE C 155 " --> pdb=" O HIS C 495 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA C 529 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 542 " --> pdb=" O ALA C 529 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 187 removed outlier: 3.630A pdb=" N SER C 396 " --> pdb=" O VAL C 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 27 through 29 Processing sheet with id=AB3, first strand: chain 'D' and resid 129 through 134 removed outlier: 5.722A pdb=" N THR D 130 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N PHE D 142 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLY D 132 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 152 through 155 removed outlier: 6.888A pdb=" N ALA D 153 " --> pdb=" O ILE D 493 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 199 through 202 removed outlier: 6.172A pdb=" N LYS D 199 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER D 396 " --> pdb=" O LYS D 199 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL D 201 " --> pdb=" O SER D 396 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N HIS D 182 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR D 395 " --> pdb=" O HIS D 182 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N HIS D 184 " --> pdb=" O TYR D 395 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU D 181 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE D 434 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE D 183 " --> pdb=" O ILE D 434 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLU D 436 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE D 185 " --> pdb=" O GLU D 436 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 27 through 29 Processing sheet with id=AB7, first strand: chain 'E' and resid 199 through 202 removed outlier: 6.421A pdb=" N PHE E 183 " --> pdb=" O ILE E 393 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N TYR E 395 " --> pdb=" O PHE E 183 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE E 185 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N HIS E 182 " --> pdb=" O VAL E 432 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ILE E 434 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N HIS E 184 " --> pdb=" O ILE E 434 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N GLU E 436 " --> pdb=" O HIS E 184 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE E 186 " --> pdb=" O GLU E 436 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA E 153 " --> pdb=" O ILE E 493 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 27 through 29 Processing sheet with id=AB9, first strand: chain 'F' and resid 128 through 129 Processing sheet with id=AC1, first strand: chain 'F' and resid 133 through 134 Processing sheet with id=AC2, first strand: chain 'F' and resid 199 through 202 removed outlier: 5.917A pdb=" N PHE F 183 " --> pdb=" O ILE F 393 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR F 395 " --> pdb=" O PHE F 183 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE F 185 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU F 436 " --> pdb=" O PHE F 186 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN F 431 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N MET F 472 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE F 433 " --> pdb=" O MET F 472 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER F 474 " --> pdb=" O PHE F 433 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE F 435 " --> pdb=" O SER F 474 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE F 493 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 4 through 6 removed outlier: 6.484A pdb=" N LEU G 374 " --> pdb=" O HIS G 398 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE G 400 " --> pdb=" O LEU G 374 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE G 376 " --> pdb=" O ILE G 400 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU G 347 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR G 39 " --> pdb=" O THR G 346 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL G 220 " --> pdb=" O ASN G 282 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE G 241 " --> pdb=" O ALA G 281 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 261 through 265 removed outlier: 3.738A pdb=" N GLN L 275 " --> pdb=" O ASP L 265 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 301 through 302 removed outlier: 3.587A pdb=" N SER G 289 " --> pdb=" O VAL G 312 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL G 312 " --> pdb=" O SER G 289 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 6 removed outlier: 6.605A pdb=" N LEU H 374 " --> pdb=" O HIS H 398 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE H 400 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE H 376 " --> pdb=" O ILE H 400 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR H 345 " --> pdb=" O ASN H 373 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE H 375 " --> pdb=" O THR H 345 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU H 347 " --> pdb=" O ILE H 375 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN H 37 " --> pdb=" O THR H 346 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE H 348 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR H 39 " --> pdb=" O ILE H 348 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA H 281 " --> pdb=" O ILE H 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 275 through 276 removed outlier: 3.557A pdb=" N GLN H 275 " --> pdb=" O ASP H 265 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL H 264 " --> pdb=" O ARG Q 262 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 292 through 293 Processing sheet with id=AC9, first strand: chain 'I' and resid 4 through 6 removed outlier: 6.858A pdb=" N LEU I 374 " --> pdb=" O HIS I 398 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE I 400 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE I 376 " --> pdb=" O ILE I 400 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU I 347 " --> pdb=" O ILE I 375 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE I 377 " --> pdb=" O LEU I 347 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE I 349 " --> pdb=" O PHE I 377 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR I 39 " --> pdb=" O ILE I 348 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL I 220 " --> pdb=" O GLU I 280 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA I 281 " --> pdb=" O ILE I 241 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 262 through 265 Processing sheet with id=AD2, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.683A pdb=" N SER I 289 " --> pdb=" O VAL I 312 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL I 312 " --> pdb=" O SER I 289 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 3 through 6 removed outlier: 7.853A pdb=" N HIS J 398 " --> pdb=" O PHE J 372 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU J 374 " --> pdb=" O HIS J 398 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE J 400 " --> pdb=" O LEU J 374 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE J 376 " --> pdb=" O ILE J 400 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N GLY J 402 " --> pdb=" O ILE J 376 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR J 345 " --> pdb=" O ASN J 373 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE J 375 " --> pdb=" O THR J 345 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU J 347 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N PHE J 377 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE J 349 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR J 39 " --> pdb=" O ILE J 348 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE J 350 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE J 41 " --> pdb=" O ILE J 350 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE J 241 " --> pdb=" O ALA J 281 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU J 283 " --> pdb=" O ILE J 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 275 through 276 Processing sheet with id=AD5, first strand: chain 'J' and resid 292 through 293 Processing sheet with id=AD6, first strand: chain 'K' and resid 3 through 6 removed outlier: 7.997A pdb=" N HIS K 398 " --> pdb=" O PHE K 372 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU K 374 " --> pdb=" O HIS K 398 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE K 400 " --> pdb=" O LEU K 374 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE K 376 " --> pdb=" O ILE K 400 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLY K 402 " --> pdb=" O ILE K 376 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR K 345 " --> pdb=" O ASN K 373 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE K 375 " --> pdb=" O THR K 345 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU K 347 " --> pdb=" O ILE K 375 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR K 39 " --> pdb=" O ILE K 348 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL K 220 " --> pdb=" O GLU K 280 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE K 241 " --> pdb=" O ALA K 281 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU K 283 " --> pdb=" O ILE K 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 4 through 6 removed outlier: 8.385A pdb=" N HIS L 398 " --> pdb=" O PHE L 372 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU L 374 " --> pdb=" O HIS L 398 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE L 400 " --> pdb=" O LEU L 374 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE L 376 " --> pdb=" O ILE L 400 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR L 39 " --> pdb=" O ILE L 348 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE L 350 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE L 41 " --> pdb=" O ILE L 350 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL L 220 " --> pdb=" O ASN L 282 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 252 through 253 removed outlier: 4.500A pdb=" N LYS L 252 " --> pdb=" O GLN L 302 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 288 through 289 removed outlier: 4.542A pdb=" N VAL L 313 " --> pdb=" O SER L 289 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'M' and resid 241 through 243 removed outlier: 3.845A pdb=" N VAL M 220 " --> pdb=" O GLU M 280 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR M 39 " --> pdb=" O ILE M 348 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR M 345 " --> pdb=" O ASN M 373 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE M 375 " --> pdb=" O THR M 345 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU M 347 " --> pdb=" O ILE M 375 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 261 through 265 removed outlier: 3.901A pdb=" N GLN P 275 " --> pdb=" O ASP P 265 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 288 through 293 removed outlier: 4.515A pdb=" N VAL M 312 " --> pdb=" O SER M 289 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 3 through 6 removed outlier: 6.248A pdb=" N THR N 345 " --> pdb=" O ASN N 373 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE N 375 " --> pdb=" O THR N 345 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU N 347 " --> pdb=" O ILE N 375 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR N 39 " --> pdb=" O ILE N 348 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE N 350 " --> pdb=" O THR N 39 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE N 41 " --> pdb=" O ILE N 350 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 220 through 221 removed outlier: 6.489A pdb=" N VAL N 220 " --> pdb=" O ASN N 282 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE N 241 " --> pdb=" O ALA N 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'N' and resid 252 through 253 removed outlier: 4.560A pdb=" N LYS N 252 " --> pdb=" O GLN N 302 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'O' and resid 241 through 243 removed outlier: 6.618A pdb=" N VAL O 220 " --> pdb=" O ASN O 282 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR O 284 " --> pdb=" O VAL O 220 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE O 222 " --> pdb=" O TYR O 284 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU O 38 " --> pdb=" O SER O 221 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE O 223 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE O 40 " --> pdb=" O PHE O 223 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR O 39 " --> pdb=" O ILE O 348 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE O 350 " --> pdb=" O THR O 39 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE O 41 " --> pdb=" O ILE O 350 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR O 345 " --> pdb=" O ASN O 373 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE O 375 " --> pdb=" O THR O 345 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU O 347 " --> pdb=" O ILE O 375 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 262 through 265 Processing sheet with id=AF2, first strand: chain 'O' and resid 300 through 302 removed outlier: 4.229A pdb=" N VAL O 312 " --> pdb=" O SER O 289 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 4 through 6 removed outlier: 6.556A pdb=" N THR P 345 " --> pdb=" O ASN P 373 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE P 375 " --> pdb=" O THR P 345 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU P 347 " --> pdb=" O ILE P 375 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE P 377 " --> pdb=" O LEU P 347 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE P 349 " --> pdb=" O PHE P 377 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR P 39 " --> pdb=" O ILE P 348 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 292 through 293 Processing sheet with id=AF5, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AF6, first strand: chain 'Q' and resid 241 through 243 removed outlier: 6.400A pdb=" N ILE Q 241 " --> pdb=" O ALA Q 281 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU Q 283 " --> pdb=" O ILE Q 241 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER Q 243 " --> pdb=" O LEU Q 283 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LYS Q 285 " --> pdb=" O SER Q 243 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL Q 220 " --> pdb=" O GLU Q 280 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU Q 38 " --> pdb=" O SER Q 221 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE Q 223 " --> pdb=" O LEU Q 38 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 223 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR Q 39 " --> pdb=" O ILE Q 348 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU Q 347 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 4 through 6 removed outlier: 7.005A pdb=" N THR R 39 " --> pdb=" O ILE R 348 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE R 350 " --> pdb=" O THR R 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 220 through 224 removed outlier: 6.520A pdb=" N ILE R 241 " --> pdb=" O ALA R 281 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU R 283 " --> pdb=" O ILE R 241 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 289 through 293 removed outlier: 6.343A pdb=" N TRP R 292 " --> pdb=" O VAL R 313 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL R 313 " --> pdb=" O TRP R 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 2523 hydrogen bonds defined for protein. 7143 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: 28.17 Time building geometry restraints manager: 15.67 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: 20991 1.34 - 1.45: 11250 1.45 - 1.57: 38809 1.57 - 1.69: 34 1.69 - 1.81: 312 Bond restraints: 71396 Sorted by residual: bond pdb=" C1' APR P 501 " pdb=" O4' APR P 501 " ideal model delta sigma weight residual 1.393 1.657 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C1' APR N 501 " pdb=" O4' APR N 501 " ideal model delta sigma weight residual 1.393 1.657 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C1' APR R 501 " pdb=" O4' APR R 501 " ideal model delta sigma weight residual 1.393 1.655 -0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1' APR L 501 " pdb=" O4' APR L 501 " ideal model delta sigma weight residual 1.393 1.654 -0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C1D APR L 501 " pdb=" O4D APR L 501 " ideal model delta sigma weight residual 1.408 1.623 -0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 71391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.83: 96092 4.83 - 9.67: 184 9.67 - 14.50: 20 14.50 - 19.34: 0 19.34 - 24.17: 8 Bond angle restraints: 96304 Sorted by residual: angle pdb=" N SER A 522 " pdb=" CA SER A 522 " pdb=" C SER A 522 " ideal model delta sigma weight residual 114.75 104.11 10.64 1.26e+00 6.30e-01 7.13e+01 angle pdb=" N1 APR P 501 " pdb=" C6 APR P 501 " pdb=" N6 APR P 501 " ideal model delta sigma weight residual 119.20 95.03 24.17 3.00e+00 1.11e-01 6.49e+01 angle pdb=" N1 APR N 501 " pdb=" C6 APR N 501 " pdb=" N6 APR N 501 " ideal model delta sigma weight residual 119.20 95.07 24.13 3.00e+00 1.11e-01 6.47e+01 angle pdb=" N1 APR L 501 " pdb=" C6 APR L 501 " pdb=" N6 APR L 501 " ideal model delta sigma weight residual 119.20 95.11 24.09 3.00e+00 1.11e-01 6.45e+01 angle pdb=" N1 APR R 501 " pdb=" C6 APR R 501 " pdb=" N6 APR R 501 " ideal model delta sigma weight residual 119.20 95.17 24.03 3.00e+00 1.11e-01 6.42e+01 ... (remaining 96299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 38048 18.10 - 36.20: 3744 36.20 - 54.31: 998 54.31 - 72.41: 237 72.41 - 90.51: 126 Dihedral angle restraints: 43153 sinusoidal: 18131 harmonic: 25022 Sorted by residual: dihedral pdb=" CD ARG C 561 " pdb=" NE ARG C 561 " pdb=" CZ ARG C 561 " pdb=" NH1 ARG C 561 " ideal model delta sinusoidal sigma weight residual 0.00 76.13 -76.13 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CA LYS J 393 " pdb=" C LYS J 393 " pdb=" N ASN J 394 " pdb=" CA ASN J 394 " ideal model delta harmonic sigma weight residual 180.00 137.64 42.36 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CA LYS N 393 " pdb=" C LYS N 393 " pdb=" N ASN N 394 " pdb=" CA ASN N 394 " ideal model delta harmonic sigma weight residual 180.00 137.84 42.16 0 5.00e+00 4.00e-02 7.11e+01 ... (remaining 43150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 9310 0.068 - 0.136: 1104 0.136 - 0.204: 41 0.204 - 0.272: 3 0.272 - 0.340: 4 Chirality restraints: 10462 Sorted by residual: chirality pdb=" C2' APR L 501 " pdb=" C1' APR L 501 " pdb=" C3' APR L 501 " pdb=" O2' APR L 501 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C2' APR P 501 " pdb=" C1' APR P 501 " pdb=" C3' APR P 501 " pdb=" O2' APR P 501 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C2' APR N 501 " pdb=" C1' APR N 501 " pdb=" C3' APR N 501 " pdb=" O2' APR N 501 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 10459 not shown) Planarity restraints: 12399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 561 " -1.073 9.50e-02 1.11e+02 4.81e-01 1.39e+02 pdb=" NE ARG C 561 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG C 561 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 561 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 561 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 197 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C GLU N 197 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU N 197 " -0.017 2.00e-02 2.50e+03 pdb=" N THR N 198 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU L 197 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C GLU L 197 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU L 197 " 0.016 2.00e-02 2.50e+03 pdb=" N THR L 198 " 0.015 2.00e-02 2.50e+03 ... (remaining 12396 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 12 1.94 - 2.68: 1628 2.68 - 3.42: 102733 3.42 - 4.16: 176558 4.16 - 4.90: 317133 Nonbonded interactions: 598064 Sorted by model distance: nonbonded pdb=" CD1 ILE D 211 " pdb=" O VAL D 334 " model vdw 1.197 3.460 nonbonded pdb=" OD1 ASN D 213 " pdb=" OE1 GLU D 418 " model vdw 1.433 3.040 nonbonded pdb=" CB PHE N 392 " pdb=" OD1 ASN N 394 " model vdw 1.593 3.440 nonbonded pdb=" OD1 ASN K 167 " pdb=" NZ LYS L 117 " model vdw 1.620 3.120 nonbonded pdb=" O PHE D 348 " pdb=" OE1 GLU D 352 " model vdw 1.653 3.040 ... (remaining 598059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 154 or (resid 155 and (name N or name CA or name \ C or name O or name CB )) or resid 156 or (resid 157 through 158 and (name N or \ name CA or name C or name O or name CB )) or resid 159 through 562)) selection = (chain 'B' and (resid 1 through 154 or (resid 155 and (name N or name CA or name \ C or name O or name CB )) or resid 156 or (resid 157 through 158 and (name N or \ name CA or name C or name O or name CB )) or resid 159 through 562)) selection = (chain 'C' and (resid 1 through 154 or (resid 155 and (name N or name CA or name \ C or name O or name CB )) or resid 156 or (resid 157 through 158 and (name N or \ name CA or name C or name O or name CB )) or resid 159 through 562)) selection = chain 'D' selection = (chain 'E' and (resid 1 through 154 or (resid 155 and (name N or name CA or name \ C or name O or name CB )) or resid 156 or (resid 157 through 158 and (name N or \ name CA or name C or name O or name CB )) or resid 159 through 562)) selection = (chain 'F' and (resid 1 through 154 or (resid 155 and (name N or name CA or name \ C or name O or name CB )) or resid 156 or (resid 157 through 158 and (name N or \ name CA or name C or name O or name CB )) or resid 159 through 562)) } ncs_group { reference = (chain 'G' and (resid 1 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 or resid 130 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 267 or resid 272 through 408)) selection = (chain 'H' and (resid 1 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 or resid 130 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 267 or resid 272 through 408)) selection = (chain 'I' and (resid 1 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 or resid 130 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 267 or resid 272 through 408)) selection = (chain 'J' and (resid 1 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 or resid 130 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 267 or resid 272 through 408)) selection = (chain 'K' and (resid 1 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 or resid 130 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 267 or resid 272 through 408)) selection = (chain 'L' and (resid 1 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 or resid 130 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 267 or resid 272 through 408)) selection = (chain 'M' and (resid 1 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 or resid 130 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 267 or resid 272 through 408)) selection = (chain 'N' and (resid 1 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 or resid 130 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 267 or resid 272 through 408)) selection = (chain 'O' and (resid 1 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 or resid 130 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 267 or resid 272 through 408)) selection = (chain 'P' and (resid 1 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 or resid 130 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 267 or resid 272 through 408)) selection = (chain 'Q' and (resid 1 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 or resid 130 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 267 or resid 272 through 405 or resid 410 through 411 or resid 419)) selection = (chain 'R' and (resid 1 through 267 or resid 272 through 408)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 2.400 Check model and map are aligned: 0.450 Set scattering table: 0.560 Process input model: 123.460 Find NCS groups from input model: 3.290 Set up NCS constraints: 0.280 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: 0.030 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 0.264 71396 Z= 0.285 Angle : 0.712 24.173 96304 Z= 0.390 Chirality : 0.043 0.340 10462 Planarity : 0.005 0.481 12399 Dihedral : 16.447 90.510 26993 Min Nonbonded Distance : 1.197 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.85 % Favored : 92.96 % Rotamer: Outliers : 0.97 % Allowed : 23.63 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.42 (0.08), residues: 8381 helix: -2.03 (0.07), residues: 3368 sheet: -3.29 (0.13), residues: 900 loop : -2.15 (0.09), residues: 4113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 125 HIS 0.013 0.001 HIS P 105 PHE 0.042 0.001 PHE B 348 TYR 0.025 0.001 TYR L 199 ARG 0.010 0.000 ARG P 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1693 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 1617 time to evaluate : 6.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7617 (t70) cc_final: 0.7135 (t70) REVERT: A 186 PHE cc_start: 0.7379 (m-80) cc_final: 0.7124 (m-80) REVERT: A 239 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5130 (mmpt) REVERT: A 298 MET cc_start: 0.0805 (mmm) cc_final: 0.0458 (mmt) REVERT: A 402 ASP cc_start: 0.6888 (m-30) cc_final: 0.6607 (m-30) REVERT: A 504 GLU cc_start: 0.7336 (pp20) cc_final: 0.7092 (pp20) REVERT: A 508 ASN cc_start: 0.8678 (m110) cc_final: 0.8425 (m110) REVERT: A 519 ASN cc_start: 0.8653 (t0) cc_final: 0.8432 (t0) REVERT: A 530 TYR cc_start: 0.7129 (t80) cc_final: 0.6879 (t80) REVERT: A 562 SER cc_start: 0.5616 (m) cc_final: 0.5408 (p) REVERT: B 23 GLU cc_start: 0.8208 (pt0) cc_final: 0.7983 (mt-10) REVERT: B 113 GLN cc_start: 0.8084 (tt0) cc_final: 0.7739 (tt0) REVERT: B 177 ASN cc_start: 0.5154 (t160) cc_final: 0.4436 (p0) REVERT: B 224 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6114 (tmtm) REVERT: B 402 ASP cc_start: 0.7429 (m-30) cc_final: 0.7077 (m-30) REVERT: B 414 LYS cc_start: 0.7731 (mppt) cc_final: 0.7508 (mppt) REVERT: B 440 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6807 (ptt90) REVERT: B 517 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7874 (mm-40) REVERT: B 519 ASN cc_start: 0.8576 (m-40) cc_final: 0.8155 (m-40) REVERT: C 339 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6405 (ttpp) REVERT: C 530 TYR cc_start: 0.7445 (t80) cc_final: 0.7206 (t80) REVERT: D 167 ARG cc_start: 0.6863 (ttm170) cc_final: 0.6641 (pmt-80) REVERT: D 196 ASN cc_start: 0.7593 (m110) cc_final: 0.7308 (t0) REVERT: D 216 MET cc_start: 0.7532 (ptm) cc_final: 0.7215 (ppp) REVERT: D 221 ASN cc_start: 0.5696 (t0) cc_final: 0.4780 (m-40) REVERT: D 457 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6417 (p90) REVERT: E 51 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7473 (mt-10) REVERT: E 131 ILE cc_start: 0.7109 (tt) cc_final: 0.6863 (tp) REVERT: E 142 PHE cc_start: 0.4953 (m-80) cc_final: 0.4546 (m-10) REVERT: E 213 ASN cc_start: 0.7343 (m-40) cc_final: 0.7041 (t0) REVERT: E 216 MET cc_start: 0.6199 (tmm) cc_final: 0.5534 (tpp) REVERT: E 400 LEU cc_start: 0.9033 (tp) cc_final: 0.8671 (tp) REVERT: E 407 PHE cc_start: 0.9032 (t80) cc_final: 0.8173 (t80) REVERT: E 437 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7627 (tp30) REVERT: E 459 LYS cc_start: 0.8404 (mtpp) cc_final: 0.7810 (ttmm) REVERT: E 486 LEU cc_start: 0.9081 (tt) cc_final: 0.8854 (tt) REVERT: E 545 PHE cc_start: 0.7786 (m-10) cc_final: 0.7417 (m-10) REVERT: F 40 ILE cc_start: 0.8631 (pt) cc_final: 0.8428 (pp) REVERT: F 175 ASN cc_start: 0.8675 (m-40) cc_final: 0.8467 (m-40) REVERT: F 216 MET cc_start: 0.7366 (ppp) cc_final: 0.6567 (tmm) REVERT: F 238 LEU cc_start: 0.5275 (pp) cc_final: 0.4367 (pt) REVERT: F 266 GLN cc_start: 0.2871 (OUTLIER) cc_final: 0.1345 (pt0) REVERT: F 404 LEU cc_start: 0.8959 (pt) cc_final: 0.8684 (pt) REVERT: F 408 PHE cc_start: 0.8326 (t80) cc_final: 0.8078 (t80) REVERT: F 424 LYS cc_start: 0.8907 (ptpt) cc_final: 0.8614 (ptpt) REVERT: F 510 ILE cc_start: 0.8685 (pt) cc_final: 0.8471 (pp) REVERT: F 535 LEU cc_start: 0.8980 (tp) cc_final: 0.8211 (tp) REVERT: G 128 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.6903 (mpp) REVERT: G 142 ASP cc_start: 0.8755 (m-30) cc_final: 0.8399 (m-30) REVERT: G 224 THR cc_start: 0.7688 (p) cc_final: 0.7484 (t) REVERT: G 319 LEU cc_start: 0.8129 (tp) cc_final: 0.7900 (tp) REVERT: H 86 LYS cc_start: 0.8795 (mtpp) cc_final: 0.8558 (tptp) REVERT: H 126 LEU cc_start: 0.8599 (mt) cc_final: 0.8256 (tt) REVERT: H 139 ASN cc_start: 0.8451 (t0) cc_final: 0.7934 (m110) REVERT: H 251 LEU cc_start: 0.7922 (tp) cc_final: 0.7646 (pt) REVERT: H 313 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7464 (m) REVERT: I 82 LYS cc_start: 0.8413 (tmtm) cc_final: 0.8164 (tptp) REVERT: I 105 HIS cc_start: 0.8663 (m-70) cc_final: 0.8429 (m90) REVERT: I 207 ARG cc_start: 0.8090 (ttp-110) cc_final: 0.7837 (ttp80) REVERT: I 241 ILE cc_start: 0.9032 (mt) cc_final: 0.8727 (mt) REVERT: J 163 HIS cc_start: 0.8210 (t-90) cc_final: 0.7997 (t-170) REVERT: J 211 ASP cc_start: 0.7927 (t0) cc_final: 0.7721 (t0) REVERT: J 383 GLU cc_start: 0.7268 (tp30) cc_final: 0.6511 (tp30) REVERT: J 387 ASN cc_start: 0.8208 (m-40) cc_final: 0.7365 (m-40) REVERT: K 100 GLU cc_start: 0.8040 (tt0) cc_final: 0.7706 (mm-30) REVERT: K 165 ASP cc_start: 0.8396 (t0) cc_final: 0.8162 (p0) REVERT: K 171 LEU cc_start: 0.8519 (mt) cc_final: 0.8088 (mt) REVERT: K 227 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: K 310 ASP cc_start: 0.7594 (t0) cc_final: 0.7225 (t0) REVERT: L 119 LEU cc_start: 0.8827 (mt) cc_final: 0.8579 (tm) REVERT: L 144 TYR cc_start: 0.7844 (t80) cc_final: 0.7318 (t80) REVERT: L 343 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7416 (ttpp) REVERT: L 419 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6945 (mt-10) REVERT: M 243 SER cc_start: 0.8587 (t) cc_final: 0.8301 (t) REVERT: N 140 PHE cc_start: 0.8754 (t80) cc_final: 0.8342 (t80) REVERT: N 297 GLU cc_start: 0.7520 (mp0) cc_final: 0.7306 (mp0) REVERT: N 350 ILE cc_start: 0.7981 (tp) cc_final: 0.7744 (tp) REVERT: O 157 TRP cc_start: 0.8031 (t60) cc_final: 0.7538 (t60) REVERT: O 162 LEU cc_start: 0.8717 (mt) cc_final: 0.8512 (mt) REVERT: O 303 ILE cc_start: 0.7545 (tp) cc_final: 0.7251 (tp) REVERT: O 357 GLU cc_start: 0.7071 (tt0) cc_final: 0.6735 (tt0) REVERT: P 150 ASN cc_start: 0.8290 (t0) cc_final: 0.8058 (t0) REVERT: P 163 HIS cc_start: 0.8830 (t-90) cc_final: 0.8531 (t-90) REVERT: P 265 ASP cc_start: 0.7760 (t0) cc_final: 0.7358 (t0) REVERT: Q 264 VAL cc_start: 0.8530 (t) cc_final: 0.8247 (p) REVERT: Q 323 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6990 (mt-10) REVERT: Q 387 ASN cc_start: 0.8585 (m-40) cc_final: 0.8170 (m-40) REVERT: R 44 SER cc_start: 0.6554 (t) cc_final: 0.5845 (p) REVERT: R 319 LEU cc_start: 0.6381 (mt) cc_final: 0.6074 (mt) REVERT: R 343 LYS cc_start: 0.7737 (tttm) cc_final: 0.7153 (ttpp) outliers start: 76 outliers final: 17 residues processed: 1679 average time/residue: 1.3798 time to fit residues: 3096.4399 Evaluate side-chains 867 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 841 time to evaluate : 6.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain D residue 192 TYR Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain J residue 261 TYR Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 227 TYR Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 54 MET Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 392 PHE Chi-restraints excluded: chain O residue 202 TYR Chi-restraints excluded: chain P residue 309 ASP Chi-restraints excluded: chain R residue 414 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 704 optimal weight: 3.9990 chunk 632 optimal weight: 0.9980 chunk 350 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 426 optimal weight: 10.0000 chunk 337 optimal weight: 20.0000 chunk 653 optimal weight: 0.6980 chunk 252 optimal weight: 6.9990 chunk 397 optimal weight: 0.3980 chunk 486 optimal weight: 2.9990 chunk 757 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 HIS ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN A 157 ASN A 175 ASN A 177 ASN A 184 HIS A 205 ASN A 297 ASN A 384 ASN A 431 ASN ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN A 508 ASN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 2 HIS B 91 HIS B 97 ASN B 137 GLN B 168 GLN B 177 ASN B 230 GLN B 235 GLN B 265 ASN B 301 ASN B 356 ASN B 372 ASN B 431 ASN B 450 GLN C 2 HIS C 32 GLN C 97 ASN C 137 GLN C 150 ASN C 168 GLN C 316 ASN C 333 ASN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 490 ASN C 519 ASN D 32 GLN D 127 ASN D 189 HIS ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN D 319 ASN D 356 ASN D 495 HIS D 519 ASN E 2 HIS E 97 ASN E 122 HIS E 157 ASN ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN E 235 GLN E 266 GLN E 267 GLN E 383 ASN E 420 ASN E 431 ASN F 32 GLN F 91 HIS F 177 ASN F 242 ASN F 265 ASN F 338 ASN F 372 ASN F 490 ASN ** F 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 ASN G 22 GLN G 36 ASN G 91 GLN G 129 GLN G 139 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN G 238 ASN G 287 HIS ** G 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN H 77 ASN H 91 GLN H 93 GLN H 226 ASN H 258 GLN H 287 HIS H 301 GLN H 302 GLN H 306 ASN I 22 GLN I 30 ASN I 139 ASN I 150 ASN ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 ASN I 301 GLN I 306 ASN I 311 GLN I 326 GLN I 415 GLN ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 ASN J 91 GLN J 147 ASN J 160 ASN ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 275 GLN J 391 ASN ** J 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN ** K 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 237 ASN ** K 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 396 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 115 ASN ** L 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 HIS L 168 ASN L 231 ASN L 238 ASN ** L 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 391 ASN L 424 ASN L 425 GLN M 22 GLN M 24 GLN M 247 GLN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 394 ASN ** N 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN N 216 GLN N 226 ASN N 238 ASN N 258 GLN N 275 GLN ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 306 ASN ** N 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 GLN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 129 GLN O 226 ASN O 231 ASN ** O 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 415 GLN ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 ASN P 110 GLN ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 258 GLN P 301 GLN ** P 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 ASN Q 115 ASN Q 139 ASN Q 159 GLN Q 391 ASN Q 420 ASN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 160 ASN R 216 GLN R 226 ASN R 258 GLN R 287 HIS ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 391 ASN R 396 ASN R 415 GLN Total number of N/Q/H flips: 145 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.151552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.108399 restraints weight = 144704.213| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.05 r_work: 0.3531 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 71396 Z= 0.226 Angle : 0.641 11.987 96304 Z= 0.335 Chirality : 0.045 0.219 10462 Planarity : 0.004 0.056 12399 Dihedral : 8.257 89.530 9404 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 4.63 % Allowed : 27.02 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.48 (0.09), residues: 8381 helix: -0.96 (0.08), residues: 3420 sheet: -3.09 (0.14), residues: 943 loop : -1.81 (0.09), residues: 4018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 125 HIS 0.018 0.001 HIS L 412 PHE 0.037 0.002 PHE P 75 TYR 0.027 0.002 TYR D 49 ARG 0.010 0.001 ARG F 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1292 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 363 poor density : 929 time to evaluate : 6.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8263 (t70) cc_final: 0.7975 (t70) REVERT: A 138 TYR cc_start: 0.7372 (m-80) cc_final: 0.6468 (m-80) REVERT: A 239 LYS cc_start: 0.6173 (OUTLIER) cc_final: 0.4927 (mmpt) REVERT: A 298 MET cc_start: 0.1215 (mmm) cc_final: 0.0833 (mmt) REVERT: A 340 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5682 (tt) REVERT: A 519 ASN cc_start: 0.8737 (t0) cc_final: 0.8461 (t0) REVERT: B 6 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8229 (mmmm) REVERT: B 88 MET cc_start: 0.8554 (ttp) cc_final: 0.8302 (ttp) REVERT: B 463 GLU cc_start: 0.7106 (mp0) cc_final: 0.6855 (mp0) REVERT: B 483 SER cc_start: 0.8888 (p) cc_final: 0.8625 (p) REVERT: B 517 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7576 (mm-40) REVERT: B 519 ASN cc_start: 0.8405 (m-40) cc_final: 0.8194 (m110) REVERT: B 544 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6986 (mp) REVERT: C 48 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: C 122 HIS cc_start: 0.5563 (OUTLIER) cc_final: 0.5168 (p-80) REVERT: C 137 GLN cc_start: 0.8371 (tt0) cc_final: 0.6947 (tt0) REVERT: C 216 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7788 (ttm) REVERT: C 459 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7957 (tptt) REVERT: D 196 ASN cc_start: 0.7780 (m110) cc_final: 0.7383 (t0) REVERT: D 209 ILE cc_start: 0.6429 (mm) cc_final: 0.5933 (mm) REVERT: D 216 MET cc_start: 0.7404 (ptm) cc_final: 0.7147 (ppp) REVERT: D 457 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6609 (p90) REVERT: D 469 CYS cc_start: 0.6801 (m) cc_final: 0.6482 (m) REVERT: D 541 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7526 (tm-30) REVERT: E 109 TYR cc_start: 0.8459 (m-80) cc_final: 0.8147 (m-80) REVERT: E 120 PHE cc_start: 0.8371 (m-10) cc_final: 0.8166 (m-10) REVERT: E 131 ILE cc_start: 0.7155 (tt) cc_final: 0.6883 (tp) REVERT: E 213 ASN cc_start: 0.7257 (m-40) cc_final: 0.6937 (t0) REVERT: E 219 TRP cc_start: 0.6584 (m100) cc_final: 0.6237 (m100) REVERT: E 291 TYR cc_start: 0.0989 (OUTLIER) cc_final: 0.0675 (t80) REVERT: E 332 TYR cc_start: 0.6061 (OUTLIER) cc_final: 0.5768 (m-80) REVERT: E 376 ARG cc_start: 0.8382 (mmm160) cc_final: 0.8100 (tpp-160) REVERT: E 407 PHE cc_start: 0.9020 (t80) cc_final: 0.8173 (t80) REVERT: E 437 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7637 (tp30) REVERT: E 505 TYR cc_start: 0.8124 (t80) cc_final: 0.7881 (t80) REVERT: E 545 PHE cc_start: 0.8049 (m-10) cc_final: 0.7148 (m-10) REVERT: F 40 ILE cc_start: 0.9122 (pt) cc_final: 0.8867 (pp) REVERT: F 80 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7841 (mtp85) REVERT: F 142 PHE cc_start: 0.7213 (m-10) cc_final: 0.6930 (m-80) REVERT: F 175 ASN cc_start: 0.8792 (m-40) cc_final: 0.8579 (m-40) REVERT: F 189 HIS cc_start: 0.8883 (m-70) cc_final: 0.8589 (m-70) REVERT: F 216 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6726 (tmm) REVERT: F 238 LEU cc_start: 0.4719 (pp) cc_final: 0.4235 (pt) REVERT: F 267 GLN cc_start: 0.4383 (OUTLIER) cc_final: 0.4072 (tp40) REVERT: F 269 ASP cc_start: 0.4275 (OUTLIER) cc_final: 0.3621 (p0) REVERT: F 424 LYS cc_start: 0.8994 (ptpt) cc_final: 0.8782 (pmtt) REVERT: F 504 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8204 (tm-30) REVERT: F 530 TYR cc_start: 0.8700 (t80) cc_final: 0.8283 (t80) REVERT: F 534 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8103 (mp0) REVERT: F 535 LEU cc_start: 0.9096 (tp) cc_final: 0.8883 (tp) REVERT: G 128 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7110 (mpp) REVERT: G 320 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8356 (pttt) REVERT: G 323 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8146 (mt-10) REVERT: G 396 ASN cc_start: 0.6504 (m110) cc_final: 0.6066 (p0) REVERT: H 86 LYS cc_start: 0.8999 (mtpp) cc_final: 0.8649 (tptp) REVERT: H 139 ASN cc_start: 0.8388 (t0) cc_final: 0.7778 (m110) REVERT: H 172 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7998 (mptp) REVERT: H 301 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: H 323 GLU cc_start: 0.7491 (pm20) cc_final: 0.7127 (mp0) REVERT: H 391 ASN cc_start: 0.7337 (m-40) cc_final: 0.7119 (m110) REVERT: I 82 LYS cc_start: 0.8523 (tmtm) cc_final: 0.8189 (tptp) REVERT: I 105 HIS cc_start: 0.8705 (m-70) cc_final: 0.8419 (m90) REVERT: I 207 ARG cc_start: 0.8441 (ttp-110) cc_final: 0.8110 (ttp80) REVERT: I 227 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: I 301 GLN cc_start: 0.8319 (mt0) cc_final: 0.7952 (mt0) REVERT: I 370 GLN cc_start: 0.8398 (pp30) cc_final: 0.8160 (pp30) REVERT: I 382 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: J 121 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8233 (pp20) REVERT: J 163 HIS cc_start: 0.8410 (t-90) cc_final: 0.8000 (t-170) REVERT: J 211 ASP cc_start: 0.8832 (t0) cc_final: 0.8389 (t0) REVERT: J 269 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.5873 (mtm-85) REVERT: J 383 GLU cc_start: 0.7986 (tp30) cc_final: 0.7759 (tp30) REVERT: K 108 MET cc_start: 0.7952 (ppp) cc_final: 0.7657 (ppp) REVERT: K 153 GLU cc_start: 0.8631 (tp30) cc_final: 0.8352 (tt0) REVERT: K 154 LEU cc_start: 0.9261 (tt) cc_final: 0.8978 (tm) REVERT: K 165 ASP cc_start: 0.8699 (t0) cc_final: 0.8235 (p0) REVERT: K 171 LEU cc_start: 0.8643 (mt) cc_final: 0.8152 (mt) REVERT: K 253 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7570 (mmtt) REVERT: K 310 ASP cc_start: 0.8171 (t0) cc_final: 0.7510 (t0) REVERT: K 343 LYS cc_start: 0.7546 (ttpp) cc_final: 0.7154 (mtpp) REVERT: K 416 PHE cc_start: 0.8191 (m-80) cc_final: 0.7942 (m-10) REVERT: L 24 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8052 (tp40) REVERT: L 105 HIS cc_start: 0.8719 (m-70) cc_final: 0.8509 (m-70) REVERT: L 208 TYR cc_start: 0.8388 (m-80) cc_final: 0.8145 (m-80) REVERT: L 419 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7957 (mt-10) REVERT: M 137 ILE cc_start: 0.7101 (mm) cc_final: 0.6361 (tt) REVERT: M 303 ILE cc_start: 0.8236 (tt) cc_final: 0.7896 (pp) REVERT: N 253 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8206 (mttt) REVERT: N 269 ARG cc_start: 0.6172 (mmm160) cc_final: 0.5907 (mmm160) REVERT: N 275 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7898 (mm110) REVERT: N 350 ILE cc_start: 0.8480 (tp) cc_final: 0.8265 (tp) REVERT: N 379 ASP cc_start: 0.8575 (t70) cc_final: 0.8340 (t0) REVERT: N 392 PHE cc_start: 0.3274 (OUTLIER) cc_final: 0.2739 (p90) REVERT: O 216 GLN cc_start: 0.7824 (pm20) cc_final: 0.7617 (pp30) REVERT: O 334 ARG cc_start: 0.7992 (ttt90) cc_final: 0.7576 (ttp-110) REVERT: O 382 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7791 (mm-30) REVERT: O 393 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8248 (mtpm) REVERT: P 73 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8359 (mptm) REVERT: P 108 MET cc_start: 0.7451 (mtp) cc_final: 0.7164 (mtt) REVERT: P 110 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: P 111 LEU cc_start: 0.8847 (pt) cc_final: 0.8242 (tm) REVERT: P 126 LEU cc_start: 0.8678 (tt) cc_final: 0.8349 (mm) REVERT: P 159 GLN cc_start: 0.8985 (tp40) cc_final: 0.8635 (mm-40) REVERT: P 163 HIS cc_start: 0.9111 (t-90) cc_final: 0.8631 (t-90) REVERT: P 299 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7344 (mm-30) REVERT: P 322 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8313 (mtpp) REVERT: P 357 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7770 (tp30) REVERT: Q 22 GLN cc_start: 0.8695 (mm110) cc_final: 0.7977 (pm20) REVERT: Q 128 MET cc_start: 0.8713 (mmp) cc_final: 0.8162 (ppp) REVERT: Q 208 TYR cc_start: 0.8229 (t80) cc_final: 0.7954 (t80) REVERT: Q 264 VAL cc_start: 0.9130 (t) cc_final: 0.8855 (p) REVERT: Q 323 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7622 (mt-10) REVERT: R 44 SER cc_start: 0.7774 (t) cc_final: 0.6963 (p) REVERT: R 150 ASN cc_start: 0.8802 (t0) cc_final: 0.8305 (t0) REVERT: R 310 ASP cc_start: 0.7366 (t0) cc_final: 0.7143 (t0) REVERT: R 343 LYS cc_start: 0.8195 (tttm) cc_final: 0.7535 (ttpp) REVERT: R 387 ASN cc_start: 0.8588 (m-40) cc_final: 0.8117 (m-40) outliers start: 363 outliers final: 88 residues processed: 1211 average time/residue: 1.2477 time to fit residues: 2085.3229 Evaluate side-chains 839 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 722 time to evaluate : 6.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain E residue 291 TYR Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 507 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 83 CYS Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 483 SER Chi-restraints excluded: chain F residue 509 SER Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 320 LYS Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 172 LYS Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 301 GLN Chi-restraints excluded: chain H residue 421 PHE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 227 TYR Chi-restraints excluded: chain I residue 330 SER Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain J residue 121 GLU Chi-restraints excluded: chain J residue 269 ARG Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 366 ASN Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 167 ASN Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 337 SER Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 154 LEU Chi-restraints excluded: chain N residue 321 HIS Chi-restraints excluded: chain N residue 392 PHE Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 393 LYS Chi-restraints excluded: chain O residue 394 ASN Chi-restraints excluded: chain P residue 73 LYS Chi-restraints excluded: chain P residue 110 GLN Chi-restraints excluded: chain P residue 322 LYS Chi-restraints excluded: chain P residue 357 GLU Chi-restraints excluded: chain P residue 414 PHE Chi-restraints excluded: chain Q residue 294 SER Chi-restraints excluded: chain Q residue 383 GLU Chi-restraints excluded: chain Q residue 404 SER Chi-restraints excluded: chain Q residue 418 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 143 CYS Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 324 THR Chi-restraints excluded: chain R residue 414 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 699 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 138 optimal weight: 50.0000 chunk 546 optimal weight: 0.6980 chunk 825 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 764 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 792 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 137 GLN A 213 ASN A 488 GLN A 508 ASN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 113 GLN B 143 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN B 495 HIS C 137 GLN D 180 ASN ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 HIS E 122 HIS E 174 ASN E 374 GLN ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 235 GLN ** F 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 306 ASN ** I 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 GLN K 160 ASN ** K 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 237 ASN ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 366 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 403 ASN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 358 HIS N 32 HIS N 60 ASN ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 403 ASN O 24 GLN O 32 HIS ** O 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 129 GLN ** O 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 168 ASN ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 268 ASN P 341 GLN P 369 ASN ** Q 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 420 ASN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 ASN ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.146332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.100844 restraints weight = 141385.015| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.08 r_work: 0.3388 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 71396 Z= 0.252 Angle : 0.623 15.629 96304 Z= 0.326 Chirality : 0.045 0.207 10462 Planarity : 0.003 0.055 12399 Dihedral : 7.565 89.871 9363 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.97 % Favored : 92.91 % Rotamer: Outliers : 4.63 % Allowed : 27.44 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.01 (0.09), residues: 8381 helix: -0.48 (0.09), residues: 3418 sheet: -2.85 (0.14), residues: 961 loop : -1.63 (0.10), residues: 4002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP P 125 HIS 0.020 0.001 HIS Q 105 PHE 0.036 0.002 PHE B 348 TYR 0.031 0.002 TYR F 49 ARG 0.008 0.001 ARG M 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 363 poor density : 788 time to evaluate : 6.215 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 35 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8867 (mt) REVERT: A 62 ASP cc_start: 0.8411 (t70) cc_final: 0.8056 (t0) REVERT: A 231 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7455 (mp) REVERT: A 239 LYS cc_start: 0.6080 (OUTLIER) cc_final: 0.4833 (mmpt) REVERT: A 298 MET cc_start: 0.1424 (mmm) cc_final: 0.1189 (mmt) REVERT: A 310 LEU cc_start: 0.5022 (OUTLIER) cc_final: 0.4654 (OUTLIER) REVERT: A 340 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5749 (tt) REVERT: A 423 MET cc_start: 0.6936 (ptp) cc_final: 0.6680 (ptp) REVERT: A 474 SER cc_start: 0.6251 (OUTLIER) cc_final: 0.5802 (p) REVERT: A 519 ASN cc_start: 0.8660 (t0) cc_final: 0.8315 (t0) REVERT: B 88 MET cc_start: 0.8686 (ttp) cc_final: 0.8448 (ttp) REVERT: B 463 GLU cc_start: 0.7267 (mp0) cc_final: 0.6880 (mp0) REVERT: B 483 SER cc_start: 0.8893 (p) cc_final: 0.8689 (p) REVERT: B 517 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7623 (mm-40) REVERT: B 519 ASN cc_start: 0.8413 (m-40) cc_final: 0.8165 (m110) REVERT: B 536 PHE cc_start: 0.6848 (m-80) cc_final: 0.6613 (m-80) REVERT: C 122 HIS cc_start: 0.5627 (OUTLIER) cc_final: 0.5171 (p-80) REVERT: C 216 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7728 (ttm) REVERT: C 222 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7840 (mp) REVERT: C 236 MET cc_start: 0.8327 (ttm) cc_final: 0.8022 (tpp) REVERT: C 441 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6572 (m-10) REVERT: D 109 TYR cc_start: 0.7851 (m-10) cc_final: 0.7424 (m-80) REVERT: D 196 ASN cc_start: 0.7786 (m110) cc_final: 0.7290 (t0) REVERT: D 407 PHE cc_start: 0.6374 (t80) cc_final: 0.6153 (t80) REVERT: D 411 PHE cc_start: 0.7864 (t80) cc_final: 0.7481 (t80) REVERT: D 447 GLU cc_start: 0.4194 (OUTLIER) cc_final: 0.2684 (pm20) REVERT: D 457 PHE cc_start: 0.6852 (OUTLIER) cc_final: 0.6407 (p90) REVERT: D 469 CYS cc_start: 0.6639 (m) cc_final: 0.6330 (m) REVERT: E 14 LYS cc_start: 0.8636 (tttm) cc_final: 0.8405 (tppt) REVERT: E 114 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: E 117 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8572 (mt-10) REVERT: E 123 PHE cc_start: 0.7532 (m-10) cc_final: 0.7266 (m-80) REVERT: E 131 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6793 (tp) REVERT: E 135 ASP cc_start: 0.8036 (t0) cc_final: 0.7720 (t70) REVERT: E 216 MET cc_start: 0.6235 (ttp) cc_final: 0.5672 (tpp) REVERT: E 233 ILE cc_start: 0.8045 (mp) cc_final: 0.7769 (tt) REVERT: E 376 ARG cc_start: 0.8355 (mmm160) cc_final: 0.7991 (tpp-160) REVERT: E 407 PHE cc_start: 0.8924 (t80) cc_final: 0.7973 (t80) REVERT: E 480 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6657 (mt-10) REVERT: E 486 LEU cc_start: 0.8962 (tp) cc_final: 0.8671 (tt) REVERT: E 492 TYR cc_start: 0.7343 (m-80) cc_final: 0.6874 (m-80) REVERT: E 505 TYR cc_start: 0.8115 (t80) cc_final: 0.7859 (t80) REVERT: E 528 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7779 (t) REVERT: E 545 PHE cc_start: 0.8113 (m-10) cc_final: 0.7142 (m-10) REVERT: E 546 GLU cc_start: 0.6667 (tm-30) cc_final: 0.6407 (tm-30) REVERT: F 40 ILE cc_start: 0.9153 (pt) cc_final: 0.8945 (pp) REVERT: F 80 ARG cc_start: 0.8327 (mtp85) cc_final: 0.7947 (mtp85) REVERT: F 142 PHE cc_start: 0.7508 (m-10) cc_final: 0.7244 (m-80) REVERT: F 216 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6721 (tmm) REVERT: F 238 LEU cc_start: 0.4729 (pp) cc_final: 0.4383 (pp) REVERT: F 266 GLN cc_start: 0.3146 (OUTLIER) cc_final: 0.1622 (pm20) REVERT: F 267 GLN cc_start: 0.4442 (OUTLIER) cc_final: 0.4026 (tp40) REVERT: F 367 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7664 (mm-30) REVERT: F 384 ASN cc_start: 0.8246 (t0) cc_final: 0.8001 (t0) REVERT: F 504 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8184 (tm-30) REVERT: F 534 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8135 (mp0) REVERT: F 535 LEU cc_start: 0.9138 (tp) cc_final: 0.8901 (tp) REVERT: G 22 GLN cc_start: 0.8782 (tp40) cc_final: 0.8443 (tp-100) REVERT: G 92 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6474 (pm20) REVERT: G 128 MET cc_start: 0.7704 (pp-130) cc_final: 0.7025 (mpp) REVERT: G 227 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8879 (m-80) REVERT: G 301 GLN cc_start: 0.8300 (mt0) cc_final: 0.8087 (mt0) REVERT: G 303 ILE cc_start: 0.8617 (mm) cc_final: 0.8354 (pp) REVERT: G 323 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8267 (mt-10) REVERT: G 396 ASN cc_start: 0.6524 (m110) cc_final: 0.5986 (p0) REVERT: H 86 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8662 (tptp) REVERT: H 139 ASN cc_start: 0.8371 (t0) cc_final: 0.7746 (m110) REVERT: H 322 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7677 (ptpp) REVERT: H 323 GLU cc_start: 0.7724 (pm20) cc_final: 0.7412 (pm20) REVERT: I 82 LYS cc_start: 0.8556 (tmtm) cc_final: 0.8204 (tptp) REVERT: I 105 HIS cc_start: 0.8730 (m-70) cc_final: 0.8438 (m90) REVERT: I 301 GLN cc_start: 0.8377 (mt0) cc_final: 0.8086 (mt0) REVERT: I 304 ASP cc_start: 0.8004 (p0) cc_final: 0.7736 (p0) REVERT: I 382 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: J 134 LYS cc_start: 0.7595 (mttt) cc_final: 0.7048 (ptmm) REVERT: J 163 HIS cc_start: 0.8458 (t-90) cc_final: 0.8136 (t-170) REVERT: J 211 ASP cc_start: 0.9044 (t0) cc_final: 0.8575 (t0) REVERT: J 383 GLU cc_start: 0.8220 (tp30) cc_final: 0.7768 (tp30) REVERT: K 109 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8297 (p0) REVERT: K 153 GLU cc_start: 0.8672 (tp30) cc_final: 0.8378 (tt0) REVERT: K 227 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: K 277 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8890 (m) REVERT: K 301 GLN cc_start: 0.8008 (tt0) cc_final: 0.7291 (tt0) REVERT: K 310 ASP cc_start: 0.8277 (t0) cc_final: 0.7526 (t0) REVERT: K 416 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7895 (m-10) REVERT: L 10 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8700 (pmmt) REVERT: L 105 HIS cc_start: 0.8819 (m-70) cc_final: 0.8534 (m-70) REVERT: L 153 GLU cc_start: 0.8407 (mp0) cc_final: 0.8171 (mp0) REVERT: L 383 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8074 (tp30) REVERT: L 419 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7984 (mt-10) REVERT: M 137 ILE cc_start: 0.7191 (mm) cc_final: 0.6448 (tt) REVERT: M 303 ILE cc_start: 0.8322 (tt) cc_final: 0.8055 (pp) REVERT: N 131 SER cc_start: 0.7290 (OUTLIER) cc_final: 0.6884 (p) REVERT: N 253 LYS cc_start: 0.8548 (mtpt) cc_final: 0.8167 (mttm) REVERT: N 275 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7938 (mm110) REVERT: N 320 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7770 (mtmt) REVERT: N 379 ASP cc_start: 0.8610 (t70) cc_final: 0.8385 (t0) REVERT: N 392 PHE cc_start: 0.3871 (OUTLIER) cc_final: 0.2718 (p90) REVERT: O 382 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7759 (mp0) REVERT: P 73 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8400 (mptm) REVERT: P 163 HIS cc_start: 0.9127 (t-90) cc_final: 0.8562 (t-90) REVERT: P 280 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8311 (mt-10) REVERT: Q 22 GLN cc_start: 0.8616 (mm110) cc_final: 0.7880 (pm20) REVERT: Q 208 TYR cc_start: 0.8311 (t80) cc_final: 0.8036 (t80) REVERT: Q 264 VAL cc_start: 0.9242 (t) cc_final: 0.8948 (m) REVERT: Q 323 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7755 (mt-10) REVERT: Q 344 ASP cc_start: 0.8699 (m-30) cc_final: 0.8391 (m-30) REVERT: Q 404 SER cc_start: 0.4242 (OUTLIER) cc_final: 0.3857 (t) REVERT: R 44 SER cc_start: 0.8203 (t) cc_final: 0.7481 (p) REVERT: R 237 ASN cc_start: 0.8411 (m-40) cc_final: 0.8188 (m-40) REVERT: R 310 ASP cc_start: 0.7598 (t0) cc_final: 0.7388 (t0) REVERT: R 343 LYS cc_start: 0.8385 (tttm) cc_final: 0.7707 (ttpp) REVERT: R 387 ASN cc_start: 0.8753 (m-40) cc_final: 0.8280 (m-40) outliers start: 363 outliers final: 124 residues processed: 1080 average time/residue: 1.2303 time to fit residues: 1838.4014 Evaluate side-chains 826 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 668 time to evaluate : 6.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 83 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 83 CYS Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 367 GLU Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 522 SER Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 227 TYR Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 320 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 322 LYS Chi-restraints excluded: chain H residue 421 PHE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 330 SER Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain J residue 143 CYS Chi-restraints excluded: chain J residue 261 TYR Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 366 ASN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 227 TYR Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 416 PHE Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 330 SER Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain M residue 405 SER Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain N residue 131 SER Chi-restraints excluded: chain N residue 215 GLU Chi-restraints excluded: chain N residue 320 LYS Chi-restraints excluded: chain N residue 392 PHE Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 183 ILE Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 73 LYS Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 414 PHE Chi-restraints excluded: chain Q residue 10 LYS Chi-restraints excluded: chain Q residue 294 SER Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 366 ASN Chi-restraints excluded: chain Q residue 404 SER Chi-restraints excluded: chain Q residue 418 VAL Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 83 GLU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 143 CYS Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 278 SER Chi-restraints excluded: chain R residue 324 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 13 optimal weight: 4.9990 chunk 379 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 553 optimal weight: 0.5980 chunk 657 optimal weight: 1.9990 chunk 368 optimal weight: 2.9990 chunk 756 optimal weight: 0.8980 chunk 480 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 247 optimal weight: 3.9990 chunk 109 optimal weight: 0.1980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS A 213 ASN B 113 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN C 91 HIS ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 ASN D 182 HIS ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 HIS E 213 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 387 ASN H 91 GLN H 105 HIS ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 358 HIS ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 ASN ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 ASN ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 ASN ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 366 ASN O 24 GLN ** O 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 129 GLN ** O 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 GLN P 226 ASN P 275 GLN P 287 HIS ** Q 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 160 ASN ** Q 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.146694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.101295 restraints weight = 140759.800| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.11 r_work: 0.3401 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 71396 Z= 0.181 Angle : 0.592 12.692 96304 Z= 0.308 Chirality : 0.044 0.188 10462 Planarity : 0.003 0.081 12399 Dihedral : 7.253 89.378 9356 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.99 % Favored : 92.97 % Rotamer: Outliers : 4.18 % Allowed : 28.19 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.76 (0.09), residues: 8381 helix: -0.18 (0.09), residues: 3408 sheet: -2.76 (0.14), residues: 967 loop : -1.57 (0.10), residues: 4006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 125 HIS 0.014 0.001 HIS H 105 PHE 0.033 0.001 PHE B 96 TYR 0.022 0.001 TYR E 291 ARG 0.012 0.001 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 328 poor density : 763 time to evaluate : 6.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7959 (ttp) cc_final: 0.7672 (tpt) REVERT: A 35 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8942 (mt) REVERT: A 62 ASP cc_start: 0.8434 (t70) cc_final: 0.8031 (t0) REVERT: A 239 LYS cc_start: 0.6103 (OUTLIER) cc_final: 0.4914 (mmpt) REVERT: A 298 MET cc_start: 0.1248 (mmm) cc_final: 0.1013 (mmt) REVERT: A 310 LEU cc_start: 0.5137 (OUTLIER) cc_final: 0.4831 (pp) REVERT: A 340 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5796 (tt) REVERT: A 384 ASN cc_start: 0.5419 (m-40) cc_final: 0.4840 (p0) REVERT: A 519 ASN cc_start: 0.8649 (t0) cc_final: 0.8292 (t0) REVERT: A 543 GLU cc_start: 0.7574 (tt0) cc_final: 0.7303 (tt0) REVERT: B 46 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8212 (mtmt) REVERT: B 88 MET cc_start: 0.8693 (ttp) cc_final: 0.8434 (ttp) REVERT: B 247 LYS cc_start: 0.5683 (OUTLIER) cc_final: 0.5466 (mmmm) REVERT: B 447 GLU cc_start: 0.7472 (pt0) cc_final: 0.7254 (pt0) REVERT: B 517 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7528 (mm-40) REVERT: B 519 ASN cc_start: 0.8413 (m-40) cc_final: 0.8161 (m110) REVERT: C 122 HIS cc_start: 0.5594 (OUTLIER) cc_final: 0.5099 (p-80) REVERT: C 222 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7843 (mp) REVERT: C 236 MET cc_start: 0.8251 (ttm) cc_final: 0.8019 (tpp) REVERT: C 298 MET cc_start: 0.3557 (ptt) cc_final: 0.3113 (ptm) REVERT: C 441 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.6588 (m-10) REVERT: D 109 TYR cc_start: 0.7892 (m-10) cc_final: 0.7524 (m-80) REVERT: D 196 ASN cc_start: 0.7821 (m110) cc_final: 0.7321 (t0) REVERT: D 216 MET cc_start: 0.7340 (ptm) cc_final: 0.7089 (ppp) REVERT: D 411 PHE cc_start: 0.7896 (t80) cc_final: 0.7480 (t80) REVERT: D 447 GLU cc_start: 0.4124 (OUTLIER) cc_final: 0.2691 (pm20) REVERT: D 457 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.6352 (p90) REVERT: D 469 CYS cc_start: 0.6707 (m) cc_final: 0.6407 (m) REVERT: E 117 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8545 (mt-10) REVERT: E 122 HIS cc_start: 0.7337 (t70) cc_final: 0.7135 (t-170) REVERT: E 131 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6620 (tp) REVERT: E 135 ASP cc_start: 0.8111 (t0) cc_final: 0.7778 (t0) REVERT: E 142 PHE cc_start: 0.5685 (m-80) cc_final: 0.4960 (m-80) REVERT: E 216 MET cc_start: 0.6245 (ttp) cc_final: 0.5644 (tpp) REVERT: E 233 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7776 (tt) REVERT: E 407 PHE cc_start: 0.8935 (t80) cc_final: 0.7921 (t80) REVERT: E 423 MET cc_start: 0.7207 (mpp) cc_final: 0.6957 (mpp) REVERT: E 486 LEU cc_start: 0.8908 (tp) cc_final: 0.8582 (tp) REVERT: E 492 TYR cc_start: 0.7285 (m-80) cc_final: 0.6834 (m-80) REVERT: E 505 TYR cc_start: 0.8089 (t80) cc_final: 0.7741 (t80) REVERT: E 528 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7786 (t) REVERT: E 545 PHE cc_start: 0.8187 (m-10) cc_final: 0.7193 (m-10) REVERT: E 546 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6402 (tm-30) REVERT: F 40 ILE cc_start: 0.8988 (pt) cc_final: 0.8714 (pp) REVERT: F 56 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: F 80 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8018 (mtp85) REVERT: F 268 THR cc_start: 0.3753 (OUTLIER) cc_final: 0.3275 (p) REVERT: F 269 ASP cc_start: 0.3479 (OUTLIER) cc_final: 0.2552 (m-30) REVERT: F 423 MET cc_start: 0.7643 (tmt) cc_final: 0.7341 (tmm) REVERT: F 504 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8203 (tm-30) REVERT: F 530 TYR cc_start: 0.8727 (t80) cc_final: 0.8258 (t80) REVERT: F 534 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8193 (mp0) REVERT: F 535 LEU cc_start: 0.9158 (tp) cc_final: 0.8889 (tp) REVERT: G 22 GLN cc_start: 0.8803 (tp40) cc_final: 0.8467 (tp-100) REVERT: G 37 ASN cc_start: 0.9118 (t0) cc_final: 0.8495 (t0) REVERT: G 92 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6474 (pm20) REVERT: G 128 MET cc_start: 0.7738 (pp-130) cc_final: 0.7028 (mpp) REVERT: G 159 GLN cc_start: 0.9155 (tt0) cc_final: 0.8771 (tt0) REVERT: G 301 GLN cc_start: 0.8317 (mt0) cc_final: 0.8086 (mt0) REVERT: G 323 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8328 (mt-10) REVERT: H 86 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8588 (tptp) REVERT: H 139 ASN cc_start: 0.8360 (t0) cc_final: 0.7730 (m110) REVERT: H 322 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7782 (ptpp) REVERT: H 323 GLU cc_start: 0.7692 (pm20) cc_final: 0.7314 (pm20) REVERT: I 82 LYS cc_start: 0.8563 (tmtm) cc_final: 0.8222 (tptp) REVERT: I 105 HIS cc_start: 0.8723 (m-70) cc_final: 0.8439 (m90) REVERT: I 227 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: I 301 GLN cc_start: 0.8402 (mt0) cc_final: 0.8139 (mt0) REVERT: I 370 GLN cc_start: 0.8459 (pp30) cc_final: 0.8238 (pp30) REVERT: I 382 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: J 121 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8273 (pp20) REVERT: J 134 LYS cc_start: 0.7596 (mttt) cc_final: 0.7016 (ptmm) REVERT: J 163 HIS cc_start: 0.8420 (t-90) cc_final: 0.8005 (t-170) REVERT: J 211 ASP cc_start: 0.9063 (t0) cc_final: 0.8583 (t0) REVERT: J 391 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8245 (t0) REVERT: K 109 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8274 (p0) REVERT: K 153 GLU cc_start: 0.8652 (tp30) cc_final: 0.8085 (tp30) REVERT: K 165 ASP cc_start: 0.8647 (t0) cc_final: 0.8218 (p0) REVERT: K 310 ASP cc_start: 0.8252 (t0) cc_final: 0.7508 (t0) REVERT: K 416 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7868 (m-10) REVERT: L 10 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8658 (pmmt) REVERT: L 105 HIS cc_start: 0.8781 (m-70) cc_final: 0.8459 (m-70) REVERT: L 137 ILE cc_start: 0.7812 (mm) cc_final: 0.7566 (mm) REVERT: L 153 GLU cc_start: 0.8421 (mp0) cc_final: 0.8117 (mp0) REVERT: L 207 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8093 (ttm-80) REVERT: L 383 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8106 (tp30) REVERT: M 76 LEU cc_start: 0.9472 (mt) cc_final: 0.9233 (mt) REVERT: M 303 ILE cc_start: 0.8413 (tt) cc_final: 0.8179 (pp) REVERT: N 1 MET cc_start: 0.6557 (tpp) cc_final: 0.6352 (tpt) REVERT: N 71 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6410 (t80) REVERT: N 77 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.6960 (p0) REVERT: N 253 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8230 (mttm) REVERT: N 321 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7574 (m90) REVERT: N 379 ASP cc_start: 0.8594 (t70) cc_final: 0.8365 (t0) REVERT: N 392 PHE cc_start: 0.3876 (OUTLIER) cc_final: 0.2654 (p90) REVERT: O 303 ILE cc_start: 0.8339 (tp) cc_final: 0.8124 (pp) REVERT: O 381 LYS cc_start: 0.8486 (mptt) cc_final: 0.8270 (mptt) REVERT: O 382 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7802 (mp0) REVERT: P 73 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8453 (tppp) REVERT: P 75 PHE cc_start: 0.7066 (t80) cc_final: 0.6105 (t80) REVERT: P 133 TYR cc_start: 0.6258 (p90) cc_final: 0.5984 (p90) REVERT: P 163 HIS cc_start: 0.9104 (t-90) cc_final: 0.8639 (t-90) REVERT: P 280 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8231 (mt-10) REVERT: Q 22 GLN cc_start: 0.8633 (mm110) cc_final: 0.7869 (pm20) REVERT: Q 165 ASP cc_start: 0.8749 (t0) cc_final: 0.8498 (t0) REVERT: Q 208 TYR cc_start: 0.8304 (t80) cc_final: 0.8042 (t80) REVERT: Q 264 VAL cc_start: 0.9203 (t) cc_final: 0.9003 (m) REVERT: Q 319 LEU cc_start: 0.7801 (mt) cc_final: 0.7568 (mp) REVERT: Q 323 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7720 (mt-10) REVERT: Q 344 ASP cc_start: 0.8727 (m-30) cc_final: 0.8502 (m-30) REVERT: R 44 SER cc_start: 0.8250 (t) cc_final: 0.7523 (p) REVERT: R 237 ASN cc_start: 0.8495 (m-40) cc_final: 0.8238 (m-40) REVERT: R 310 ASP cc_start: 0.7641 (t0) cc_final: 0.7415 (t0) REVERT: R 343 LYS cc_start: 0.8396 (tttm) cc_final: 0.7850 (ttpp) REVERT: R 387 ASN cc_start: 0.8812 (m-40) cc_final: 0.8351 (m-40) outliers start: 328 outliers final: 124 residues processed: 1018 average time/residue: 1.1987 time to fit residues: 1701.1864 Evaluate side-chains 808 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 651 time to evaluate : 6.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 83 CYS Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 522 SER Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 320 LYS Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 322 LYS Chi-restraints excluded: chain H residue 421 PHE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 227 TYR Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 121 GLU Chi-restraints excluded: chain J residue 143 CYS Chi-restraints excluded: chain J residue 261 TYR Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 366 ASN Chi-restraints excluded: chain J residue 391 ASN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 224 THR Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 416 PHE Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 71 TYR Chi-restraints excluded: chain N residue 74 LYS Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 211 ASP Chi-restraints excluded: chain N residue 215 GLU Chi-restraints excluded: chain N residue 321 HIS Chi-restraints excluded: chain N residue 392 PHE Chi-restraints excluded: chain N residue 394 ASN Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 294 SER Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 394 ASN Chi-restraints excluded: chain P residue 58 MET Chi-restraints excluded: chain P residue 73 LYS Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 414 PHE Chi-restraints excluded: chain Q residue 10 LYS Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 294 SER Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 366 ASN Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 143 CYS Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 364 optimal weight: 4.9990 chunk 516 optimal weight: 2.9990 chunk 772 optimal weight: 1.9990 chunk 635 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 426 optimal weight: 1.9990 chunk 362 optimal weight: 0.5980 chunk 587 optimal weight: 0.4980 chunk 319 optimal weight: 9.9990 chunk 769 optimal weight: 2.9990 chunk 759 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 97 ASN B 113 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN C 137 GLN C 235 GLN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN D 221 ASN E 213 ASN ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 GLN I 37 ASN I 159 GLN ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN J 166 ASN ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 ASN ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 GLN ** K 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN L 110 GLN ** L 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 361 ASN O 97 GLN ** O 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN O 168 ASN ** O 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 GLN P 226 ASN ** Q 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 166 ASN Q 238 ASN ** Q 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.144929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.098467 restraints weight = 141082.135| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.11 r_work: 0.3356 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 71396 Z= 0.226 Angle : 0.600 12.332 96304 Z= 0.313 Chirality : 0.044 0.175 10462 Planarity : 0.003 0.049 12399 Dihedral : 7.049 87.526 9354 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.92 % Favored : 93.02 % Rotamer: Outliers : 4.42 % Allowed : 28.17 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.60 (0.09), residues: 8381 helix: -0.02 (0.09), residues: 3419 sheet: -2.58 (0.14), residues: 987 loop : -1.53 (0.10), residues: 3975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP P 125 HIS 0.009 0.001 HIS O 105 PHE 0.034 0.001 PHE B 348 TYR 0.024 0.001 TYR P 145 ARG 0.010 0.001 ARG K 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 347 poor density : 695 time to evaluate : 6.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7984 (ttp) cc_final: 0.7756 (tpt) REVERT: A 62 ASP cc_start: 0.8487 (t70) cc_final: 0.8003 (t0) REVERT: A 239 LYS cc_start: 0.6057 (OUTLIER) cc_final: 0.4915 (mmpt) REVERT: A 298 MET cc_start: 0.0480 (mmm) cc_final: 0.0021 (mmt) REVERT: A 340 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5628 (tt) REVERT: A 384 ASN cc_start: 0.5520 (m-40) cc_final: 0.4904 (p0) REVERT: A 519 ASN cc_start: 0.8671 (t0) cc_final: 0.8287 (t0) REVERT: B 247 LYS cc_start: 0.5847 (OUTLIER) cc_final: 0.5469 (mmmm) REVERT: B 436 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6722 (tp30) REVERT: B 517 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7747 (mm-40) REVERT: B 519 ASN cc_start: 0.8412 (m-40) cc_final: 0.8098 (m110) REVERT: B 536 PHE cc_start: 0.6923 (m-80) cc_final: 0.6441 (m-80) REVERT: C 122 HIS cc_start: 0.5716 (OUTLIER) cc_final: 0.5162 (p-80) REVERT: C 222 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7883 (mp) REVERT: C 298 MET cc_start: 0.2664 (ptt) cc_final: 0.2059 (ptm) REVERT: C 441 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6797 (m-10) REVERT: C 455 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8161 (pt0) REVERT: D 95 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: D 109 TYR cc_start: 0.8197 (m-10) cc_final: 0.7880 (m-80) REVERT: D 119 VAL cc_start: 0.9090 (t) cc_final: 0.8825 (p) REVERT: D 216 MET cc_start: 0.7340 (ptm) cc_final: 0.7031 (ppp) REVERT: D 411 PHE cc_start: 0.7997 (t80) cc_final: 0.7653 (t80) REVERT: D 447 GLU cc_start: 0.4023 (OUTLIER) cc_final: 0.2636 (pm20) REVERT: D 457 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.6239 (p90) REVERT: D 469 CYS cc_start: 0.7278 (m) cc_final: 0.6852 (m) REVERT: D 536 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8340 (t80) REVERT: E 117 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8535 (mt-10) REVERT: E 131 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6760 (tp) REVERT: E 135 ASP cc_start: 0.8133 (t0) cc_final: 0.7808 (t0) REVERT: E 142 PHE cc_start: 0.5729 (m-80) cc_final: 0.5106 (m-80) REVERT: E 216 MET cc_start: 0.6260 (ttp) cc_final: 0.5629 (tpp) REVERT: E 233 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7826 (tt) REVERT: E 291 TYR cc_start: 0.1131 (OUTLIER) cc_final: 0.0695 (m-80) REVERT: E 340 LEU cc_start: 0.7282 (mm) cc_final: 0.6972 (mm) REVERT: E 407 PHE cc_start: 0.8876 (t80) cc_final: 0.7855 (t80) REVERT: E 423 MET cc_start: 0.7211 (mpp) cc_final: 0.6937 (mpp) REVERT: E 486 LEU cc_start: 0.8895 (tp) cc_final: 0.8524 (tp) REVERT: E 492 TYR cc_start: 0.7350 (m-80) cc_final: 0.6854 (m-80) REVERT: E 505 TYR cc_start: 0.8060 (t80) cc_final: 0.7664 (t80) REVERT: E 545 PHE cc_start: 0.8229 (m-10) cc_final: 0.7247 (m-10) REVERT: E 546 GLU cc_start: 0.6625 (tm-30) cc_final: 0.6378 (tm-30) REVERT: F 40 ILE cc_start: 0.9009 (pt) cc_final: 0.8709 (pp) REVERT: F 56 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: F 80 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8019 (mtp85) REVERT: F 216 MET cc_start: 0.7617 (tmm) cc_final: 0.7318 (tmm) REVERT: F 268 THR cc_start: 0.3317 (OUTLIER) cc_final: 0.3032 (p) REVERT: F 269 ASP cc_start: 0.3519 (OUTLIER) cc_final: 0.2683 (m-30) REVERT: F 504 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8212 (tm-30) REVERT: F 506 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8580 (mp) REVERT: F 534 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8188 (mp0) REVERT: G 22 GLN cc_start: 0.8797 (tp40) cc_final: 0.8464 (tp-100) REVERT: G 37 ASN cc_start: 0.9093 (t0) cc_final: 0.8441 (t0) REVERT: G 128 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7111 (mpp) REVERT: G 216 GLN cc_start: 0.8171 (mp10) cc_final: 0.7867 (mp10) REVERT: G 301 GLN cc_start: 0.8542 (mt0) cc_final: 0.8305 (mt0) REVERT: G 323 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8354 (mt-10) REVERT: H 86 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8583 (tptp) REVERT: H 139 ASN cc_start: 0.8383 (t0) cc_final: 0.7729 (m110) REVERT: H 192 LYS cc_start: 0.9133 (ptpp) cc_final: 0.8781 (pmtt) REVERT: H 322 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7791 (ptpp) REVERT: H 323 GLU cc_start: 0.7777 (pm20) cc_final: 0.7385 (pm20) REVERT: I 82 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8239 (tptp) REVERT: I 105 HIS cc_start: 0.8755 (m-70) cc_final: 0.8423 (m90) REVERT: I 301 GLN cc_start: 0.8436 (mt0) cc_final: 0.8203 (mt0) REVERT: I 319 LEU cc_start: 0.7788 (mp) cc_final: 0.7545 (tt) REVERT: I 370 GLN cc_start: 0.8520 (pp30) cc_final: 0.8277 (pp30) REVERT: I 382 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: I 413 TYR cc_start: 0.8106 (t80) cc_final: 0.7872 (t80) REVERT: J 134 LYS cc_start: 0.7535 (mttt) cc_final: 0.6944 (tmmt) REVERT: J 163 HIS cc_start: 0.8489 (t-90) cc_final: 0.8213 (t-170) REVERT: J 211 ASP cc_start: 0.9118 (t0) cc_final: 0.8652 (t0) REVERT: J 295 ASN cc_start: 0.8335 (t0) cc_final: 0.8000 (t0) REVERT: J 391 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8334 (t0) REVERT: K 109 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8307 (p0) REVERT: K 153 GLU cc_start: 0.8663 (tp30) cc_final: 0.8105 (tp30) REVERT: K 165 ASP cc_start: 0.8635 (t0) cc_final: 0.8140 (p0) REVERT: K 310 ASP cc_start: 0.8271 (t0) cc_final: 0.7525 (t0) REVERT: K 416 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7869 (m-10) REVERT: L 10 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8676 (pmmt) REVERT: L 153 GLU cc_start: 0.8510 (mp0) cc_final: 0.8171 (mp0) REVERT: L 207 ARG cc_start: 0.8568 (mtp85) cc_final: 0.8277 (ttm-80) REVERT: L 383 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: M 76 LEU cc_start: 0.9506 (mt) cc_final: 0.9252 (mt) REVERT: M 108 MET cc_start: 0.8305 (mmm) cc_final: 0.7310 (ptm) REVERT: M 160 ASN cc_start: 0.8207 (t0) cc_final: 0.7958 (t0) REVERT: M 303 ILE cc_start: 0.8462 (tt) cc_final: 0.8250 (pp) REVERT: M 326 GLN cc_start: 0.7151 (pp30) cc_final: 0.6881 (pp30) REVERT: N 77 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.6995 (p0) REVERT: N 197 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: N 253 LYS cc_start: 0.8599 (mtpt) cc_final: 0.8212 (mttm) REVERT: N 297 GLU cc_start: 0.8259 (mp0) cc_final: 0.7862 (pm20) REVERT: N 321 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7742 (m90) REVERT: N 343 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8093 (ttpt) REVERT: N 379 ASP cc_start: 0.8602 (t70) cc_final: 0.8380 (t0) REVERT: N 392 PHE cc_start: 0.4197 (OUTLIER) cc_final: 0.3533 (p90) REVERT: N 394 ASN cc_start: 0.6569 (OUTLIER) cc_final: 0.6189 (m110) REVERT: O 166 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8349 (t0) REVERT: O 303 ILE cc_start: 0.8423 (tp) cc_final: 0.8195 (pp) REVERT: O 323 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7649 (mt-10) REVERT: O 370 GLN cc_start: 0.8463 (pp30) cc_final: 0.8236 (tm-30) REVERT: O 382 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7847 (mp0) REVERT: P 75 PHE cc_start: 0.7126 (t80) cc_final: 0.6177 (t80) REVERT: P 133 TYR cc_start: 0.6437 (p90) cc_final: 0.6203 (p90) REVERT: P 163 HIS cc_start: 0.9151 (t-90) cc_final: 0.8647 (t-90) REVERT: P 280 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: Q 22 GLN cc_start: 0.8615 (mm110) cc_final: 0.7828 (pm20) REVERT: Q 165 ASP cc_start: 0.8749 (t0) cc_final: 0.8529 (t0) REVERT: Q 319 LEU cc_start: 0.7817 (mt) cc_final: 0.7586 (mp) REVERT: Q 323 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7763 (mt-10) REVERT: Q 344 ASP cc_start: 0.8741 (m-30) cc_final: 0.8450 (m-30) REVERT: Q 382 GLU cc_start: 0.8659 (mp0) cc_final: 0.8029 (mp0) REVERT: R 44 SER cc_start: 0.8262 (t) cc_final: 0.7555 (p) REVERT: R 237 ASN cc_start: 0.8554 (m-40) cc_final: 0.8294 (m-40) REVERT: R 275 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8221 (mm-40) REVERT: R 387 ASN cc_start: 0.8866 (m-40) cc_final: 0.8434 (m-40) outliers start: 347 outliers final: 146 residues processed: 970 average time/residue: 1.2407 time to fit residues: 1662.2873 Evaluate side-chains 801 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 622 time to evaluate : 6.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 83 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 536 PHE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 291 TYR Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 83 CYS Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 522 SER Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 320 LYS Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 322 LYS Chi-restraints excluded: chain H residue 366 ASN Chi-restraints excluded: chain H residue 421 PHE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 82 LYS Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 330 SER Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 143 CYS Chi-restraints excluded: chain J residue 261 TYR Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 391 ASN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 217 LYS Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 227 TYR Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 416 PHE Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain M residue 394 ASN Chi-restraints excluded: chain M residue 405 SER Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 74 LYS Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 197 GLU Chi-restraints excluded: chain N residue 321 HIS Chi-restraints excluded: chain N residue 331 GLU Chi-restraints excluded: chain N residue 392 PHE Chi-restraints excluded: chain N residue 394 ASN Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 278 SER Chi-restraints excluded: chain O residue 294 SER Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 394 ASN Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 414 PHE Chi-restraints excluded: chain Q residue 10 LYS Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 294 SER Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 366 ASN Chi-restraints excluded: chain Q residue 418 VAL Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 143 CYS Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 324 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 415 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 773 optimal weight: 0.9990 chunk 543 optimal weight: 0.0070 chunk 246 optimal weight: 0.8980 chunk 458 optimal weight: 7.9990 chunk 655 optimal weight: 5.9990 chunk 373 optimal weight: 4.9990 chunk 446 optimal weight: 3.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN C 72 HIS ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 HIS E 213 ASN ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 369 ASN ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 398 HIS ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN L 77 ASN ** L 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN ** O 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 321 HIS ** O 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 ASN ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 415 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 412 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.143572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096709 restraints weight = 139953.720| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.95 r_work: 0.3319 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 71396 Z= 0.236 Angle : 0.607 14.211 96304 Z= 0.316 Chirality : 0.044 0.225 10462 Planarity : 0.003 0.058 12399 Dihedral : 6.916 86.698 9352 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.15 % Favored : 92.76 % Rotamer: Outliers : 4.26 % Allowed : 28.33 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.53 (0.09), residues: 8381 helix: 0.07 (0.09), residues: 3438 sheet: -2.53 (0.14), residues: 1005 loop : -1.53 (0.10), residues: 3938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP P 125 HIS 0.012 0.001 HIS J 105 PHE 0.039 0.002 PHE B 96 TYR 0.023 0.001 TYR C 560 ARG 0.009 0.001 ARG K 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 334 poor density : 670 time to evaluate : 6.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8532 (t70) cc_final: 0.8060 (t0) REVERT: A 236 MET cc_start: 0.5969 (tpt) cc_final: 0.5735 (tpp) REVERT: A 340 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5709 (tt) REVERT: A 384 ASN cc_start: 0.5554 (m-40) cc_final: 0.4888 (p0) REVERT: A 519 ASN cc_start: 0.8660 (t0) cc_final: 0.8273 (t0) REVERT: A 530 TYR cc_start: 0.7008 (t80) cc_final: 0.6600 (t80) REVERT: B 247 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5588 (mmmm) REVERT: B 428 ARG cc_start: 0.3919 (OUTLIER) cc_final: 0.3616 (ppt-90) REVERT: B 436 GLU cc_start: 0.7546 (mm-30) cc_final: 0.6727 (tp30) REVERT: B 517 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7840 (mm-40) REVERT: C 122 HIS cc_start: 0.5786 (OUTLIER) cc_final: 0.5168 (p-80) REVERT: C 216 MET cc_start: 0.8476 (ttm) cc_final: 0.8175 (tpt) REVERT: C 222 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7894 (mp) REVERT: C 437 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7872 (tp30) REVERT: C 441 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6837 (m-10) REVERT: C 455 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8140 (pt0) REVERT: D 411 PHE cc_start: 0.7948 (t80) cc_final: 0.7641 (t80) REVERT: D 447 GLU cc_start: 0.4203 (OUTLIER) cc_final: 0.2817 (pm20) REVERT: D 457 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.6193 (p90) REVERT: D 469 CYS cc_start: 0.7272 (m) cc_final: 0.6843 (m) REVERT: D 536 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8142 (t80) REVERT: E 14 LYS cc_start: 0.8675 (tttm) cc_final: 0.8301 (tppt) REVERT: E 117 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8534 (mt-10) REVERT: E 131 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.7013 (tp) REVERT: E 135 ASP cc_start: 0.8166 (t0) cc_final: 0.7845 (t0) REVERT: E 216 MET cc_start: 0.6255 (ttp) cc_final: 0.5659 (tpp) REVERT: E 291 TYR cc_start: 0.0991 (OUTLIER) cc_final: 0.0526 (m-80) REVERT: E 340 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7034 (mm) REVERT: E 376 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8140 (tpp-160) REVERT: E 407 PHE cc_start: 0.8870 (t80) cc_final: 0.7840 (t80) REVERT: E 486 LEU cc_start: 0.8887 (tp) cc_final: 0.8483 (tp) REVERT: E 492 TYR cc_start: 0.7351 (m-80) cc_final: 0.6822 (m-80) REVERT: E 505 TYR cc_start: 0.8011 (t80) cc_final: 0.7584 (t80) REVERT: E 545 PHE cc_start: 0.8271 (m-10) cc_final: 0.7296 (m-10) REVERT: E 546 GLU cc_start: 0.6652 (tm-30) cc_final: 0.6393 (tm-30) REVERT: F 40 ILE cc_start: 0.8977 (pt) cc_final: 0.8651 (pp) REVERT: F 56 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: F 80 ARG cc_start: 0.8405 (mtp85) cc_final: 0.7964 (mtp85) REVERT: F 268 THR cc_start: 0.3175 (OUTLIER) cc_final: 0.2883 (p) REVERT: F 269 ASP cc_start: 0.3601 (OUTLIER) cc_final: 0.2940 (m-30) REVERT: F 423 MET cc_start: 0.7821 (tmt) cc_final: 0.7573 (tmm) REVERT: F 500 ASN cc_start: 0.8733 (t0) cc_final: 0.8520 (t0) REVERT: F 504 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8256 (tm-30) REVERT: F 506 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8529 (mp) REVERT: F 534 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8168 (mp0) REVERT: G 22 GLN cc_start: 0.8826 (tp40) cc_final: 0.8474 (tp-100) REVERT: G 37 ASN cc_start: 0.9083 (t0) cc_final: 0.8420 (t0) REVERT: G 92 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6479 (pm20) REVERT: G 128 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7072 (mpp) REVERT: G 301 GLN cc_start: 0.8549 (mt0) cc_final: 0.8263 (mt0) REVERT: G 323 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8251 (mt-10) REVERT: H 54 MET cc_start: 0.8582 (tpp) cc_final: 0.8225 (ttm) REVERT: H 86 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8579 (tptp) REVERT: H 139 ASN cc_start: 0.8375 (t0) cc_final: 0.7720 (m110) REVERT: H 192 LYS cc_start: 0.9142 (ptpp) cc_final: 0.8777 (pmtt) REVERT: H 322 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7800 (ptpp) REVERT: H 323 GLU cc_start: 0.7844 (pm20) cc_final: 0.7470 (pm20) REVERT: I 82 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8255 (tptp) REVERT: I 105 HIS cc_start: 0.8719 (m-70) cc_final: 0.8364 (m90) REVERT: I 301 GLN cc_start: 0.8439 (mt0) cc_final: 0.8199 (mt0) REVERT: I 370 GLN cc_start: 0.8533 (pp30) cc_final: 0.8293 (pp30) REVERT: I 382 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: J 134 LYS cc_start: 0.7623 (mttt) cc_final: 0.7307 (pptt) REVERT: J 295 ASN cc_start: 0.8245 (t0) cc_final: 0.7830 (t0) REVERT: J 391 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8422 (t0) REVERT: K 109 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8311 (p0) REVERT: K 153 GLU cc_start: 0.8609 (tp30) cc_final: 0.8056 (tp30) REVERT: K 165 ASP cc_start: 0.8667 (t0) cc_final: 0.8123 (p0) REVERT: K 310 ASP cc_start: 0.8348 (t0) cc_final: 0.7548 (t0) REVERT: K 357 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7766 (mp0) REVERT: K 416 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7878 (m-10) REVERT: L 10 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8708 (pmmt) REVERT: L 137 ILE cc_start: 0.7828 (mm) cc_final: 0.7554 (mm) REVERT: L 207 ARG cc_start: 0.8607 (mtp85) cc_final: 0.8318 (ttm-80) REVERT: L 383 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8142 (tp30) REVERT: M 44 SER cc_start: 0.8483 (t) cc_final: 0.7733 (p) REVERT: M 76 LEU cc_start: 0.9472 (mt) cc_final: 0.9221 (mt) REVERT: M 105 HIS cc_start: 0.7807 (m-70) cc_final: 0.7605 (m170) REVERT: M 160 ASN cc_start: 0.8178 (m-40) cc_final: 0.7917 (t0) REVERT: M 303 ILE cc_start: 0.8455 (tt) cc_final: 0.8247 (pp) REVERT: M 326 GLN cc_start: 0.7332 (pp30) cc_final: 0.7126 (pp30) REVERT: N 71 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6525 (t80) REVERT: N 77 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.6966 (p0) REVERT: N 197 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: N 253 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8135 (mttm) REVERT: N 280 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8167 (mt-10) REVERT: N 297 GLU cc_start: 0.8277 (mp0) cc_final: 0.7858 (pm20) REVERT: N 321 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7817 (m90) REVERT: N 357 GLU cc_start: 0.8417 (tt0) cc_final: 0.8111 (tp30) REVERT: N 379 ASP cc_start: 0.8589 (t70) cc_final: 0.8361 (t0) REVERT: N 392 PHE cc_start: 0.4325 (OUTLIER) cc_final: 0.3200 (p90) REVERT: N 394 ASN cc_start: 0.6515 (OUTLIER) cc_final: 0.6094 (m110) REVERT: O 114 GLU cc_start: 0.5172 (OUTLIER) cc_final: 0.4082 (mp0) REVERT: O 165 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8106 (t0) REVERT: O 166 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8456 (t0) REVERT: O 323 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7758 (mt-10) REVERT: O 370 GLN cc_start: 0.8570 (pp30) cc_final: 0.8302 (tm-30) REVERT: O 382 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7869 (mp0) REVERT: P 75 PHE cc_start: 0.7148 (t80) cc_final: 0.6225 (t80) REVERT: P 133 TYR cc_start: 0.6336 (p90) cc_final: 0.6018 (p90) REVERT: P 150 ASN cc_start: 0.7949 (t0) cc_final: 0.7359 (t0) REVERT: P 163 HIS cc_start: 0.9131 (t-90) cc_final: 0.8652 (t-90) REVERT: P 280 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: Q 22 GLN cc_start: 0.8571 (mm110) cc_final: 0.7780 (pm20) REVERT: Q 165 ASP cc_start: 0.8767 (t0) cc_final: 0.8548 (t0) REVERT: Q 207 ARG cc_start: 0.8783 (ttm-80) cc_final: 0.8565 (ttm-80) REVERT: Q 227 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8550 (m-10) REVERT: Q 319 LEU cc_start: 0.7832 (mt) cc_final: 0.7586 (mp) REVERT: Q 323 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7920 (mt-10) REVERT: Q 344 ASP cc_start: 0.8722 (m-30) cc_final: 0.8400 (m-30) REVERT: Q 382 GLU cc_start: 0.8682 (mp0) cc_final: 0.8006 (mp0) REVERT: R 44 SER cc_start: 0.8335 (t) cc_final: 0.7629 (p) REVERT: R 237 ASN cc_start: 0.8588 (m-40) cc_final: 0.8317 (m-40) REVERT: R 275 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8247 (mm-40) outliers start: 334 outliers final: 153 residues processed: 937 average time/residue: 1.2057 time to fit residues: 1569.2629 Evaluate side-chains 799 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 608 time to evaluate : 6.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 83 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 536 PHE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 291 TYR Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 376 ARG Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 83 CYS Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 522 SER Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 320 LYS Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 271 LYS Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 322 LYS Chi-restraints excluded: chain H residue 366 ASN Chi-restraints excluded: chain H residue 421 PHE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 82 LYS Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 330 SER Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 404 SER Chi-restraints excluded: chain I residue 412 HIS Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 143 CYS Chi-restraints excluded: chain J residue 261 TYR Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 391 ASN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 217 LYS Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 227 TYR Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 416 PHE Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 330 SER Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain M residue 394 ASN Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 71 TYR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 197 GLU Chi-restraints excluded: chain N residue 321 HIS Chi-restraints excluded: chain N residue 331 GLU Chi-restraints excluded: chain N residue 392 PHE Chi-restraints excluded: chain N residue 394 ASN Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 165 ASP Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 278 SER Chi-restraints excluded: chain O residue 294 SER Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 394 ASN Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 414 PHE Chi-restraints excluded: chain Q residue 10 LYS Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 227 TYR Chi-restraints excluded: chain Q residue 294 SER Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 366 ASN Chi-restraints excluded: chain Q residue 418 VAL Chi-restraints excluded: chain Q residue 419 GLU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 143 CYS Chi-restraints excluded: chain R residue 236 GLU Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 278 SER Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 324 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 47 optimal weight: 20.0000 chunk 345 optimal weight: 9.9990 chunk 2 optimal weight: 0.0170 chunk 247 optimal weight: 3.9990 chunk 318 optimal weight: 0.0470 chunk 306 optimal weight: 30.0000 chunk 373 optimal weight: 4.9990 chunk 604 optimal weight: 3.9990 chunk 723 optimal weight: 10.0000 chunk 560 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 overall best weight: 2.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 265 ASN A 495 HIS ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 HIS D 127 ASN ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 HIS E 213 ASN ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 415 GLN ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 238 ASN ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 287 HIS ** J 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN L 105 HIS ** L 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN ** O 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 159 GLN ** Q 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.140320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.092413 restraints weight = 140220.630| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.95 r_work: 0.3216 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 71396 Z= 0.338 Angle : 0.670 15.013 96304 Z= 0.348 Chirality : 0.046 0.299 10462 Planarity : 0.003 0.056 12399 Dihedral : 7.037 88.631 9348 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.39 % Favored : 92.47 % Rotamer: Outliers : 4.04 % Allowed : 28.65 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.50 (0.09), residues: 8381 helix: 0.08 (0.09), residues: 3439 sheet: -2.43 (0.14), residues: 1019 loop : -1.52 (0.10), residues: 3923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP P 125 HIS 0.013 0.001 HIS L 105 PHE 0.035 0.002 PHE E 408 TYR 0.028 0.002 TYR C 560 ARG 0.009 0.001 ARG M 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 317 poor density : 642 time to evaluate : 6.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8662 (t70) cc_final: 0.8169 (t0) REVERT: A 340 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5871 (tt) REVERT: A 384 ASN cc_start: 0.5438 (m-40) cc_final: 0.4796 (p0) REVERT: A 519 ASN cc_start: 0.8671 (t0) cc_final: 0.8291 (t0) REVERT: A 530 TYR cc_start: 0.7129 (t80) cc_final: 0.6670 (t80) REVERT: B 428 ARG cc_start: 0.3913 (OUTLIER) cc_final: 0.3552 (ppt-90) REVERT: B 436 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6775 (tp30) REVERT: B 517 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7925 (mm-40) REVERT: B 561 ARG cc_start: 0.8634 (ttt-90) cc_final: 0.8135 (ptp-110) REVERT: C 61 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8443 (mt-10) REVERT: C 122 HIS cc_start: 0.5918 (OUTLIER) cc_final: 0.5240 (p-80) REVERT: C 216 MET cc_start: 0.8496 (ttm) cc_final: 0.7996 (tpt) REVERT: C 222 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7932 (mp) REVERT: C 298 MET cc_start: 0.4886 (ptt) cc_final: 0.3692 (ptm) REVERT: C 366 LEU cc_start: 0.8206 (mt) cc_final: 0.7889 (pt) REVERT: C 437 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7706 (tp30) REVERT: C 441 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6905 (m-10) REVERT: D 411 PHE cc_start: 0.7900 (t80) cc_final: 0.7673 (t80) REVERT: D 447 GLU cc_start: 0.4277 (OUTLIER) cc_final: 0.3018 (pm20) REVERT: D 457 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.6097 (p90) REVERT: D 469 CYS cc_start: 0.7294 (m) cc_final: 0.6849 (m) REVERT: D 477 ARG cc_start: 0.3619 (mmt180) cc_final: 0.3097 (mmp80) REVERT: D 536 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8211 (t80) REVERT: E 14 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8513 (ttmm) REVERT: E 117 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8617 (mt-10) REVERT: E 131 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7246 (tp) REVERT: E 216 MET cc_start: 0.6192 (ttp) cc_final: 0.5599 (tpp) REVERT: E 291 TYR cc_start: 0.0915 (OUTLIER) cc_final: 0.0518 (m-80) REVERT: E 340 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7025 (mm) REVERT: E 407 PHE cc_start: 0.8789 (t80) cc_final: 0.7788 (t80) REVERT: E 492 TYR cc_start: 0.7330 (m-80) cc_final: 0.6969 (m-80) REVERT: E 505 TYR cc_start: 0.7954 (t80) cc_final: 0.7421 (t80) REVERT: E 545 PHE cc_start: 0.8327 (m-10) cc_final: 0.7279 (m-10) REVERT: E 546 GLU cc_start: 0.6724 (tm-30) cc_final: 0.6487 (tm-30) REVERT: F 40 ILE cc_start: 0.9091 (pt) cc_final: 0.8775 (pp) REVERT: F 56 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: F 80 ARG cc_start: 0.8456 (mtp85) cc_final: 0.8054 (mtp85) REVERT: F 268 THR cc_start: 0.2793 (OUTLIER) cc_final: 0.2466 (p) REVERT: F 269 ASP cc_start: 0.3396 (OUTLIER) cc_final: 0.2642 (m-30) REVERT: F 500 ASN cc_start: 0.8790 (t0) cc_final: 0.8582 (t0) REVERT: F 504 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8286 (tm-30) REVERT: F 506 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8577 (mp) REVERT: F 519 ASN cc_start: 0.8778 (m-40) cc_final: 0.8237 (t0) REVERT: F 534 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8155 (mp0) REVERT: G 22 GLN cc_start: 0.8868 (tp40) cc_final: 0.8540 (tp-100) REVERT: G 92 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6492 (pm20) REVERT: G 128 MET cc_start: 0.7871 (pp-130) cc_final: 0.7126 (mpp) REVERT: G 301 GLN cc_start: 0.8628 (mt0) cc_final: 0.8358 (mt0) REVERT: G 323 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8394 (mt-10) REVERT: H 54 MET cc_start: 0.8733 (tpp) cc_final: 0.8417 (ttm) REVERT: H 86 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8655 (tptp) REVERT: H 139 ASN cc_start: 0.8407 (t0) cc_final: 0.7757 (m110) REVERT: H 322 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7802 (ptpp) REVERT: H 323 GLU cc_start: 0.8036 (pm20) cc_final: 0.7615 (pm20) REVERT: I 82 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8282 (tptp) REVERT: I 90 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8802 (mm-30) REVERT: I 382 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: J 134 LYS cc_start: 0.7532 (mttt) cc_final: 0.7286 (pptt) REVERT: K 153 GLU cc_start: 0.8595 (tp30) cc_final: 0.8034 (tp30) REVERT: K 165 ASP cc_start: 0.8756 (t0) cc_final: 0.8150 (p0) REVERT: K 227 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: K 310 ASP cc_start: 0.8460 (t0) cc_final: 0.7601 (t0) REVERT: K 357 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7808 (mp0) REVERT: K 416 PHE cc_start: 0.8310 (m-80) cc_final: 0.8039 (m-10) REVERT: L 10 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8780 (pmmt) REVERT: L 153 GLU cc_start: 0.8625 (mp0) cc_final: 0.8159 (mp0) REVERT: L 207 ARG cc_start: 0.8692 (mtp85) cc_final: 0.8379 (ttm-80) REVERT: L 383 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8266 (tp30) REVERT: L 419 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8106 (mm-30) REVERT: M 76 LEU cc_start: 0.9475 (mt) cc_final: 0.9212 (mt) REVERT: M 108 MET cc_start: 0.8343 (mmm) cc_final: 0.7457 (ptm) REVERT: M 160 ASN cc_start: 0.8285 (m-40) cc_final: 0.8065 (t0) REVERT: M 303 ILE cc_start: 0.8517 (tt) cc_final: 0.8290 (pp) REVERT: M 326 GLN cc_start: 0.7619 (pp30) cc_final: 0.7186 (pp30) REVERT: N 71 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: N 77 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7219 (p0) REVERT: N 131 SER cc_start: 0.7328 (OUTLIER) cc_final: 0.6956 (p) REVERT: N 197 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: N 280 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8215 (mt-10) REVERT: N 321 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.8000 (m90) REVERT: N 357 GLU cc_start: 0.8541 (tt0) cc_final: 0.8310 (tp30) REVERT: N 379 ASP cc_start: 0.8603 (t0) cc_final: 0.8387 (t0) REVERT: N 392 PHE cc_start: 0.5017 (OUTLIER) cc_final: 0.3234 (p90) REVERT: N 394 ASN cc_start: 0.6542 (OUTLIER) cc_final: 0.6096 (m110) REVERT: O 114 GLU cc_start: 0.5621 (OUTLIER) cc_final: 0.4357 (mp0) REVERT: O 166 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8585 (t0) REVERT: O 201 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8711 (tp) REVERT: O 260 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9102 (pttp) REVERT: O 323 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7939 (mt-10) REVERT: O 370 GLN cc_start: 0.8675 (pp30) cc_final: 0.8376 (tm-30) REVERT: O 382 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7816 (mp0) REVERT: P 75 PHE cc_start: 0.7236 (t80) cc_final: 0.6303 (t80) REVERT: P 77 ASN cc_start: 0.7980 (p0) cc_final: 0.7091 (t0) REVERT: P 133 TYR cc_start: 0.6508 (p90) cc_final: 0.6122 (p90) REVERT: P 163 HIS cc_start: 0.9158 (t-90) cc_final: 0.8781 (t-90) REVERT: P 280 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: Q 22 GLN cc_start: 0.8621 (mm110) cc_final: 0.7833 (pm20) REVERT: Q 165 ASP cc_start: 0.8795 (t0) cc_final: 0.8543 (t0) REVERT: Q 208 TYR cc_start: 0.8437 (t80) cc_final: 0.8153 (t80) REVERT: Q 323 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8139 (mt-10) REVERT: Q 342 ILE cc_start: 0.8674 (mm) cc_final: 0.8458 (mp) REVERT: Q 344 ASP cc_start: 0.8758 (m-30) cc_final: 0.8350 (m-30) REVERT: Q 382 GLU cc_start: 0.8700 (mp0) cc_final: 0.7985 (mp0) REVERT: Q 419 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: R 10 LYS cc_start: 0.8342 (pptt) cc_final: 0.7940 (pmtt) REVERT: R 44 SER cc_start: 0.8456 (t) cc_final: 0.7752 (p) REVERT: R 224 THR cc_start: 0.9442 (OUTLIER) cc_final: 0.9231 (t) REVERT: R 237 ASN cc_start: 0.8621 (m-40) cc_final: 0.8385 (m-40) REVERT: R 275 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8198 (mm110) REVERT: R 326 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7176 (mp10) REVERT: R 343 LYS cc_start: 0.8575 (tttm) cc_final: 0.7846 (ttpp) outliers start: 317 outliers final: 144 residues processed: 900 average time/residue: 1.2432 time to fit residues: 1549.3274 Evaluate side-chains 766 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 583 time to evaluate : 6.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 83 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 536 PHE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 291 TYR Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 83 CYS Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 522 SER Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 271 LYS Chi-restraints excluded: chain H residue 322 LYS Chi-restraints excluded: chain H residue 421 PHE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 82 LYS Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 330 SER Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain I residue 404 SER Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 143 CYS Chi-restraints excluded: chain J residue 253 LYS Chi-restraints excluded: chain J residue 261 TYR Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 391 ASN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 217 LYS Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 227 TYR Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 337 SER Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain M residue 394 ASN Chi-restraints excluded: chain M residue 405 SER Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 71 TYR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 131 SER Chi-restraints excluded: chain N residue 197 GLU Chi-restraints excluded: chain N residue 321 HIS Chi-restraints excluded: chain N residue 331 GLU Chi-restraints excluded: chain N residue 392 PHE Chi-restraints excluded: chain N residue 394 ASN Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 260 LYS Chi-restraints excluded: chain O residue 278 SER Chi-restraints excluded: chain O residue 294 SER Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 394 ASN Chi-restraints excluded: chain O residue 397 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain Q residue 10 LYS Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 294 SER Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 419 GLU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 143 CYS Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 253 LYS Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 278 SER Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 326 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 295 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 517 optimal weight: 0.9990 chunk 711 optimal weight: 4.9990 chunk 259 optimal weight: 7.9990 chunk 408 optimal weight: 0.9990 chunk 667 optimal weight: 3.9990 chunk 245 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 708 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 ASN E 122 HIS E 213 ASN ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** I 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 275 GLN J 358 HIS ** J 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 366 ASN ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN ** L 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN ** O 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.139155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.091320 restraints weight = 139945.514| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.95 r_work: 0.3221 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 71396 Z= 0.356 Angle : 0.685 16.716 96304 Z= 0.356 Chirality : 0.047 0.400 10462 Planarity : 0.003 0.055 12399 Dihedral : 7.086 88.968 9348 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.65 % Favored : 92.21 % Rotamer: Outliers : 3.71 % Allowed : 29.13 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.09), residues: 8381 helix: 0.08 (0.09), residues: 3444 sheet: -2.38 (0.15), residues: 1024 loop : -1.60 (0.10), residues: 3913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP P 125 HIS 0.015 0.001 HIS J 105 PHE 0.028 0.002 PHE E 408 TYR 0.024 0.002 TYR N 329 ARG 0.009 0.001 ARG M 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 631 time to evaluate : 6.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8693 (t70) cc_final: 0.8184 (t0) REVERT: A 384 ASN cc_start: 0.5382 (m-40) cc_final: 0.4678 (p0) REVERT: A 519 ASN cc_start: 0.8662 (t0) cc_final: 0.8284 (t0) REVERT: A 530 TYR cc_start: 0.7201 (t80) cc_final: 0.6733 (t80) REVERT: B 146 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7562 (mtpp) REVERT: B 436 GLU cc_start: 0.7641 (mm-30) cc_final: 0.6713 (tp30) REVERT: B 451 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7438 (t80) REVERT: B 517 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8026 (mm-40) REVERT: B 561 ARG cc_start: 0.8588 (ttt-90) cc_final: 0.8179 (ptp-170) REVERT: C 61 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8445 (mt-10) REVERT: C 67 LEU cc_start: 0.4231 (OUTLIER) cc_final: 0.3613 (mm) REVERT: C 112 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8877 (p) REVERT: C 189 HIS cc_start: 0.7885 (t-170) cc_final: 0.7475 (t70) REVERT: C 216 MET cc_start: 0.8500 (ttm) cc_final: 0.8096 (ttm) REVERT: C 222 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7952 (mp) REVERT: C 298 MET cc_start: 0.4710 (ptt) cc_final: 0.3632 (ptm) REVERT: C 366 LEU cc_start: 0.8226 (mt) cc_final: 0.7928 (pt) REVERT: C 441 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.6914 (m-10) REVERT: C 455 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8031 (pm20) REVERT: D 64 GLU cc_start: 0.8260 (mp0) cc_final: 0.7991 (mm-30) REVERT: D 209 ILE cc_start: 0.6345 (mm) cc_final: 0.5980 (OUTLIER) REVERT: D 395 TYR cc_start: 0.5784 (m-80) cc_final: 0.5476 (m-80) REVERT: D 411 PHE cc_start: 0.7964 (t80) cc_final: 0.7703 (t80) REVERT: D 447 GLU cc_start: 0.4160 (OUTLIER) cc_final: 0.2819 (pm20) REVERT: D 457 PHE cc_start: 0.6347 (OUTLIER) cc_final: 0.5959 (p90) REVERT: D 469 CYS cc_start: 0.7237 (m) cc_final: 0.6804 (m) REVERT: D 536 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8316 (t80) REVERT: E 14 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8511 (ttmm) REVERT: E 48 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7994 (mm-30) REVERT: E 117 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8620 (mt-10) REVERT: E 142 PHE cc_start: 0.6481 (m-80) cc_final: 0.6218 (m-10) REVERT: E 291 TYR cc_start: 0.1000 (OUTLIER) cc_final: 0.0589 (m-80) REVERT: E 340 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7059 (mm) REVERT: E 407 PHE cc_start: 0.8813 (t80) cc_final: 0.7841 (t80) REVERT: E 492 TYR cc_start: 0.7420 (m-80) cc_final: 0.7070 (m-80) REVERT: E 505 TYR cc_start: 0.7969 (t80) cc_final: 0.7386 (t80) REVERT: E 545 PHE cc_start: 0.8382 (m-10) cc_final: 0.7372 (m-10) REVERT: E 546 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6567 (tm-30) REVERT: F 40 ILE cc_start: 0.9090 (pt) cc_final: 0.8783 (pp) REVERT: F 56 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: F 80 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8042 (mtp85) REVERT: F 268 THR cc_start: 0.2627 (OUTLIER) cc_final: 0.2277 (p) REVERT: F 269 ASP cc_start: 0.3431 (OUTLIER) cc_final: 0.2534 (m-30) REVERT: F 500 ASN cc_start: 0.8849 (t0) cc_final: 0.8644 (t0) REVERT: F 504 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8293 (tm-30) REVERT: F 506 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8662 (mp) REVERT: F 519 ASN cc_start: 0.8751 (m-40) cc_final: 0.8279 (t0) REVERT: F 534 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8179 (mp0) REVERT: G 22 GLN cc_start: 0.8882 (tp40) cc_final: 0.8593 (tp-100) REVERT: G 37 ASN cc_start: 0.9067 (t0) cc_final: 0.8347 (t0) REVERT: G 92 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6480 (pm20) REVERT: G 128 MET cc_start: 0.7780 (pp-130) cc_final: 0.7065 (mpp) REVERT: G 323 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8360 (mt-10) REVERT: H 54 MET cc_start: 0.8778 (tpp) cc_final: 0.8521 (ttm) REVERT: H 86 LYS cc_start: 0.9067 (mtpp) cc_final: 0.8674 (tptp) REVERT: H 139 ASN cc_start: 0.8438 (t0) cc_final: 0.7778 (m110) REVERT: H 271 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6597 (ptpt) REVERT: H 322 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7763 (ptpp) REVERT: H 323 GLU cc_start: 0.8087 (pm20) cc_final: 0.7704 (pm20) REVERT: I 82 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8340 (tptp) REVERT: I 382 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: J 269 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6338 (mtm-85) REVERT: J 295 ASN cc_start: 0.8203 (t0) cc_final: 0.7714 (t0) REVERT: K 153 GLU cc_start: 0.8522 (tp30) cc_final: 0.7975 (tp30) REVERT: K 165 ASP cc_start: 0.8796 (t0) cc_final: 0.8144 (p0) REVERT: K 217 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7802 (mptt) REVERT: K 227 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: K 310 ASP cc_start: 0.8481 (t0) cc_final: 0.7514 (t0) REVERT: K 357 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7871 (mp0) REVERT: K 416 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.8013 (m-10) REVERT: K 427 ARG cc_start: 0.2770 (OUTLIER) cc_final: 0.2453 (mmp80) REVERT: L 10 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8806 (pmmt) REVERT: L 153 GLU cc_start: 0.8611 (mp0) cc_final: 0.8109 (mp0) REVERT: L 207 ARG cc_start: 0.8743 (mtp85) cc_final: 0.8452 (ttm-80) REVERT: L 383 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: L 419 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8113 (mm-30) REVERT: M 76 LEU cc_start: 0.9495 (mt) cc_final: 0.9210 (mt) REVERT: M 82 LYS cc_start: 0.9199 (mppt) cc_final: 0.8516 (ttpp) REVERT: M 105 HIS cc_start: 0.7846 (m-70) cc_final: 0.7641 (m170) REVERT: M 160 ASN cc_start: 0.8339 (m-40) cc_final: 0.8104 (t0) REVERT: M 326 GLN cc_start: 0.7789 (pp30) cc_final: 0.7390 (pp30) REVERT: N 77 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7220 (p0) REVERT: N 131 SER cc_start: 0.7280 (OUTLIER) cc_final: 0.6908 (p) REVERT: N 197 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: N 321 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.8059 (m90) REVERT: N 326 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7016 (mm110) REVERT: N 394 ASN cc_start: 0.6320 (OUTLIER) cc_final: 0.5974 (m110) REVERT: O 114 GLU cc_start: 0.5541 (OUTLIER) cc_final: 0.4189 (mp0) REVERT: O 165 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8436 (t0) REVERT: O 166 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8482 (t0) REVERT: O 260 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9123 (pttp) REVERT: O 305 PHE cc_start: 0.8574 (t80) cc_final: 0.8144 (t80) REVERT: O 370 GLN cc_start: 0.8730 (pp30) cc_final: 0.8427 (tm-30) REVERT: O 382 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7824 (mp0) REVERT: P 75 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6252 (t80) REVERT: P 133 TYR cc_start: 0.6433 (p90) cc_final: 0.5925 (p90) REVERT: P 163 HIS cc_start: 0.9161 (t-90) cc_final: 0.8779 (t-90) REVERT: P 270 TYR cc_start: 0.5620 (OUTLIER) cc_final: 0.4977 (m-80) REVERT: P 280 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: P 309 ASP cc_start: 0.7724 (p0) cc_final: 0.7465 (p0) REVERT: P 318 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8494 (mmt) REVERT: Q 10 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7679 (ptpp) REVERT: Q 22 GLN cc_start: 0.8620 (mm110) cc_final: 0.7806 (pm20) REVERT: Q 165 ASP cc_start: 0.8802 (t0) cc_final: 0.8363 (t0) REVERT: Q 318 MET cc_start: 0.8269 (ttm) cc_final: 0.8061 (ptp) REVERT: Q 323 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8190 (mt-10) REVERT: Q 342 ILE cc_start: 0.8699 (mm) cc_final: 0.8474 (mp) REVERT: Q 344 ASP cc_start: 0.8839 (m-30) cc_final: 0.8391 (m-30) REVERT: R 10 LYS cc_start: 0.8383 (pptt) cc_final: 0.7993 (pmtt) REVERT: R 44 SER cc_start: 0.8462 (t) cc_final: 0.7736 (p) REVERT: R 86 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8331 (ptpp) REVERT: R 224 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9219 (t) REVERT: R 237 ASN cc_start: 0.8647 (m-40) cc_final: 0.8427 (m-40) REVERT: R 275 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8490 (mm110) outliers start: 291 outliers final: 154 residues processed: 865 average time/residue: 1.2356 time to fit residues: 1480.2423 Evaluate side-chains 758 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 558 time to evaluate : 6.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 536 PHE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 291 TYR Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 83 CYS Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 522 SER Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 271 LYS Chi-restraints excluded: chain H residue 322 LYS Chi-restraints excluded: chain H residue 326 GLN Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 421 PHE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 82 LYS Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 330 SER Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 404 SER Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 143 CYS Chi-restraints excluded: chain J residue 261 TYR Chi-restraints excluded: chain J residue 269 ARG Chi-restraints excluded: chain J residue 391 ASN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 217 LYS Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 227 TYR Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 337 SER Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 366 ASN Chi-restraints excluded: chain K residue 416 PHE Chi-restraints excluded: chain K residue 427 ARG Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain M residue 394 ASN Chi-restraints excluded: chain M residue 405 SER Chi-restraints excluded: chain M residue 422 LEU Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LYS Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 131 SER Chi-restraints excluded: chain N residue 197 GLU Chi-restraints excluded: chain N residue 321 HIS Chi-restraints excluded: chain N residue 326 GLN Chi-restraints excluded: chain N residue 331 GLU Chi-restraints excluded: chain N residue 392 PHE Chi-restraints excluded: chain N residue 394 ASN Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 165 ASP Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 260 LYS Chi-restraints excluded: chain O residue 278 SER Chi-restraints excluded: chain O residue 294 SER Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 397 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 75 PHE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 270 TYR Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 318 MET Chi-restraints excluded: chain Q residue 10 LYS Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 294 SER Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 382 GLU Chi-restraints excluded: chain Q residue 419 GLU Chi-restraints excluded: chain Q residue 421 PHE Chi-restraints excluded: chain R residue 86 LYS Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 143 CYS Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 253 LYS Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 278 SER Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 326 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 179 optimal weight: 0.0670 chunk 112 optimal weight: 3.9990 chunk 802 optimal weight: 0.7980 chunk 774 optimal weight: 0.9990 chunk 777 optimal weight: 0.7980 chunk 784 optimal weight: 3.9990 chunk 716 optimal weight: 1.9990 chunk 367 optimal weight: 0.7980 chunk 289 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B 372 ASN B 500 ASN C 72 HIS ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 HIS E 213 ASN ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 500 ASN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN ** L 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 306 ASN ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 238 ASN N 403 ASN ** O 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN ** O 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 ASN ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 275 GLN ** Q 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.142071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095056 restraints weight = 139814.530| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.05 r_work: 0.3262 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 71396 Z= 0.192 Angle : 0.659 16.390 96304 Z= 0.338 Chirality : 0.045 0.372 10462 Planarity : 0.003 0.057 12399 Dihedral : 6.924 88.388 9348 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.34 % Favored : 92.57 % Rotamer: Outliers : 2.78 % Allowed : 30.54 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.49 (0.09), residues: 8381 helix: 0.13 (0.09), residues: 3471 sheet: -2.42 (0.15), residues: 1020 loop : -1.58 (0.10), residues: 3890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP J 125 HIS 0.015 0.001 HIS J 105 PHE 0.068 0.001 PHE Q 421 TYR 0.029 0.001 TYR C 560 ARG 0.011 0.001 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 625 time to evaluate : 6.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8632 (t70) cc_final: 0.8148 (t0) REVERT: A 158 THR cc_start: 0.5488 (OUTLIER) cc_final: 0.4977 (p) REVERT: A 384 ASN cc_start: 0.5421 (m-40) cc_final: 0.4795 (p0) REVERT: A 404 LEU cc_start: 0.7843 (tm) cc_final: 0.7585 (mm) REVERT: A 519 ASN cc_start: 0.8648 (t0) cc_final: 0.8268 (t0) REVERT: A 530 TYR cc_start: 0.7096 (t80) cc_final: 0.6616 (t80) REVERT: B 88 MET cc_start: 0.8706 (ttp) cc_final: 0.8392 (ttp) REVERT: B 282 ASP cc_start: 0.6612 (t0) cc_final: 0.6299 (p0) REVERT: B 436 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6566 (tp30) REVERT: B 451 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7542 (t80) REVERT: B 517 GLN cc_start: 0.8214 (mm-40) cc_final: 0.8003 (mm-40) REVERT: B 543 GLU cc_start: 0.7887 (tp30) cc_final: 0.7245 (tm-30) REVERT: B 561 ARG cc_start: 0.8652 (ttt-90) cc_final: 0.8143 (ptp-110) REVERT: C 14 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8148 (tttp) REVERT: C 67 LEU cc_start: 0.4514 (OUTLIER) cc_final: 0.3890 (mm) REVERT: C 189 HIS cc_start: 0.7851 (t-170) cc_final: 0.7468 (t70) REVERT: C 216 MET cc_start: 0.8483 (ttm) cc_final: 0.7968 (tpt) REVERT: C 222 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7933 (mp) REVERT: C 298 MET cc_start: 0.5135 (ptt) cc_final: 0.4163 (ptm) REVERT: C 366 LEU cc_start: 0.8249 (mt) cc_final: 0.8004 (pt) REVERT: C 441 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6825 (m-10) REVERT: C 455 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8016 (pt0) REVERT: D 137 GLN cc_start: 0.5536 (OUTLIER) cc_final: 0.5289 (tm130) REVERT: D 395 TYR cc_start: 0.5796 (m-80) cc_final: 0.5497 (m-80) REVERT: D 411 PHE cc_start: 0.7942 (t80) cc_final: 0.7594 (t80) REVERT: D 447 GLU cc_start: 0.4173 (OUTLIER) cc_final: 0.2764 (pm20) REVERT: D 457 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.5878 (p90) REVERT: D 469 CYS cc_start: 0.7096 (m) cc_final: 0.6660 (m) REVERT: D 536 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8321 (t80) REVERT: E 14 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8409 (ttmm) REVERT: E 117 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8594 (mt-10) REVERT: E 131 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7101 (tp) REVERT: E 142 PHE cc_start: 0.6376 (m-80) cc_final: 0.6159 (m-10) REVERT: E 216 MET cc_start: 0.6254 (ttp) cc_final: 0.5711 (tpp) REVERT: E 291 TYR cc_start: 0.0977 (OUTLIER) cc_final: 0.0605 (m-80) REVERT: E 340 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6979 (mm) REVERT: E 407 PHE cc_start: 0.8896 (t80) cc_final: 0.7897 (t80) REVERT: E 486 LEU cc_start: 0.8922 (tp) cc_final: 0.8531 (tp) REVERT: E 492 TYR cc_start: 0.7397 (m-80) cc_final: 0.6900 (m-80) REVERT: E 505 TYR cc_start: 0.7941 (t80) cc_final: 0.7360 (t80) REVERT: E 510 ILE cc_start: 0.8865 (mt) cc_final: 0.8486 (mp) REVERT: E 545 PHE cc_start: 0.8394 (m-10) cc_final: 0.7336 (m-10) REVERT: E 546 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6470 (tm-30) REVERT: F 40 ILE cc_start: 0.8975 (pt) cc_final: 0.8656 (pp) REVERT: F 56 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: F 80 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8121 (mtp-110) REVERT: F 268 THR cc_start: 0.2429 (OUTLIER) cc_final: 0.2103 (p) REVERT: F 269 ASP cc_start: 0.3648 (OUTLIER) cc_final: 0.3135 (m-30) REVERT: F 423 MET cc_start: 0.7978 (tmt) cc_final: 0.7777 (tmm) REVERT: F 500 ASN cc_start: 0.8803 (t0) cc_final: 0.8594 (t0) REVERT: F 504 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8290 (tm-30) REVERT: F 506 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8625 (mp) REVERT: F 519 ASN cc_start: 0.8722 (m-40) cc_final: 0.8176 (t0) REVERT: F 534 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8083 (mp0) REVERT: G 22 GLN cc_start: 0.8880 (tp40) cc_final: 0.8570 (tp-100) REVERT: G 37 ASN cc_start: 0.8959 (t0) cc_final: 0.8367 (t0) REVERT: G 92 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: G 128 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7180 (mpp) REVERT: G 301 GLN cc_start: 0.8589 (mt0) cc_final: 0.8329 (mt0) REVERT: G 323 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8218 (mt-10) REVERT: H 54 MET cc_start: 0.8705 (tpp) cc_final: 0.8403 (ttm) REVERT: H 86 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8677 (tptp) REVERT: H 139 ASN cc_start: 0.8391 (t0) cc_final: 0.7745 (m110) REVERT: H 322 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7697 (ptpp) REVERT: H 323 GLU cc_start: 0.7913 (pm20) cc_final: 0.7522 (pm20) REVERT: I 82 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8329 (tptp) REVERT: I 117 LYS cc_start: 0.9044 (tppp) cc_final: 0.8503 (ttmt) REVERT: I 382 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: J 295 ASN cc_start: 0.8201 (t0) cc_final: 0.7728 (t0) REVERT: J 391 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8572 (t0) REVERT: K 109 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8438 (m-30) REVERT: K 153 GLU cc_start: 0.8465 (tp30) cc_final: 0.8265 (tt0) REVERT: K 165 ASP cc_start: 0.8747 (t0) cc_final: 0.8181 (p0) REVERT: K 217 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7834 (mptt) REVERT: K 310 ASP cc_start: 0.8367 (t0) cc_final: 0.7400 (t0) REVERT: K 357 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7809 (mp0) REVERT: K 416 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7982 (m-10) REVERT: L 10 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8738 (pmmt) REVERT: L 153 GLU cc_start: 0.8636 (mp0) cc_final: 0.8145 (mp0) REVERT: L 207 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8325 (ttm-80) REVERT: L 419 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8049 (mm-30) REVERT: M 37 ASN cc_start: 0.8718 (t0) cc_final: 0.8262 (t0) REVERT: M 76 LEU cc_start: 0.9479 (mt) cc_final: 0.9203 (mt) REVERT: M 82 LYS cc_start: 0.9177 (mppt) cc_final: 0.8521 (ttpp) REVERT: M 108 MET cc_start: 0.8328 (mmm) cc_final: 0.7421 (ptt) REVERT: M 207 ARG cc_start: 0.8423 (ttp80) cc_final: 0.7810 (ttp80) REVERT: M 326 GLN cc_start: 0.7573 (pp30) cc_final: 0.7215 (pp30) REVERT: N 77 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7022 (p0) REVERT: N 197 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: N 321 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.8026 (m90) REVERT: O 114 GLU cc_start: 0.5335 (OUTLIER) cc_final: 0.3954 (mp0) REVERT: O 166 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8456 (t0) REVERT: O 305 PHE cc_start: 0.8548 (t80) cc_final: 0.8114 (t80) REVERT: O 323 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7578 (mt-10) REVERT: O 370 GLN cc_start: 0.8740 (pp30) cc_final: 0.8489 (pp30) REVERT: O 382 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7849 (mp0) REVERT: P 75 PHE cc_start: 0.7258 (t80) cc_final: 0.6242 (t80) REVERT: P 133 TYR cc_start: 0.6409 (p90) cc_final: 0.5891 (p90) REVERT: P 150 ASN cc_start: 0.7660 (t0) cc_final: 0.7035 (t0) REVERT: P 153 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8726 (tt0) REVERT: P 163 HIS cc_start: 0.9151 (t-90) cc_final: 0.8660 (t-90) REVERT: P 270 TYR cc_start: 0.5640 (OUTLIER) cc_final: 0.4985 (m-80) REVERT: P 280 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: P 318 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8498 (mmt) REVERT: P 331 GLU cc_start: 0.8387 (pt0) cc_final: 0.7845 (pm20) REVERT: Q 22 GLN cc_start: 0.8555 (mm110) cc_final: 0.7763 (pm20) REVERT: Q 165 ASP cc_start: 0.8892 (t0) cc_final: 0.8484 (t0) REVERT: Q 323 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8087 (mt-10) REVERT: Q 342 ILE cc_start: 0.8557 (mm) cc_final: 0.8338 (mp) REVERT: Q 344 ASP cc_start: 0.8809 (m-30) cc_final: 0.8360 (m-30) REVERT: Q 382 GLU cc_start: 0.8753 (mp0) cc_final: 0.8100 (mp0) REVERT: Q 416 PHE cc_start: 0.8954 (t80) cc_final: 0.8721 (t80) REVERT: R 10 LYS cc_start: 0.8323 (pptt) cc_final: 0.7934 (pmtt) REVERT: R 44 SER cc_start: 0.8211 (t) cc_final: 0.7430 (p) REVERT: R 224 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9198 (t) REVERT: R 237 ASN cc_start: 0.8589 (m-40) cc_final: 0.8340 (m-40) REVERT: R 275 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8390 (mm110) outliers start: 218 outliers final: 117 residues processed: 798 average time/residue: 1.2509 time to fit residues: 1385.1384 Evaluate side-chains 736 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 583 time to evaluate : 6.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 536 PHE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 291 TYR Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 77 TYR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 322 LYS Chi-restraints excluded: chain H residue 421 PHE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain I residue 82 LYS Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 404 SER Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 143 CYS Chi-restraints excluded: chain J residue 261 TYR Chi-restraints excluded: chain J residue 391 ASN Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 217 LYS Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 227 TYR Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 337 SER Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 416 PHE Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LYS Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 197 GLU Chi-restraints excluded: chain N residue 321 HIS Chi-restraints excluded: chain N residue 331 GLU Chi-restraints excluded: chain N residue 392 PHE Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 278 SER Chi-restraints excluded: chain O residue 294 SER Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 394 ASN Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 270 TYR Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 318 MET Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 294 SER Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 366 ASN Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 253 LYS Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 278 SER Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 690 optimal weight: 3.9990 chunk 348 optimal weight: 7.9990 chunk 590 optimal weight: 0.9990 chunk 746 optimal weight: 0.7980 chunk 355 optimal weight: 0.0570 chunk 782 optimal weight: 0.5980 chunk 630 optimal weight: 4.9990 chunk 699 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 566 optimal weight: 3.9990 chunk 188 optimal weight: 20.0000 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 HIS E 213 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN ** L 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 306 ASN ** O 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.141495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094433 restraints weight = 139414.817| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.01 r_work: 0.3267 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 71396 Z= 0.231 Angle : 0.666 17.290 96304 Z= 0.341 Chirality : 0.045 0.398 10462 Planarity : 0.003 0.059 12399 Dihedral : 6.865 89.390 9348 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.33 % Favored : 92.55 % Rotamer: Outliers : 2.37 % Allowed : 31.12 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.46 (0.09), residues: 8381 helix: 0.18 (0.09), residues: 3470 sheet: -2.40 (0.15), residues: 1030 loop : -1.58 (0.10), residues: 3881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP P 125 HIS 0.016 0.001 HIS J 105 PHE 0.047 0.002 PHE B 96 TYR 0.026 0.001 TYR A 192 ARG 0.009 0.001 ARG M 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16762 Ramachandran restraints generated. 8381 Oldfield, 0 Emsley, 8381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 592 time to evaluate : 6.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8687 (t70) cc_final: 0.8188 (t0) REVERT: A 158 THR cc_start: 0.5530 (OUTLIER) cc_final: 0.5023 (p) REVERT: A 384 ASN cc_start: 0.5505 (m-40) cc_final: 0.4749 (p0) REVERT: A 519 ASN cc_start: 0.8638 (t0) cc_final: 0.8268 (t0) REVERT: A 530 TYR cc_start: 0.7059 (t80) cc_final: 0.6582 (t80) REVERT: B 88 MET cc_start: 0.8688 (ttp) cc_final: 0.8388 (ttp) REVERT: B 96 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7611 (t80) REVERT: B 282 ASP cc_start: 0.6637 (t0) cc_final: 0.6247 (p0) REVERT: B 436 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6599 (tp30) REVERT: B 451 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7428 (t80) REVERT: B 517 GLN cc_start: 0.8234 (mm-40) cc_final: 0.8012 (mm-40) REVERT: B 543 GLU cc_start: 0.7914 (tp30) cc_final: 0.7153 (tm-30) REVERT: B 561 ARG cc_start: 0.8552 (ttt-90) cc_final: 0.8162 (ptp-170) REVERT: C 14 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8174 (mttp) REVERT: C 67 LEU cc_start: 0.4418 (OUTLIER) cc_final: 0.3821 (mm) REVERT: C 189 HIS cc_start: 0.7870 (t-170) cc_final: 0.7459 (t70) REVERT: C 216 MET cc_start: 0.8522 (ttm) cc_final: 0.8049 (tpt) REVERT: C 222 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7920 (mp) REVERT: C 298 MET cc_start: 0.3684 (ptt) cc_final: 0.2010 (ptm) REVERT: C 366 LEU cc_start: 0.8230 (mt) cc_final: 0.7977 (pt) REVERT: C 423 MET cc_start: 0.8594 (ptp) cc_final: 0.8366 (ptm) REVERT: C 437 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7629 (tp30) REVERT: C 441 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6739 (m-10) REVERT: C 455 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8050 (pt0) REVERT: D 395 TYR cc_start: 0.5852 (m-80) cc_final: 0.5523 (m-80) REVERT: D 411 PHE cc_start: 0.8013 (t80) cc_final: 0.7654 (t80) REVERT: D 447 GLU cc_start: 0.3985 (OUTLIER) cc_final: 0.2566 (pm20) REVERT: D 457 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5818 (p90) REVERT: D 469 CYS cc_start: 0.7081 (m) cc_final: 0.6626 (m) REVERT: D 536 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8270 (t80) REVERT: E 117 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8617 (mt-10) REVERT: E 131 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7091 (tp) REVERT: E 142 PHE cc_start: 0.6443 (m-80) cc_final: 0.6196 (m-10) REVERT: E 216 MET cc_start: 0.6231 (ttp) cc_final: 0.5702 (tpp) REVERT: E 291 TYR cc_start: 0.1185 (OUTLIER) cc_final: 0.0676 (m-80) REVERT: E 340 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6978 (mm) REVERT: E 407 PHE cc_start: 0.8909 (t80) cc_final: 0.7949 (t80) REVERT: E 486 LEU cc_start: 0.8880 (tp) cc_final: 0.8462 (tp) REVERT: E 492 TYR cc_start: 0.7353 (m-80) cc_final: 0.6826 (m-80) REVERT: E 505 TYR cc_start: 0.7943 (t80) cc_final: 0.7350 (t80) REVERT: E 510 ILE cc_start: 0.8910 (mt) cc_final: 0.8530 (mp) REVERT: E 545 PHE cc_start: 0.8416 (m-10) cc_final: 0.7369 (m-10) REVERT: E 546 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6508 (tm-30) REVERT: F 40 ILE cc_start: 0.8973 (pt) cc_final: 0.8664 (pp) REVERT: F 56 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: F 61 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8627 (mt-10) REVERT: F 80 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8051 (mtp85) REVERT: F 122 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7795 (t-170) REVERT: F 216 MET cc_start: 0.7973 (tmm) cc_final: 0.7372 (tmm) REVERT: F 268 THR cc_start: 0.2792 (OUTLIER) cc_final: 0.2496 (p) REVERT: F 269 ASP cc_start: 0.3768 (OUTLIER) cc_final: 0.3217 (m-30) REVERT: F 500 ASN cc_start: 0.8832 (t0) cc_final: 0.8594 (t0) REVERT: F 504 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8271 (tm-30) REVERT: F 506 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8608 (mp) REVERT: F 519 ASN cc_start: 0.8737 (m-40) cc_final: 0.8204 (t0) REVERT: F 534 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8053 (mp0) REVERT: G 22 GLN cc_start: 0.8886 (tp40) cc_final: 0.8570 (tp-100) REVERT: G 37 ASN cc_start: 0.9015 (t0) cc_final: 0.8422 (t0) REVERT: G 92 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6430 (pm20) REVERT: G 128 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7162 (mpp) REVERT: G 217 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8423 (mppt) REVERT: G 301 GLN cc_start: 0.8609 (mt0) cc_final: 0.8349 (mt0) REVERT: G 323 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8175 (mt-10) REVERT: H 54 MET cc_start: 0.8739 (tpp) cc_final: 0.8448 (ttm) REVERT: H 86 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8679 (tptp) REVERT: H 139 ASN cc_start: 0.8398 (t0) cc_final: 0.7767 (m110) REVERT: H 322 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7734 (ptpp) REVERT: H 323 GLU cc_start: 0.7910 (pm20) cc_final: 0.7516 (pm20) REVERT: I 82 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8332 (tptp) REVERT: I 117 LYS cc_start: 0.8998 (tppp) cc_final: 0.8463 (ttmt) REVERT: I 304 ASP cc_start: 0.7740 (p0) cc_final: 0.7476 (p0) REVERT: I 382 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: J 295 ASN cc_start: 0.8231 (t0) cc_final: 0.7779 (t0) REVERT: J 391 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8574 (t0) REVERT: K 82 LYS cc_start: 0.9017 (mppt) cc_final: 0.8142 (tppp) REVERT: K 109 ASP cc_start: 0.8934 (m-30) cc_final: 0.8455 (m-30) REVERT: K 153 GLU cc_start: 0.8470 (tp30) cc_final: 0.7861 (tp30) REVERT: K 165 ASP cc_start: 0.8754 (t0) cc_final: 0.8165 (p0) REVERT: K 217 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7833 (mptt) REVERT: K 310 ASP cc_start: 0.8346 (t0) cc_final: 0.7373 (t0) REVERT: K 357 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7810 (mp0) REVERT: K 416 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7985 (m-10) REVERT: L 10 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8741 (pmmt) REVERT: L 153 GLU cc_start: 0.8619 (mp0) cc_final: 0.8133 (mp0) REVERT: L 207 ARG cc_start: 0.8663 (mtp85) cc_final: 0.8228 (ttm-80) REVERT: L 419 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8072 (mm-30) REVERT: M 37 ASN cc_start: 0.8708 (t0) cc_final: 0.8264 (t0) REVERT: M 44 SER cc_start: 0.8455 (m) cc_final: 0.7775 (p) REVERT: M 76 LEU cc_start: 0.9485 (mt) cc_final: 0.9221 (mt) REVERT: M 82 LYS cc_start: 0.9193 (mppt) cc_final: 0.8535 (ttpp) REVERT: M 108 MET cc_start: 0.8329 (mmm) cc_final: 0.7408 (ptp) REVERT: M 207 ARG cc_start: 0.8396 (ttp80) cc_final: 0.7795 (ttp80) REVERT: M 227 TYR cc_start: 0.9146 (OUTLIER) cc_final: 0.8924 (m-80) REVERT: M 326 GLN cc_start: 0.7604 (pp30) cc_final: 0.7292 (pp30) REVERT: N 77 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7060 (p0) REVERT: N 197 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: N 321 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.8026 (m90) REVERT: N 392 PHE cc_start: 0.4953 (OUTLIER) cc_final: 0.3735 (p90) REVERT: O 89 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8727 (pp20) REVERT: O 114 GLU cc_start: 0.5331 (OUTLIER) cc_final: 0.3958 (mp0) REVERT: O 165 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8358 (t0) REVERT: O 305 PHE cc_start: 0.8549 (t80) cc_final: 0.8093 (t80) REVERT: O 323 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7608 (mt-10) REVERT: O 370 GLN cc_start: 0.8767 (pp30) cc_final: 0.8514 (pp30) REVERT: O 382 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7879 (mp0) REVERT: P 75 PHE cc_start: 0.7256 (t80) cc_final: 0.6230 (t80) REVERT: P 133 TYR cc_start: 0.6405 (p90) cc_final: 0.6022 (p90) REVERT: P 150 ASN cc_start: 0.7630 (t0) cc_final: 0.6845 (t0) REVERT: P 153 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8735 (tt0) REVERT: P 163 HIS cc_start: 0.9157 (t-90) cc_final: 0.8672 (t-90) REVERT: P 270 TYR cc_start: 0.5708 (OUTLIER) cc_final: 0.5035 (m-80) REVERT: P 280 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: P 318 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8474 (mmt) REVERT: P 331 GLU cc_start: 0.8383 (pt0) cc_final: 0.7854 (pm20) REVERT: Q 22 GLN cc_start: 0.8525 (mm110) cc_final: 0.7717 (pm20) REVERT: Q 165 ASP cc_start: 0.8919 (t0) cc_final: 0.8523 (t0) REVERT: Q 323 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7993 (mt-10) REVERT: Q 342 ILE cc_start: 0.8593 (mm) cc_final: 0.8371 (mp) REVERT: Q 344 ASP cc_start: 0.8817 (m-30) cc_final: 0.8372 (m-30) REVERT: Q 382 GLU cc_start: 0.8740 (mp0) cc_final: 0.8111 (mp0) REVERT: R 10 LYS cc_start: 0.8315 (pptt) cc_final: 0.7921 (pmtt) REVERT: R 44 SER cc_start: 0.8222 (t) cc_final: 0.7430 (p) REVERT: R 224 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9212 (t) REVERT: R 237 ASN cc_start: 0.8610 (m-40) cc_final: 0.8358 (m-40) REVERT: R 275 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8408 (mm110) outliers start: 186 outliers final: 119 residues processed: 741 average time/residue: 1.2606 time to fit residues: 1299.3013 Evaluate side-chains 737 residues out of total 7850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 580 time to evaluate : 6.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 381 PHE Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 536 PHE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 291 TYR Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 77 TYR Chi-restraints excluded: chain F residue 122 HIS Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 322 LYS Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 421 PHE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain I residue 82 LYS Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 382 GLU Chi-restraints excluded: chain I residue 404 SER Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 143 CYS Chi-restraints excluded: chain J residue 261 TYR Chi-restraints excluded: chain J residue 391 ASN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 189 VAL Chi-restraints excluded: chain K residue 217 LYS Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 227 TYR Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 416 PHE Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 189 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 74 LYS Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 197 GLU Chi-restraints excluded: chain N residue 321 HIS Chi-restraints excluded: chain N residue 331 GLU Chi-restraints excluded: chain N residue 392 PHE Chi-restraints excluded: chain O residue 89 GLU Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 165 ASP Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 278 SER Chi-restraints excluded: chain O residue 294 SER Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 394 ASN Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 270 TYR Chi-restraints excluded: chain P residue 280 GLU Chi-restraints excluded: chain P residue 318 MET Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 294 SER Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 366 ASN Chi-restraints excluded: chain Q residue 419 GLU Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 253 LYS Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 278 SER Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 439 optimal weight: 0.6980 chunk 239 optimal weight: 7.9990 chunk 577 optimal weight: 3.9990 chunk 755 optimal weight: 20.0000 chunk 689 optimal weight: 0.0980 chunk 751 optimal weight: 2.9990 chunk 655 optimal weight: 2.9990 chunk 739 optimal weight: 0.9980 chunk 761 optimal weight: 0.9990 chunk 733 optimal weight: 0.9980 chunk 832 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B 500 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN ** O 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.141682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.094816 restraints weight = 139797.015| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.91 r_work: 0.3284 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 71396 Z= 0.260 Angle : 0.714 59.190 96304 Z= 0.383 Chirality : 0.047 1.215 10462 Planarity : 0.004 0.165 12399 Dihedral : 6.870 89.423 9348 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.41 % Favored : 92.47 % Rotamer: Outliers : 2.50 % Allowed : 31.01 % Favored : 66.49 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.45 (0.09), residues: 8381 helix: 0.19 (0.09), residues: 3469 sheet: -2.40 (0.15), residues: 1030 loop : -1.57 (0.10), residues: 3882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP P 125 HIS 0.015 0.001 HIS J 105 PHE 0.329 0.002 PHE C 516 TYR 0.039 0.001 TYR I 133 ARG 0.009 0.000 ARG N 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54764.04 seconds wall clock time: 937 minutes 32.98 seconds (56252.98 seconds total)