Starting phenix.real_space_refine on Mon Dec 30 05:36:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wux_37863/12_2024/8wux_37863.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wux_37863/12_2024/8wux_37863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wux_37863/12_2024/8wux_37863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wux_37863/12_2024/8wux_37863.map" model { file = "/net/cci-nas-00/data/ceres_data/8wux_37863/12_2024/8wux_37863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wux_37863/12_2024/8wux_37863.cif" } resolution = 2.6 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= 0.016 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: 7 Type Number sf(0) Gaussians K 7 8.98 5 P 42 5.49 5 Mg 14 5.21 5 S 154 5.16 5 C 38262 2.51 5 N 10521 2.21 5 O 12026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 256 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 61026 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "H" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "a" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "B" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "I" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "b" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "C" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "J" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "c" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "D" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "K" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "d" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "E" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "L" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "e" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "F" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "M" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "f" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "G" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "N" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "g" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 27.23, per 1000 atoms: 0.45 Number of scatterers: 61026 At special positions: 0 Unit cell: (166.944, 169.2, 221.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 7 19.00 S 154 16.00 P 42 15.00 Mg 14 11.99 O 12026 8.00 N 10521 7.00 C 38262 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.32 Conformation dependent library (CDL) restraints added in 6.3 seconds 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14700 Finding SS restraints... Secondary structure from input PDB file: 339 helices and 101 sheets defined 56.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.72 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.703A pdb=" N ALA A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.810A pdb=" N GLU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 85 removed outlier: 3.616A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.554A pdb=" N PHE A 204 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.769A pdb=" N LEU A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.510A pdb=" N ASN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.994A pdb=" N THR A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 297 removed outlier: 4.361A pdb=" N TYR A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.583A pdb=" N VAL A 312 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 removed outlier: 3.520A pdb=" N ARG A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.989A pdb=" N GLU A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 410 removed outlier: 3.631A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 424 removed outlier: 3.519A pdb=" N GLU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 428 Processing helix chain 'A' and resid 433 through 448 removed outlier: 3.610A pdb=" N ARG A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.847A pdb=" N ARG A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 removed outlier: 4.201A pdb=" N LYS A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 501 through 520 removed outlier: 3.763A pdb=" N THR A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 28 removed outlier: 3.637A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 53 through 60 removed outlier: 3.644A pdb=" N GLU H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 86 removed outlier: 3.618A pdb=" N GLY H 70 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 109 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 removed outlier: 3.514A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 244 removed outlier: 3.701A pdb=" N LEU H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) Proline residue: H 235 - end of helix removed outlier: 3.623A pdb=" N VAL H 241 " --> pdb=" O LEU H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 266 removed outlier: 3.675A pdb=" N VAL H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 296 removed outlier: 3.524A pdb=" N TYR H 288 " --> pdb=" O ARG H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 306 Processing helix chain 'H' and resid 308 through 312 removed outlier: 3.814A pdb=" N VAL H 312 " --> pdb=" O LEU H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 356 removed outlier: 4.124A pdb=" N GLN H 348 " --> pdb=" O ALA H 344 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE H 349 " --> pdb=" O ARG H 345 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU H 354 " --> pdb=" O LYS H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 365 removed outlier: 3.923A pdb=" N LYS H 364 " --> pdb=" O TYR H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 374 removed outlier: 3.650A pdb=" N ALA H 370 " --> pdb=" O GLN H 366 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU H 372 " --> pdb=" O ARG H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 410 removed outlier: 3.551A pdb=" N ALA H 394 " --> pdb=" O LYS H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 424 Processing helix chain 'H' and resid 425 through 428 Processing helix chain 'H' and resid 433 through 448 removed outlier: 3.543A pdb=" N ARG H 448 " --> pdb=" O LYS H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 459 removed outlier: 3.783A pdb=" N ARG H 452 " --> pdb=" O ARG H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 476 removed outlier: 4.012A pdb=" N LYS H 474 " --> pdb=" O LEU H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 496 Processing helix chain 'H' and resid 501 through 520 removed outlier: 3.544A pdb=" N THR H 520 " --> pdb=" O GLY H 516 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 34 removed outlier: 3.734A pdb=" N LYS a 34 " --> pdb=" O ASP a 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.648A pdb=" N ALA B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 59 removed outlier: 3.783A pdb=" N GLU B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 85 removed outlier: 3.501A pdb=" N GLY B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.628A pdb=" N LEU B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.609A pdb=" N ASN B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 269 removed outlier: 4.046A pdb=" N THR B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 removed outlier: 3.667A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 287 " --> pdb=" O GLN B 283 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 340 through 356 removed outlier: 4.050A pdb=" N ALA B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 363 through 374 removed outlier: 4.285A pdb=" N LEU B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 410 removed outlier: 3.695A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 424 removed outlier: 3.526A pdb=" N GLU B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 428 Processing helix chain 'B' and resid 433 through 448 removed outlier: 3.631A pdb=" N ARG B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.868A pdb=" N ARG B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 476 removed outlier: 4.304A pdb=" N LYS B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 501 through 520 removed outlier: 3.782A pdb=" N THR B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 28 removed outlier: 3.588A pdb=" N ALA I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 53 through 60 removed outlier: 3.626A pdb=" N GLU I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 86 removed outlier: 3.643A pdb=" N GLY I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 109 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.694A pdb=" N PHE I 204 " --> pdb=" O SER I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 244 removed outlier: 3.571A pdb=" N LEU I 233 " --> pdb=" O ASN I 229 " (cutoff:3.500A) Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 258 through 266 removed outlier: 4.669A pdb=" N VAL I 264 " --> pdb=" O ALA I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 296 removed outlier: 3.795A pdb=" N ASP I 287 " --> pdb=" O GLN I 283 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE I 292 " --> pdb=" O TYR I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 306 Processing helix chain 'I' and resid 313 through 317 Processing helix chain 'I' and resid 338 through 351 removed outlier: 3.880A pdb=" N GLU I 347 " --> pdb=" O GLN I 343 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN I 348 " --> pdb=" O ALA I 344 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE I 349 " --> pdb=" O ARG I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 356 Processing helix chain 'I' and resid 367 through 374 Processing helix chain 'I' and resid 385 through 410 removed outlier: 3.503A pdb=" N ARG I 395 " --> pdb=" O GLU I 391 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 424 Processing helix chain 'I' and resid 425 through 428 Processing helix chain 'I' and resid 433 through 448 removed outlier: 3.541A pdb=" N ARG I 448 " --> pdb=" O LYS I 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 459 removed outlier: 3.807A pdb=" N ARG I 452 " --> pdb=" O ARG I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 476 removed outlier: 4.173A pdb=" N LYS I 474 " --> pdb=" O LEU I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 496 Processing helix chain 'I' and resid 501 through 520 removed outlier: 3.582A pdb=" N THR I 520 " --> pdb=" O GLY I 516 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 34 removed outlier: 3.618A pdb=" N LYS b 34 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.689A pdb=" N ALA C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.664A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 85 removed outlier: 3.535A pdb=" N GLY C 70 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 229 through 244 Proline residue: C 235 - end of helix removed outlier: 3.838A pdb=" N ARG C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 269 removed outlier: 4.509A pdb=" N THR C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 296 removed outlier: 4.317A pdb=" N LYS C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP C 287 " --> pdb=" O GLN C 283 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR C 288 " --> pdb=" O ARG C 284 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 340 through 356 removed outlier: 4.064A pdb=" N ALA C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU C 347 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 363 through 374 removed outlier: 4.081A pdb=" N LEU C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 372 " --> pdb=" O ARG C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 410 removed outlier: 3.831A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 424 removed outlier: 3.536A pdb=" N GLU C 424 " --> pdb=" O VAL C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 428 Processing helix chain 'C' and resid 433 through 448 removed outlier: 3.786A pdb=" N ARG C 448 " --> pdb=" O LYS C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.854A pdb=" N ARG C 452 " --> pdb=" O ARG C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 476 removed outlier: 4.194A pdb=" N LYS C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 501 through 520 removed outlier: 3.806A pdb=" N THR C 520 " --> pdb=" O GLY C 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 28 removed outlier: 3.594A pdb=" N ALA J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 53 through 60 removed outlier: 3.697A pdb=" N GLU J 59 " --> pdb=" O THR J 55 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 86 removed outlier: 3.663A pdb=" N GLY J 70 " --> pdb=" O TYR J 66 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 109 Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 Processing helix chain 'J' and resid 229 through 244 Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 258 through 268 removed outlier: 3.918A pdb=" N VAL J 263 " --> pdb=" O LEU J 259 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL J 264 " --> pdb=" O ALA J 260 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE J 267 " --> pdb=" O VAL J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 296 Processing helix chain 'J' and resid 302 through 306 removed outlier: 3.633A pdb=" N GLY J 306 " --> pdb=" O GLU J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 312 removed outlier: 4.001A pdb=" N VAL J 312 " --> pdb=" O LEU J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 351 removed outlier: 3.829A pdb=" N GLN J 348 " --> pdb=" O ALA J 344 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE J 349 " --> pdb=" O ARG J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 356 Processing helix chain 'J' and resid 367 through 374 removed outlier: 3.574A pdb=" N GLY J 374 " --> pdb=" O ALA J 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 410 removed outlier: 3.768A pdb=" N GLU J 391 " --> pdb=" O ALA J 387 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA J 394 " --> pdb=" O LYS J 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 424 Processing helix chain 'J' and resid 425 through 428 Processing helix chain 'J' and resid 433 through 448 removed outlier: 3.526A pdb=" N ARG J 448 " --> pdb=" O LYS J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 459 removed outlier: 3.799A pdb=" N ARG J 452 " --> pdb=" O ARG J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 476 removed outlier: 4.075A pdb=" N LYS J 474 " --> pdb=" O LEU J 470 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 496 Processing helix chain 'J' and resid 501 through 520 removed outlier: 3.524A pdb=" N THR J 520 " --> pdb=" O GLY J 516 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 34 removed outlier: 3.662A pdb=" N LYS c 34 " --> pdb=" O ASP c 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 28 removed outlier: 3.660A pdb=" N ALA D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.804A pdb=" N GLU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 85 removed outlier: 3.641A pdb=" N MET D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY D 70 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 229 through 244 removed outlier: 4.043A pdb=" N LEU D 233 " --> pdb=" O ASN D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.739A pdb=" N VAL D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG D 242 " --> pdb=" O GLU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.805A pdb=" N THR D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 297 removed outlier: 4.235A pdb=" N ASP D 287 " --> pdb=" O GLN D 283 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR D 288 " --> pdb=" O ARG D 284 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 removed outlier: 4.083A pdb=" N LYS D 350 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG D 351 " --> pdb=" O GLU D 347 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 357 Processing helix chain 'D' and resid 363 through 374 removed outlier: 3.511A pdb=" N GLU D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 410 removed outlier: 3.764A pdb=" N GLU D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 424 removed outlier: 3.540A pdb=" N GLU D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 428 Processing helix chain 'D' and resid 433 through 448 removed outlier: 3.776A pdb=" N ARG D 448 " --> pdb=" O LYS D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.857A pdb=" N ARG D 452 " --> pdb=" O ARG D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 476 removed outlier: 4.291A pdb=" N LYS D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 501 through 520 removed outlier: 3.769A pdb=" N THR D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 28 removed outlier: 3.573A pdb=" N ALA K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 53 through 60 removed outlier: 3.608A pdb=" N GLU K 59 " --> pdb=" O THR K 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 removed outlier: 3.597A pdb=" N GLY K 70 " --> pdb=" O TYR K 66 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 109 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 removed outlier: 3.602A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 229 through 244 removed outlier: 3.504A pdb=" N LEU K 233 " --> pdb=" O ASN K 229 " (cutoff:3.500A) Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 258 through 266 removed outlier: 4.499A pdb=" N VAL K 264 " --> pdb=" O ALA K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 283 No H-bonds generated for 'chain 'K' and resid 281 through 283' Processing helix chain 'K' and resid 284 through 297 removed outlier: 3.751A pdb=" N TYR K 288 " --> pdb=" O ARG K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 312 Processing helix chain 'K' and resid 338 through 356 removed outlier: 4.514A pdb=" N LEU K 354 " --> pdb=" O LYS K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 365 removed outlier: 3.790A pdb=" N ARG K 362 " --> pdb=" O SER K 358 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 374 Processing helix chain 'K' and resid 385 through 410 removed outlier: 3.697A pdb=" N GLU K 391 " --> pdb=" O ALA K 387 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA K 394 " --> pdb=" O LYS K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 424 Processing helix chain 'K' and resid 425 through 428 Processing helix chain 'K' and resid 433 through 448 removed outlier: 3.512A pdb=" N ARG K 448 " --> pdb=" O LYS K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 459 removed outlier: 3.804A pdb=" N ARG K 452 " --> pdb=" O ARG K 448 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 476 removed outlier: 4.066A pdb=" N LYS K 474 " --> pdb=" O LEU K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 496 Processing helix chain 'K' and resid 501 through 520 Processing helix chain 'd' and resid 30 through 34 removed outlier: 3.789A pdb=" N LYS d 34 " --> pdb=" O ASP d 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 28 removed outlier: 3.727A pdb=" N ALA E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.947A pdb=" N GLU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 85 removed outlier: 3.672A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.644A pdb=" N LEU E 233 " --> pdb=" O ASN E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.570A pdb=" N ARG E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 268 removed outlier: 3.569A pdb=" N THR E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 removed outlier: 4.368A pdb=" N LYS E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP E 287 " --> pdb=" O GLN E 283 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 341 through 356 removed outlier: 3.599A pdb=" N ARG E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 363 through 374 removed outlier: 3.733A pdb=" N LEU E 369 " --> pdb=" O LEU E 365 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 372 " --> pdb=" O ARG E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 410 removed outlier: 3.674A pdb=" N GLU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 424 removed outlier: 3.514A pdb=" N GLU E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 428 Processing helix chain 'E' and resid 433 through 448 removed outlier: 3.734A pdb=" N ARG E 448 " --> pdb=" O LYS E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.849A pdb=" N ARG E 452 " --> pdb=" O ARG E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 476 removed outlier: 4.281A pdb=" N LYS E 474 " --> pdb=" O LEU E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 496 Processing helix chain 'E' and resid 501 through 520 removed outlier: 3.796A pdb=" N THR E 520 " --> pdb=" O GLY E 516 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 28 removed outlier: 3.601A pdb=" N ALA L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 53 through 60 removed outlier: 3.699A pdb=" N GLU L 59 " --> pdb=" O THR L 55 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 86 removed outlier: 3.653A pdb=" N GLY L 70 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 109 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 168 Processing helix chain 'L' and resid 201 through 205 removed outlier: 3.669A pdb=" N PHE L 204 " --> pdb=" O SER L 201 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL L 205 " --> pdb=" O PRO L 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 201 through 205' Processing helix chain 'L' and resid 230 through 232 No H-bonds generated for 'chain 'L' and resid 230 through 232' Processing helix chain 'L' and resid 233 through 244 removed outlier: 4.085A pdb=" N ASN L 239 " --> pdb=" O PRO L 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 269 removed outlier: 4.148A pdb=" N ILE L 267 " --> pdb=" O VAL L 263 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY L 269 " --> pdb=" O ASN L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 283 No H-bonds generated for 'chain 'L' and resid 281 through 283' Processing helix chain 'L' and resid 284 through 297 removed outlier: 3.900A pdb=" N TYR L 288 " --> pdb=" O ARG L 284 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 306 Processing helix chain 'L' and resid 338 through 356 removed outlier: 3.692A pdb=" N ILE L 342 " --> pdb=" O SER L 338 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU L 354 " --> pdb=" O LYS L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 365 removed outlier: 3.776A pdb=" N LYS L 364 " --> pdb=" O TYR L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 374 removed outlier: 3.702A pdb=" N ALA L 370 " --> pdb=" O GLN L 366 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU L 372 " --> pdb=" O ARG L 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 410 removed outlier: 3.719A pdb=" N GLU L 391 " --> pdb=" O ALA L 387 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 424 Processing helix chain 'L' and resid 425 through 428 Processing helix chain 'L' and resid 433 through 448 removed outlier: 3.523A pdb=" N ARG L 448 " --> pdb=" O LYS L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 459 removed outlier: 3.807A pdb=" N ARG L 452 " --> pdb=" O ARG L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 476 removed outlier: 4.089A pdb=" N LYS L 474 " --> pdb=" O LEU L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 496 Processing helix chain 'L' and resid 501 through 520 removed outlier: 3.562A pdb=" N THR L 520 " --> pdb=" O GLY L 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 3.721A pdb=" N ALA F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.804A pdb=" N GLU F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 60 " --> pdb=" O VAL F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 85 removed outlier: 3.705A pdb=" N GLY F 70 " --> pdb=" O TYR F 66 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 109 removed outlier: 3.520A pdb=" N ARG F 105 " --> pdb=" O ASN F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 232 through 244 removed outlier: 4.268A pdb=" N VAL F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.948A pdb=" N THR F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 296 Processing helix chain 'F' and resid 308 through 312 removed outlier: 3.588A pdb=" N VAL F 312 " --> pdb=" O LEU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 357 removed outlier: 3.521A pdb=" N GLU F 347 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 374 removed outlier: 3.746A pdb=" N LEU F 372 " --> pdb=" O ARG F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 410 removed outlier: 3.706A pdb=" N GLU F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 424 Processing helix chain 'F' and resid 425 through 429 Processing helix chain 'F' and resid 433 through 448 removed outlier: 3.670A pdb=" N ARG F 448 " --> pdb=" O LYS F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.854A pdb=" N ARG F 452 " --> pdb=" O ARG F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 476 removed outlier: 4.271A pdb=" N LYS F 474 " --> pdb=" O LEU F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 501 through 520 removed outlier: 3.826A pdb=" N THR F 520 " --> pdb=" O GLY F 516 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 28 removed outlier: 3.670A pdb=" N ALA M 26 " --> pdb=" O LYS M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 53 through 59 removed outlier: 3.741A pdb=" N GLU M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 86 removed outlier: 3.751A pdb=" N GLY M 70 " --> pdb=" O TYR M 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER M 82 " --> pdb=" O ALA M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 109 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 removed outlier: 3.764A pdb=" N GLY M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 229 through 244 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 258 through 266 removed outlier: 3.755A pdb=" N VAL M 263 " --> pdb=" O LEU M 259 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 296 removed outlier: 4.139A pdb=" N TYR M 288 " --> pdb=" O ARG M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 306 Processing helix chain 'M' and resid 338 through 356 removed outlier: 3.526A pdb=" N ILE M 346 " --> pdb=" O ILE M 342 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU M 347 " --> pdb=" O GLN M 343 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN M 348 " --> pdb=" O ALA M 344 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU M 354 " --> pdb=" O LYS M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 364 removed outlier: 3.917A pdb=" N ARG M 362 " --> pdb=" O SER M 358 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS M 364 " --> pdb=" O TYR M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 374 removed outlier: 4.003A pdb=" N LEU M 369 " --> pdb=" O LEU M 365 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA M 370 " --> pdb=" O GLN M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 410 removed outlier: 3.816A pdb=" N GLU M 391 " --> pdb=" O ALA M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 424 Processing helix chain 'M' and resid 425 through 428 Processing helix chain 'M' and resid 433 through 448 removed outlier: 3.502A pdb=" N ARG M 448 " --> pdb=" O LYS M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 459 removed outlier: 3.797A pdb=" N ARG M 452 " --> pdb=" O ARG M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 476 removed outlier: 3.997A pdb=" N LYS M 474 " --> pdb=" O LEU M 470 " (cutoff:3.500A) Processing helix chain 'M' and resid 492 through 496 Processing helix chain 'M' and resid 501 through 520 Processing helix chain 'f' and resid 30 through 34 removed outlier: 3.513A pdb=" N LYS f 34 " --> pdb=" O ASP f 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 28 removed outlier: 3.628A pdb=" N ALA G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 52 through 59 removed outlier: 3.757A pdb=" N GLU G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 85 removed outlier: 3.649A pdb=" N GLY G 70 " --> pdb=" O TYR G 66 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 109 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 229 through 244 removed outlier: 4.002A pdb=" N LEU G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) Proline residue: G 235 - end of helix removed outlier: 3.559A pdb=" N ARG G 242 " --> pdb=" O GLU G 238 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA G 243 " --> pdb=" O ASN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 268 removed outlier: 3.996A pdb=" N THR G 261 " --> pdb=" O GLU G 257 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU G 262 " --> pdb=" O ALA G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 283 No H-bonds generated for 'chain 'G' and resid 281 through 283' Processing helix chain 'G' and resid 284 through 297 removed outlier: 3.699A pdb=" N TYR G 288 " --> pdb=" O ARG G 284 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN G 290 " --> pdb=" O LYS G 286 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU G 295 " --> pdb=" O ASP G 291 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY G 297 " --> pdb=" O ALA G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 312 removed outlier: 3.575A pdb=" N VAL G 312 " --> pdb=" O LEU G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 317 Processing helix chain 'G' and resid 340 through 357 removed outlier: 3.939A pdb=" N ALA G 344 " --> pdb=" O GLU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 374 removed outlier: 3.757A pdb=" N LEU G 369 " --> pdb=" O LEU G 365 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU G 372 " --> pdb=" O ARG G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 410 removed outlier: 3.749A pdb=" N GLU G 391 " --> pdb=" O ALA G 387 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU G 408 " --> pdb=" O LYS G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 424 removed outlier: 3.511A pdb=" N GLU G 424 " --> pdb=" O VAL G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 Processing helix chain 'G' and resid 433 through 448 removed outlier: 3.705A pdb=" N ARG G 448 " --> pdb=" O LYS G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 458 removed outlier: 3.848A pdb=" N ARG G 452 " --> pdb=" O ARG G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 476 removed outlier: 4.280A pdb=" N LYS G 474 " --> pdb=" O LEU G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 496 Processing helix chain 'G' and resid 501 through 520 removed outlier: 3.794A pdb=" N THR G 520 " --> pdb=" O GLY G 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 28 removed outlier: 3.591A pdb=" N ALA N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 53 through 59 removed outlier: 3.656A pdb=" N GLU N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 86 removed outlier: 3.623A pdb=" N GLY N 70 " --> pdb=" O TYR N 66 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER N 82 " --> pdb=" O ALA N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 109 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 Processing helix chain 'N' and resid 201 through 205 removed outlier: 3.895A pdb=" N PHE N 204 " --> pdb=" O SER N 201 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL N 205 " --> pdb=" O PRO N 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 201 through 205' Processing helix chain 'N' and resid 229 through 244 Proline residue: N 235 - end of helix removed outlier: 3.613A pdb=" N ASN N 239 " --> pdb=" O PRO N 235 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 269 removed outlier: 5.009A pdb=" N VAL N 264 " --> pdb=" O ALA N 260 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE N 267 " --> pdb=" O VAL N 263 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY N 269 " --> pdb=" O ASN N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 297 Processing helix chain 'N' and resid 302 through 306 Processing helix chain 'N' and resid 338 through 356 removed outlier: 4.044A pdb=" N GLU N 347 " --> pdb=" O GLN N 343 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN N 348 " --> pdb=" O ALA N 344 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE N 349 " --> pdb=" O ARG N 345 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU N 354 " --> pdb=" O LYS N 350 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 365 removed outlier: 3.768A pdb=" N LYS N 364 " --> pdb=" O TYR N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 374 Processing helix chain 'N' and resid 385 through 410 removed outlier: 3.748A pdb=" N GLU N 391 " --> pdb=" O ALA N 387 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA N 394 " --> pdb=" O LYS N 390 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 424 Processing helix chain 'N' and resid 425 through 428 Processing helix chain 'N' and resid 433 through 448 removed outlier: 3.515A pdb=" N ARG N 448 " --> pdb=" O LYS N 444 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 459 removed outlier: 3.804A pdb=" N ARG N 452 " --> pdb=" O ARG N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 476 removed outlier: 4.321A pdb=" N LYS N 474 " --> pdb=" O LEU N 470 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 496 Processing helix chain 'N' and resid 501 through 520 removed outlier: 3.696A pdb=" N THR N 520 " --> pdb=" O GLY N 516 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 34 removed outlier: 3.791A pdb=" N LYS g 34 " --> pdb=" O ASP g 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 7.402A pdb=" N ILE G 39 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 524 " --> pdb=" O ILE G 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 7.506A pdb=" N GLU A 37 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 524 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 39 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA B 526 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.672A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.452A pdb=" N LEU A 247 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'A' and resid 480 through 483 Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.242A pdb=" N GLU I 37 " --> pdb=" O ALA H 521 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA H 523 " --> pdb=" O GLU I 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 48 through 50 removed outlier: 7.133A pdb=" N GLU H 37 " --> pdb=" O ALA N 523 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N VAL N 525 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE H 39 " --> pdb=" O VAL N 525 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLU N 527 " --> pdb=" O ILE H 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 175 through 179 removed outlier: 3.650A pdb=" N VAL H 190 " --> pdb=" O VAL H 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 192 through 195 Processing sheet with id=AB3, first strand: chain 'H' and resid 274 through 276 removed outlier: 6.496A pdb=" N LEU H 247 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 274 through 276 removed outlier: 6.496A pdb=" N LEU H 247 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AB6, first strand: chain 'H' and resid 480 through 483 removed outlier: 3.542A pdb=" N ASP H 488 " --> pdb=" O ASP H 483 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'a' and resid 5 through 6 removed outlier: 7.179A pdb=" N VAL b 12 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL b 45 " --> pdb=" O LYS b 10 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS b 10 " --> pdb=" O VAL b 45 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ARG b 15 " --> pdb=" O LYS b 83 " (cutoff:3.500A) removed outlier: 9.515A pdb=" N LYS b 83 " --> pdb=" O ARG b 15 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 85 through 88 removed outlier: 7.556A pdb=" N LYS a 10 " --> pdb=" O VAL a 45 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL a 45 " --> pdb=" O LYS a 10 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL a 12 " --> pdb=" O ILE a 43 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS a 66 " --> pdb=" O VAL a 95 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL a 95 " --> pdb=" O LYS a 66 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL a 68 " --> pdb=" O LEU a 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 49 through 50 removed outlier: 3.701A pdb=" N LYS a 49 " --> pdb=" O VAL a 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 50 removed outlier: 7.428A pdb=" N GLU B 37 " --> pdb=" O GLU C 522 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 524 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 39 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ALA C 526 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 174 through 179 removed outlier: 3.535A pdb=" N VAL B 376 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC4, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.439A pdb=" N LEU B 247 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AC6, first strand: chain 'B' and resid 480 through 483 Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 8 Processing sheet with id=AC8, first strand: chain 'I' and resid 175 through 179 removed outlier: 7.113A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL I 381 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU I 178 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 193 through 195 removed outlier: 4.272A pdb=" N VAL I 323 " --> pdb=" O LEU I 215 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU I 215 " --> pdb=" O VAL I 323 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 274 through 277 removed outlier: 6.167A pdb=" N LEU I 247 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY I 318 " --> pdb=" O ILE I 220 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AD3, first strand: chain 'I' and resid 480 through 483 removed outlier: 3.798A pdb=" N ASP I 488 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'b' and resid 5 through 6 removed outlier: 7.096A pdb=" N VAL c 68 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL c 95 " --> pdb=" O LYS c 66 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS c 66 " --> pdb=" O VAL c 95 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL c 12 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL c 45 " --> pdb=" O LYS c 10 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LYS c 10 " --> pdb=" O VAL c 45 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b' and resid 49 through 50 removed outlier: 3.539A pdb=" N LYS b 49 " --> pdb=" O VAL b 57 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 50 removed outlier: 7.496A pdb=" N GLU C 37 " --> pdb=" O GLU D 522 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU D 524 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE C 39 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA D 526 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 174 through 179 removed outlier: 6.577A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 376 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 193 through 195 Processing sheet with id=AD9, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.279A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY C 318 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AE2, first strand: chain 'C' and resid 480 through 483 Processing sheet with id=AE3, first strand: chain 'J' and resid 4 through 8 removed outlier: 7.516A pdb=" N ILE K 39 " --> pdb=" O GLU J 522 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU J 524 " --> pdb=" O ILE K 39 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 175 through 179 removed outlier: 6.601A pdb=" N THR J 176 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL J 381 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU J 178 " --> pdb=" O VAL J 381 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 193 through 195 removed outlier: 3.501A pdb=" N ILE J 332 " --> pdb=" O MET J 193 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL J 323 " --> pdb=" O LEU J 215 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA J 213 " --> pdb=" O VAL J 325 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 274 through 277 removed outlier: 5.720A pdb=" N LEU J 247 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL J 276 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE J 249 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AE8, first strand: chain 'J' and resid 480 through 483 Processing sheet with id=AE9, first strand: chain 'c' and resid 5 through 6 removed outlier: 6.850A pdb=" N VAL d 68 " --> pdb=" O LEU d 93 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL d 95 " --> pdb=" O LYS d 66 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS d 66 " --> pdb=" O VAL d 95 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL d 12 " --> pdb=" O ILE d 43 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL d 45 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LYS d 10 " --> pdb=" O VAL d 45 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG d 15 " --> pdb=" O LYS d 83 " (cutoff:3.500A) removed outlier: 9.848A pdb=" N LYS d 83 " --> pdb=" O ARG d 15 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 48 through 50 removed outlier: 7.458A pdb=" N GLU D 37 " --> pdb=" O GLU E 522 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU E 524 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE D 39 " --> pdb=" O LEU E 524 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ALA E 526 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 174 through 179 removed outlier: 6.641A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.532A pdb=" N ASN D 329 " --> pdb=" O ASP D 326 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.507A pdb=" N LEU D 247 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 226 through 227 Processing sheet with id=AF6, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AF7, first strand: chain 'D' and resid 480 through 483 Processing sheet with id=AF8, first strand: chain 'K' and resid 4 through 8 removed outlier: 7.450A pdb=" N ILE L 39 " --> pdb=" O GLU K 522 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU K 524 " --> pdb=" O ILE L 39 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 175 through 179 removed outlier: 6.793A pdb=" N THR K 176 " --> pdb=" O ILE K 379 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL K 381 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU K 178 " --> pdb=" O VAL K 381 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 193 through 195 removed outlier: 3.989A pdb=" N MET K 193 " --> pdb=" O ILE K 332 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE K 332 " --> pdb=" O MET K 193 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR K 330 " --> pdb=" O PHE K 195 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL K 323 " --> pdb=" O LEU K 215 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 274 through 276 removed outlier: 6.551A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AG4, first strand: chain 'K' and resid 480 through 483 removed outlier: 3.819A pdb=" N ASP K 488 " --> pdb=" O ASP K 483 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 5 through 6 removed outlier: 3.659A pdb=" N ALA e 94 " --> pdb=" O VAL e 68 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL e 12 " --> pdb=" O ILE e 43 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL e 45 " --> pdb=" O LYS e 10 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LYS e 10 " --> pdb=" O VAL e 45 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG e 15 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N LYS e 83 " --> pdb=" O ARG e 15 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'd' and resid 49 through 50 removed outlier: 3.614A pdb=" N LYS d 49 " --> pdb=" O VAL d 57 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL d 57 " --> pdb=" O LYS d 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'E' and resid 48 through 50 removed outlier: 7.468A pdb=" N GLU E 37 " --> pdb=" O GLU F 522 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU F 524 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE E 39 " --> pdb=" O LEU F 524 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ALA F 526 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 174 through 179 removed outlier: 6.557A pdb=" N VAL E 174 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE E 379 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR E 176 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL E 381 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU E 178 " --> pdb=" O VAL E 381 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 193 through 195 removed outlier: 3.501A pdb=" N LEU E 215 " --> pdb=" O VAL E 323 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.537A pdb=" N LEU E 247 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AH3, first strand: chain 'E' and resid 480 through 483 Processing sheet with id=AH4, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.534A pdb=" N GLU M 37 " --> pdb=" O ALA L 521 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA L 523 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 175 through 179 Processing sheet with id=AH6, first strand: chain 'L' and resid 193 through 195 removed outlier: 3.505A pdb=" N ILE L 332 " --> pdb=" O MET L 193 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL L 325 " --> pdb=" O ALA L 213 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA L 213 " --> pdb=" O VAL L 325 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 219 through 222 Processing sheet with id=AH8, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AH9, first strand: chain 'L' and resid 480 through 483 removed outlier: 3.840A pdb=" N ASP L 488 " --> pdb=" O ASP L 483 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 5 through 6 removed outlier: 6.860A pdb=" N VAL f 68 " --> pdb=" O LEU f 93 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL f 95 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS f 66 " --> pdb=" O VAL f 95 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL f 12 " --> pdb=" O ILE f 43 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL f 45 " --> pdb=" O LYS f 10 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LYS f 10 " --> pdb=" O VAL f 45 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'e' and resid 49 through 50 removed outlier: 3.643A pdb=" N LYS e 49 " --> pdb=" O VAL e 57 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 48 through 50 removed outlier: 7.457A pdb=" N GLU F 37 " --> pdb=" O GLU G 522 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU G 524 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE F 39 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ALA G 526 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 174 through 179 Processing sheet with id=AI5, first strand: chain 'F' and resid 193 through 195 removed outlier: 3.775A pdb=" N VAL F 323 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU F 215 " --> pdb=" O VAL F 323 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 273 through 277 removed outlier: 6.432A pdb=" N LEU F 247 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY F 318 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 226 through 227 Processing sheet with id=AI8, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AI9, first strand: chain 'F' and resid 480 through 483 Processing sheet with id=AJ1, first strand: chain 'M' and resid 4 through 8 removed outlier: 7.506A pdb=" N ILE N 39 " --> pdb=" O GLU M 522 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU M 524 " --> pdb=" O ILE N 39 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'M' and resid 176 through 179 Processing sheet with id=AJ3, first strand: chain 'M' and resid 193 through 195 removed outlier: 3.604A pdb=" N MET M 193 " --> pdb=" O ILE M 332 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'M' and resid 274 through 277 removed outlier: 5.790A pdb=" N LEU M 247 " --> pdb=" O CYS M 274 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL M 276 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE M 249 " --> pdb=" O VAL M 276 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ILE M 301 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE M 222 " --> pdb=" O ILE M 301 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'M' and resid 274 through 277 removed outlier: 5.790A pdb=" N LEU M 247 " --> pdb=" O CYS M 274 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL M 276 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE M 249 " --> pdb=" O VAL M 276 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AJ7, first strand: chain 'M' and resid 480 through 483 removed outlier: 3.510A pdb=" N ASP M 488 " --> pdb=" O ASP M 483 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'f' and resid 5 through 6 removed outlier: 3.909A pdb=" N ALA g 94 " --> pdb=" O VAL g 68 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL g 12 " --> pdb=" O ILE g 43 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL g 45 " --> pdb=" O LYS g 10 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS g 10 " --> pdb=" O VAL g 45 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARG g 15 " --> pdb=" O LYS g 83 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N LYS g 83 " --> pdb=" O ARG g 15 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'f' and resid 49 through 50 Processing sheet with id=AK1, first strand: chain 'G' and resid 174 through 179 removed outlier: 6.621A pdb=" N VAL G 174 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE G 379 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR G 176 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL G 381 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU G 178 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'G' and resid 193 through 195 removed outlier: 3.594A pdb=" N ASN G 329 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 273 through 277 removed outlier: 6.485A pdb=" N LEU G 247 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AK5, first strand: chain 'G' and resid 480 through 483 Processing sheet with id=AK6, first strand: chain 'N' and resid 175 through 178 removed outlier: 6.934A pdb=" N THR N 176 " --> pdb=" O ILE N 379 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'N' and resid 193 through 195 removed outlier: 3.645A pdb=" N THR N 330 " --> pdb=" O PHE N 195 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA N 213 " --> pdb=" O VAL N 325 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'N' and resid 273 through 276 removed outlier: 6.284A pdb=" N LEU N 247 " --> pdb=" O CYS N 274 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AL1, first strand: chain 'N' and resid 480 through 483 removed outlier: 3.502A pdb=" N ASP N 488 " --> pdb=" O ASP N 483 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'g' and resid 49 through 50 removed outlier: 3.525A pdb=" N LYS g 49 " --> pdb=" O VAL g 57 " (cutoff:3.500A) 3480 hydrogen bonds defined for protein. 9948 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: 32.95 Time building geometry restraints manager: 13.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 19469 1.34 - 1.46: 7678 1.46 - 1.58: 34109 1.58 - 1.70: 57 1.70 - 1.82: 294 Bond restraints: 61607 Sorted by residual: bond pdb=" CB GLU c 76 " pdb=" CG GLU c 76 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.50e+00 bond pdb=" CA ASN d 70 " pdb=" CB ASN d 70 " ideal model delta sigma weight residual 1.527 1.550 -0.024 1.15e-02 7.56e+03 4.24e+00 bond pdb=" N ASP g 80 " pdb=" CA ASP g 80 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.58e+00 bond pdb=" C ARG A 284 " pdb=" O ARG A 284 " ideal model delta sigma weight residual 1.236 1.213 0.024 1.47e-02 4.63e+03 2.57e+00 bond pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.56e+00 ... (remaining 61602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 82376 2.51 - 5.01: 730 5.01 - 7.52: 109 7.52 - 10.02: 32 10.02 - 12.53: 11 Bond angle restraints: 83258 Sorted by residual: angle pdb=" CA GLU c 76 " pdb=" CB GLU c 76 " pdb=" CG GLU c 76 " ideal model delta sigma weight residual 114.10 125.74 -11.64 2.00e+00 2.50e-01 3.39e+01 angle pdb=" C THR I 206 " pdb=" N ASN I 207 " pdb=" CA ASN I 207 " ideal model delta sigma weight residual 120.09 127.21 -7.12 1.25e+00 6.40e-01 3.24e+01 angle pdb=" CA LYS D 231 " pdb=" CB LYS D 231 " pdb=" CG LYS D 231 " ideal model delta sigma weight residual 114.10 123.67 -9.57 2.00e+00 2.50e-01 2.29e+01 angle pdb=" CB GLU c 76 " pdb=" CG GLU c 76 " pdb=" CD GLU c 76 " ideal model delta sigma weight residual 112.60 120.29 -7.69 1.70e+00 3.46e-01 2.05e+01 angle pdb=" CA LYS G 231 " pdb=" CB LYS G 231 " pdb=" CG LYS G 231 " ideal model delta sigma weight residual 114.10 122.87 -8.77 2.00e+00 2.50e-01 1.92e+01 ... (remaining 83253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 34422 17.87 - 35.73: 2890 35.73 - 53.60: 758 53.60 - 71.47: 215 71.47 - 89.33: 152 Dihedral angle restraints: 38437 sinusoidal: 15561 harmonic: 22876 Sorted by residual: dihedral pdb=" CA ILE c 86 " pdb=" C ILE c 86 " pdb=" N MET c 87 " pdb=" CA MET c 87 " ideal model delta harmonic sigma weight residual 180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA TYR C 223 " pdb=" C TYR C 223 " pdb=" N GLU C 224 " pdb=" CA GLU C 224 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG A 285 " pdb=" C ARG A 285 " pdb=" N LYS A 286 " pdb=" CA LYS A 286 " ideal model delta harmonic sigma weight residual 180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 38434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 7320 0.040 - 0.081: 1896 0.081 - 0.121: 704 0.121 - 0.162: 84 0.162 - 0.202: 6 Chirality restraints: 10010 Sorted by residual: chirality pdb=" CA GLU d 17 " pdb=" N GLU d 17 " pdb=" C GLU d 17 " pdb=" CB GLU d 17 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLU c 76 " pdb=" N GLU c 76 " pdb=" C GLU c 76 " pdb=" CB GLU c 76 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CB ILE G 307 " pdb=" CA ILE G 307 " pdb=" CG1 ILE G 307 " pdb=" CG2 ILE G 307 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 10007 not shown) Planarity restraints: 10668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU c 76 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" CD GLU c 76 " -0.070 2.00e-02 2.50e+03 pdb=" OE1 GLU c 76 " 0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU c 76 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU d 17 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" CD GLU d 17 " -0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU d 17 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU d 17 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN d 70 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C ASN d 70 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN d 70 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS d 71 " -0.013 2.00e-02 2.50e+03 ... (remaining 10665 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.64: 736 2.64 - 3.27: 65833 3.27 - 3.89: 119579 3.89 - 4.52: 161578 4.52 - 5.14: 251354 Nonbonded interactions: 599080 Sorted by model distance: nonbonded pdb="MG MG H 601 " pdb=" O1G ANP H 603 " model vdw 2.017 2.170 nonbonded pdb="MG MG J 601 " pdb=" O1G ANP J 603 " model vdw 2.036 2.170 nonbonded pdb="MG MG M 601 " pdb=" O1G ANP M 603 " model vdw 2.037 2.170 nonbonded pdb="MG MG N 601 " pdb=" O1G ANP N 603 " model vdw 2.043 2.170 nonbonded pdb="MG MG I 601 " pdb=" O1G ANP I 603 " model vdw 2.049 2.170 ... (remaining 599075 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 3 through 529 or resid 602)) selection = (chain 'B' and (resid 3 through 529 or resid 602)) selection = (chain 'C' and (resid 3 through 529 or resid 602)) selection = (chain 'D' and (resid 3 through 529 or resid 602)) selection = (chain 'E' and (resid 3 through 529 or resid 602)) selection = (chain 'F' and (resid 3 through 529 or resid 602)) selection = (chain 'G' and (resid 3 through 529 or resid 602)) selection = (chain 'H' and (resid 3 through 529 or resid 603)) selection = (chain 'I' and (resid 3 through 529 or resid 603)) selection = (chain 'J' and (resid 3 through 529 or resid 603)) selection = (chain 'K' and (resid 3 through 529 or resid 603)) selection = (chain 'L' and (resid 3 through 529 or resid 603)) selection = (chain 'M' and (resid 3 through 529 or resid 603)) selection = (chain 'N' and (resid 3 through 529 or resid 603)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.200 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: 0.060 Extract box with map and model: 1.820 Check model and map are aligned: 0.330 Set scattering table: 0.420 Process input model: 119.770 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.550 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 61607 Z= 0.182 Angle : 0.634 12.525 83258 Z= 0.345 Chirality : 0.042 0.202 10010 Planarity : 0.004 0.050 10668 Dihedral : 16.056 89.332 23737 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 1.06 % Allowed : 15.10 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.09), residues: 8008 helix: 1.14 (0.08), residues: 3722 sheet: 0.09 (0.16), residues: 1090 loop : 0.22 (0.11), residues: 3196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 44 HIS 0.003 0.000 HIS H 266 PHE 0.016 0.001 PHE F 281 TYR 0.018 0.001 TYR C 223 ARG 0.012 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 532 time to evaluate : 5.222 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: H 189 THR cc_start: 0.9164 (p) cc_final: 0.8876 (m) REVERT: B 223 TYR cc_start: 0.8417 (t80) cc_final: 0.7859 (t80) REVERT: I 395 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8572 (mtm110) REVERT: C 114 MET cc_start: 0.9280 (tpp) cc_final: 0.8988 (tpp) REVERT: C 223 TYR cc_start: 0.7756 (t80) cc_final: 0.7541 (t80) REVERT: c 69 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: c 84 TYR cc_start: 0.8510 (m-80) cc_final: 0.8270 (m-80) REVERT: c 85 LEU cc_start: 0.9031 (pt) cc_final: 0.8829 (pt) REVERT: D 114 MET cc_start: 0.9305 (tpp) cc_final: 0.9053 (tpt) REVERT: D 172 ASP cc_start: 0.7682 (p0) cc_final: 0.7433 (p0) REVERT: D 223 TYR cc_start: 0.8414 (t80) cc_final: 0.8146 (t80) REVERT: D 368 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7923 (ttp80) REVERT: K 348 GLN cc_start: 0.6328 (OUTLIER) cc_final: 0.6099 (pt0) REVERT: K 395 ARG cc_start: 0.8486 (ttp80) cc_final: 0.7990 (ttp80) REVERT: d 69 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: E 229 ASN cc_start: 0.8095 (m110) cc_final: 0.7528 (p0) REVERT: L 121 ASP cc_start: 0.8640 (m-30) cc_final: 0.8308 (m-30) REVERT: L 316 MET cc_start: 0.4363 (ppp) cc_final: 0.3981 (pmm) REVERT: F 199 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6626 (t80) REVERT: M 395 ARG cc_start: 0.8540 (ttp80) cc_final: 0.7820 (ttp80) REVERT: f 56 ILE cc_start: 0.9389 (mp) cc_final: 0.9170 (mp) REVERT: f 69 PHE cc_start: 0.8406 (m-80) cc_final: 0.7908 (m-80) REVERT: f 84 TYR cc_start: 0.8182 (m-80) cc_final: 0.7824 (m-80) outliers start: 68 outliers final: 49 residues processed: 588 average time/residue: 1.3216 time to fit residues: 1006.7054 Evaluate side-chains 521 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 468 time to evaluate : 5.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 348 GLN Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain e residue 69 PHE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 352 GLN Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 289 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 0.8980 chunk 599 optimal weight: 6.9990 chunk 332 optimal weight: 9.9990 chunk 204 optimal weight: 0.9990 chunk 404 optimal weight: 4.9990 chunk 320 optimal weight: 1.9990 chunk 619 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 376 optimal weight: 8.9990 chunk 461 optimal weight: 3.9990 chunk 718 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN b 55 GLN c 55 GLN ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 61607 Z= 0.245 Angle : 0.625 10.145 83258 Z= 0.325 Chirality : 0.045 0.187 10010 Planarity : 0.004 0.077 10668 Dihedral : 11.018 70.514 9050 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.49 % Rotamer: Outliers : 2.87 % Allowed : 13.37 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 8008 helix: 1.43 (0.08), residues: 3954 sheet: 0.06 (0.16), residues: 1004 loop : 0.09 (0.11), residues: 3050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 44 HIS 0.003 0.001 HIS J 266 PHE 0.017 0.001 PHE G 195 TYR 0.016 0.002 TYR C 223 ARG 0.010 0.001 ARG G 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 514 time to evaluate : 5.205 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: A 199 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6651 (t80) REVERT: A 223 TYR cc_start: 0.8159 (t80) cc_final: 0.7784 (t80) REVERT: A 225 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8962 (mppt) REVERT: A 284 ARG cc_start: 0.8418 (tpt90) cc_final: 0.7949 (tpt90) REVERT: H 143 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: B 223 TYR cc_start: 0.8392 (t80) cc_final: 0.7885 (t80) REVERT: B 226 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8186 (mmmt) REVERT: B 285 ARG cc_start: 0.9009 (tpp80) cc_final: 0.8730 (tpp80) REVERT: B 303 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: I 143 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: I 475 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: b 88 SER cc_start: 0.7546 (p) cc_final: 0.6789 (t) REVERT: C 199 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7315 (t80) REVERT: C 223 TYR cc_start: 0.7847 (t80) cc_final: 0.7399 (t80) REVERT: J 143 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: J 193 MET cc_start: 0.3255 (mmt) cc_final: 0.0733 (pmm) REVERT: J 395 ARG cc_start: 0.8512 (ttp80) cc_final: 0.7865 (ttp80) REVERT: J 475 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: c 5 ARG cc_start: 0.8387 (ptt90) cc_final: 0.8090 (ptm160) REVERT: c 84 TYR cc_start: 0.8498 (m-80) cc_final: 0.8115 (m-80) REVERT: c 87 MET cc_start: 0.6745 (tpt) cc_final: 0.6404 (tpt) REVERT: D 172 ASP cc_start: 0.7628 (p0) cc_final: 0.7389 (p0) REVERT: D 272 ARG cc_start: 0.8687 (mtm180) cc_final: 0.7947 (ptt-90) REVERT: K 395 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8038 (ttp80) REVERT: d 69 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: d 84 TYR cc_start: 0.7878 (m-80) cc_final: 0.7397 (m-80) REVERT: E 199 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.7069 (t80) REVERT: E 229 ASN cc_start: 0.8142 (m110) cc_final: 0.7608 (p0) REVERT: E 272 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8288 (ptt-90) REVERT: L 143 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: L 193 MET cc_start: 0.4609 (ppp) cc_final: 0.4198 (tmm) REVERT: L 316 MET cc_start: 0.4388 (ppp) cc_final: 0.4079 (pmm) REVERT: F 225 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8564 (mppt) REVERT: M 143 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: M 391 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: f 5 ARG cc_start: 0.8590 (ptm160) cc_final: 0.8317 (ptm-80) REVERT: f 87 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5868 (tmt) REVERT: f 88 SER cc_start: 0.6294 (p) cc_final: 0.5707 (t) REVERT: G 199 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6212 (t80) REVERT: G 327 LYS cc_start: 0.9275 (mmmt) cc_final: 0.9074 (mmmt) REVERT: N 395 ARG cc_start: 0.8528 (ttp80) cc_final: 0.7644 (ttt90) outliers start: 184 outliers final: 62 residues processed: 651 average time/residue: 1.3142 time to fit residues: 1113.2656 Evaluate side-chains 543 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 464 time to evaluate : 5.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 87 MET Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain g residue 85 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 597 optimal weight: 8.9990 chunk 489 optimal weight: 7.9990 chunk 198 optimal weight: 50.0000 chunk 719 optimal weight: 3.9990 chunk 777 optimal weight: 0.0050 chunk 640 optimal weight: 8.9990 chunk 713 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 chunk 577 optimal weight: 3.9990 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 348 GLN a 70 ASN C 329 ASN ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 19 GLN ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 61607 Z= 0.468 Angle : 0.656 8.973 83258 Z= 0.338 Chirality : 0.048 0.227 10010 Planarity : 0.004 0.059 10668 Dihedral : 11.088 70.544 9009 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 3.57 % Allowed : 14.27 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.09), residues: 8008 helix: 1.42 (0.08), residues: 3948 sheet: -0.13 (0.16), residues: 990 loop : -0.05 (0.11), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 44 HIS 0.004 0.001 HIS J 401 PHE 0.013 0.001 PHE A 195 TYR 0.022 0.002 TYR A 288 ARG 0.013 0.001 ARG G 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 482 time to evaluate : 5.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7647 (p0) cc_final: 0.7411 (p0) REVERT: A 199 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.6661 (t80) REVERT: A 223 TYR cc_start: 0.8156 (t80) cc_final: 0.7709 (t80) REVERT: A 225 LYS cc_start: 0.9259 (mmmm) cc_final: 0.8966 (mppt) REVERT: A 226 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8421 (mtpp) REVERT: H 143 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: H 189 THR cc_start: 0.9063 (p) cc_final: 0.8654 (m) REVERT: H 395 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8407 (tmm-80) REVERT: a 15 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6418 (ptp-110) REVERT: a 87 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6426 (tpt) REVERT: B 225 LYS cc_start: 0.8924 (mtmm) cc_final: 0.7655 (mppt) REVERT: B 226 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8189 (mmmt) REVERT: B 303 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: I 143 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: I 475 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: C 199 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.7283 (t80) REVERT: C 223 TYR cc_start: 0.7983 (t80) cc_final: 0.7485 (t80) REVERT: C 225 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8134 (mppt) REVERT: J 143 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: J 201 SER cc_start: 0.0978 (OUTLIER) cc_final: 0.0761 (p) REVERT: J 211 MET cc_start: 0.6341 (mpt) cc_final: 0.5918 (tpt) REVERT: J 475 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: c 5 ARG cc_start: 0.8441 (ptt90) cc_final: 0.8159 (ptm160) REVERT: c 14 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8156 (tptp) REVERT: c 84 TYR cc_start: 0.8492 (m-80) cc_final: 0.8252 (m-80) REVERT: D 226 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8441 (mmmm) REVERT: D 285 ARG cc_start: 0.8916 (mmm-85) cc_final: 0.8687 (mmm-85) REVERT: d 69 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: d 84 TYR cc_start: 0.7956 (m-80) cc_final: 0.7546 (m-80) REVERT: d 87 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6969 (tpt) REVERT: E 199 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.6846 (t80) REVERT: E 229 ASN cc_start: 0.8161 (m110) cc_final: 0.7693 (p0) REVERT: E 272 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8073 (pmt100) REVERT: L 143 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: L 211 MET cc_start: 0.4354 (OUTLIER) cc_final: 0.4094 (tmt) REVERT: L 316 MET cc_start: 0.4429 (ppp) cc_final: 0.4199 (pmm) REVERT: e 84 TYR cc_start: 0.7054 (m-80) cc_final: 0.6830 (m-10) REVERT: F 225 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8511 (mppt) REVERT: F 285 ARG cc_start: 0.9146 (tpp80) cc_final: 0.8864 (ttm-80) REVERT: F 287 ASP cc_start: 0.8687 (m-30) cc_final: 0.8417 (p0) REVERT: M 143 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: f 5 ARG cc_start: 0.8636 (ptm160) cc_final: 0.8425 (ptm-80) REVERT: f 88 SER cc_start: 0.6446 (p) cc_final: 0.5786 (t) REVERT: G 199 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6595 (t80) REVERT: G 327 LYS cc_start: 0.9257 (mmmt) cc_final: 0.8923 (tppp) REVERT: G 345 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8702 (mmm160) REVERT: G 368 ARG cc_start: 0.8227 (ttt180) cc_final: 0.7971 (ttt-90) REVERT: N 143 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: N 193 MET cc_start: 0.5171 (mpt) cc_final: 0.4140 (ppp) REVERT: N 379 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8435 (mm) REVERT: g 15 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7138 (ptp-110) outliers start: 229 outliers final: 90 residues processed: 657 average time/residue: 1.3494 time to fit residues: 1151.1071 Evaluate side-chains 569 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 452 time to evaluate : 5.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain a residue 87 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 14 LYS Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain c residue 72 TYR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 87 MET Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 92 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 166 MET Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain g residue 15 ARG Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 9.9990 chunk 541 optimal weight: 7.9990 chunk 373 optimal weight: 8.9990 chunk 79 optimal weight: 0.3980 chunk 343 optimal weight: 3.9990 chunk 483 optimal weight: 9.9990 chunk 722 optimal weight: 1.9990 chunk 764 optimal weight: 7.9990 chunk 377 optimal weight: 0.9990 chunk 684 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN a 70 ASN ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 61607 Z= 0.183 Angle : 0.584 11.094 83258 Z= 0.295 Chirality : 0.044 0.175 10010 Planarity : 0.004 0.064 10668 Dihedral : 10.182 63.813 9006 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.51 % Favored : 97.42 % Rotamer: Outliers : 2.87 % Allowed : 15.25 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.09), residues: 8008 helix: 1.64 (0.08), residues: 3926 sheet: -0.13 (0.16), residues: 1013 loop : -0.02 (0.11), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 44 HIS 0.002 0.000 HIS J 266 PHE 0.013 0.001 PHE A 195 TYR 0.027 0.001 TYR A 288 ARG 0.013 0.000 ARG G 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 482 time to evaluate : 5.872 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: A 172 ASP cc_start: 0.7721 (p0) cc_final: 0.7505 (p0) REVERT: A 199 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6613 (t80) REVERT: A 223 TYR cc_start: 0.8197 (t80) cc_final: 0.7714 (t80) REVERT: A 225 LYS cc_start: 0.9281 (mmmm) cc_final: 0.8997 (mppt) REVERT: A 226 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8400 (mtpp) REVERT: H 143 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: H 189 THR cc_start: 0.9085 (p) cc_final: 0.8697 (m) REVERT: H 395 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8234 (ttp80) REVERT: a 87 MET cc_start: 0.6614 (tpt) cc_final: 0.6362 (tpt) REVERT: B 225 LYS cc_start: 0.8920 (mtmm) cc_final: 0.7763 (mppt) REVERT: B 226 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8158 (mmmt) REVERT: B 272 ARG cc_start: 0.8665 (mtm180) cc_final: 0.7866 (ptt-90) REVERT: B 285 ARG cc_start: 0.8973 (tpp80) cc_final: 0.8747 (tpp80) REVERT: B 303 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: I 143 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: I 475 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: C 199 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.7161 (t80) REVERT: C 223 TYR cc_start: 0.8041 (t80) cc_final: 0.7619 (t80) REVERT: C 225 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8189 (mppt) REVERT: J 143 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: J 201 SER cc_start: 0.1115 (OUTLIER) cc_final: 0.0908 (p) REVERT: J 211 MET cc_start: 0.6319 (mpt) cc_final: 0.5828 (tpt) REVERT: J 475 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: c 5 ARG cc_start: 0.8469 (ptt90) cc_final: 0.8102 (ptm160) REVERT: c 14 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8341 (tptp) REVERT: c 84 TYR cc_start: 0.8509 (m-80) cc_final: 0.8281 (m-80) REVERT: c 87 MET cc_start: 0.6901 (tpt) cc_final: 0.6660 (tpt) REVERT: D 223 TYR cc_start: 0.8330 (t80) cc_final: 0.7916 (t80) REVERT: D 226 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8460 (mmmm) REVERT: D 255 GLU cc_start: 0.7481 (mp0) cc_final: 0.7270 (mp0) REVERT: D 284 ARG cc_start: 0.8453 (mmm160) cc_final: 0.8214 (mmm160) REVERT: K 492 MET cc_start: 0.9012 (mmm) cc_final: 0.8680 (mmm) REVERT: d 69 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: d 84 TYR cc_start: 0.7962 (m-80) cc_final: 0.7549 (m-80) REVERT: d 87 MET cc_start: 0.7171 (tpt) cc_final: 0.6911 (tpt) REVERT: E 199 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6840 (t80) REVERT: E 229 ASN cc_start: 0.8155 (m110) cc_final: 0.7760 (p0) REVERT: E 272 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8069 (pmt100) REVERT: L 143 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: L 193 MET cc_start: 0.4337 (ppp) cc_final: 0.3961 (mmm) REVERT: L 211 MET cc_start: 0.4788 (OUTLIER) cc_final: 0.4571 (tmt) REVERT: L 316 MET cc_start: 0.4375 (ppp) cc_final: 0.4169 (pmm) REVERT: e 38 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: e 82 GLU cc_start: 0.6838 (pm20) cc_final: 0.6500 (pm20) REVERT: e 84 TYR cc_start: 0.7084 (m-80) cc_final: 0.6827 (m-10) REVERT: F 225 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8525 (mppt) REVERT: F 287 ASP cc_start: 0.8734 (m-30) cc_final: 0.8467 (p0) REVERT: F 295 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8344 (pt) REVERT: M 143 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: f 5 ARG cc_start: 0.8624 (ptm160) cc_final: 0.8395 (ptm-80) REVERT: f 84 TYR cc_start: 0.8258 (m-80) cc_final: 0.8006 (m-80) REVERT: G 59 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8789 (mp0) REVERT: G 199 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6568 (t80) REVERT: G 214 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8989 (t) REVERT: G 303 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8192 (mp0) REVERT: G 327 LYS cc_start: 0.9263 (mmmt) cc_final: 0.8924 (tppp) REVERT: G 345 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8559 (mtp85) REVERT: N 143 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: N 193 MET cc_start: 0.5124 (mpt) cc_final: 0.4233 (ppp) REVERT: N 379 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8419 (mm) REVERT: N 475 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8031 (mp0) outliers start: 184 outliers final: 82 residues processed: 627 average time/residue: 1.3247 time to fit residues: 1081.1734 Evaluate side-chains 563 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 453 time to evaluate : 5.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 14 LYS Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain c residue 72 TYR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 38 GLN Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain e residue 92 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 69 PHE Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 85 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 30.0000 chunk 434 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 569 optimal weight: 1.9990 chunk 315 optimal weight: 7.9990 chunk 652 optimal weight: 1.9990 chunk 528 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 390 optimal weight: 3.9990 chunk 686 optimal weight: 7.9990 chunk 192 optimal weight: 50.0000 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN a 55 GLN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 GLN ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 61607 Z= 0.230 Angle : 0.589 10.011 83258 Z= 0.295 Chirality : 0.044 0.170 10010 Planarity : 0.004 0.059 10668 Dihedral : 9.511 59.432 9005 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 2.80 % Allowed : 15.83 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.09), residues: 8008 helix: 1.73 (0.08), residues: 3945 sheet: -0.16 (0.16), residues: 1013 loop : -0.07 (0.11), residues: 3050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 44 HIS 0.002 0.000 HIS J 266 PHE 0.012 0.001 PHE A 195 TYR 0.020 0.001 TYR A 288 ARG 0.010 0.000 ARG G 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 472 time to evaluate : 5.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7726 (p0) cc_final: 0.7498 (p0) REVERT: A 223 TYR cc_start: 0.8192 (t80) cc_final: 0.7676 (t80) REVERT: A 225 LYS cc_start: 0.9286 (mmmm) cc_final: 0.8996 (mppt) REVERT: A 226 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8383 (mtpp) REVERT: H 143 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: H 189 THR cc_start: 0.9078 (p) cc_final: 0.8705 (m) REVERT: H 193 MET cc_start: 0.3334 (mmt) cc_final: 0.1270 (pmm) REVERT: H 395 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8302 (ttp80) REVERT: a 82 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: a 84 TYR cc_start: 0.8152 (m-80) cc_final: 0.7344 (m-80) REVERT: a 87 MET cc_start: 0.6626 (tpt) cc_final: 0.6375 (tpt) REVERT: B 225 LYS cc_start: 0.8905 (mtmm) cc_final: 0.7749 (mppt) REVERT: B 226 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8164 (mmmt) REVERT: B 303 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8308 (mp0) REVERT: B 368 ARG cc_start: 0.8852 (mtm110) cc_final: 0.8585 (mtm110) REVERT: I 5 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8659 (ttmt) REVERT: I 143 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: I 379 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8358 (mm) REVERT: I 475 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: C 199 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.7202 (t80) REVERT: C 223 TYR cc_start: 0.8036 (t80) cc_final: 0.7469 (t80) REVERT: C 225 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8201 (mppt) REVERT: C 295 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8102 (pt) REVERT: J 143 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: J 201 SER cc_start: 0.1148 (OUTLIER) cc_final: 0.0909 (p) REVERT: J 475 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: c 5 ARG cc_start: 0.8440 (ptt90) cc_final: 0.8118 (ptm160) REVERT: c 87 MET cc_start: 0.6759 (tpt) cc_final: 0.6448 (tpt) REVERT: D 223 TYR cc_start: 0.8404 (t80) cc_final: 0.8125 (t80) REVERT: D 226 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8442 (mmmm) REVERT: D 255 GLU cc_start: 0.7569 (mp0) cc_final: 0.7319 (mp0) REVERT: d 69 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: d 84 TYR cc_start: 0.7941 (m-80) cc_final: 0.7566 (m-80) REVERT: d 87 MET cc_start: 0.7192 (tpt) cc_final: 0.6929 (tpt) REVERT: E 229 ASN cc_start: 0.8160 (m110) cc_final: 0.7779 (p0) REVERT: E 272 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8043 (pmt100) REVERT: L 143 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: L 193 MET cc_start: 0.4429 (ppp) cc_final: 0.4064 (mmm) REVERT: L 211 MET cc_start: 0.4675 (OUTLIER) cc_final: 0.4425 (tmt) REVERT: e 79 LEU cc_start: 0.8840 (tm) cc_final: 0.8615 (tm) REVERT: e 84 TYR cc_start: 0.7139 (m-80) cc_final: 0.6832 (m-10) REVERT: F 199 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6554 (t80) REVERT: F 225 LYS cc_start: 0.8803 (mtmm) cc_final: 0.8561 (mppt) REVERT: F 287 ASP cc_start: 0.8762 (m-30) cc_final: 0.8388 (p0) REVERT: F 345 ARG cc_start: 0.9180 (mmm160) cc_final: 0.8972 (mtp85) REVERT: M 143 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: M 211 MET cc_start: 0.3297 (tmt) cc_final: 0.3049 (tmm) REVERT: f 5 ARG cc_start: 0.8614 (ptm160) cc_final: 0.8398 (ptm-80) REVERT: f 87 MET cc_start: 0.6398 (tpt) cc_final: 0.6023 (tpt) REVERT: G 59 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8818 (mp0) REVERT: G 199 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6329 (t80) REVERT: G 214 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8989 (t) REVERT: G 229 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8115 (t0) REVERT: G 303 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8181 (mp0) REVERT: G 345 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8569 (mtp85) REVERT: N 143 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: N 193 MET cc_start: 0.5079 (mpt) cc_final: 0.4167 (ppp) REVERT: N 379 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8424 (mm) REVERT: N 475 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8002 (mp0) outliers start: 180 outliers final: 82 residues processed: 610 average time/residue: 1.3117 time to fit residues: 1043.6430 Evaluate side-chains 556 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 445 time to evaluate : 5.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 82 GLU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 379 ILE Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain c residue 72 TYR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain e residue 92 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 69 PHE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 85 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 7.9990 chunk 688 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 448 optimal weight: 0.0670 chunk 188 optimal weight: 10.0000 chunk 765 optimal weight: 8.9990 chunk 635 optimal weight: 8.9990 chunk 354 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 253 optimal weight: 9.9990 chunk 401 optimal weight: 0.7980 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 70 ASN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 61607 Z= 0.228 Angle : 0.596 11.039 83258 Z= 0.296 Chirality : 0.044 0.168 10010 Planarity : 0.003 0.063 10668 Dihedral : 8.805 59.994 9001 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.30 % Rotamer: Outliers : 2.84 % Allowed : 16.36 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.09), residues: 8008 helix: 1.79 (0.08), residues: 3940 sheet: -0.18 (0.16), residues: 1024 loop : -0.08 (0.11), residues: 3044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 44 HIS 0.002 0.000 HIS J 266 PHE 0.012 0.001 PHE C 195 TYR 0.028 0.001 TYR A 288 ARG 0.010 0.000 ARG c 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 467 time to evaluate : 5.309 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: A 172 ASP cc_start: 0.7696 (p0) cc_final: 0.7465 (p0) REVERT: A 199 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6589 (t80) REVERT: A 223 TYR cc_start: 0.8225 (t80) cc_final: 0.7742 (t80) REVERT: A 225 LYS cc_start: 0.9290 (mmmm) cc_final: 0.9000 (mppt) REVERT: A 226 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8384 (mtpp) REVERT: A 272 ARG cc_start: 0.8282 (mtm110) cc_final: 0.8011 (mtm110) REVERT: H 143 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: H 189 THR cc_start: 0.9055 (p) cc_final: 0.8685 (m) REVERT: H 193 MET cc_start: 0.3658 (mmt) cc_final: 0.1534 (pmm) REVERT: a 82 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: a 84 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: a 87 MET cc_start: 0.6724 (tpt) cc_final: 0.6461 (tpt) REVERT: B 225 LYS cc_start: 0.8909 (mtmm) cc_final: 0.7591 (mppt) REVERT: B 226 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8173 (mmmt) REVERT: B 272 ARG cc_start: 0.8631 (mtm180) cc_final: 0.8426 (mtm180) REVERT: B 303 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8319 (mp0) REVERT: B 330 THR cc_start: 0.8956 (m) cc_final: 0.8563 (p) REVERT: B 345 ARG cc_start: 0.8904 (tpt-90) cc_final: 0.8687 (tpt-90) REVERT: B 368 ARG cc_start: 0.8846 (mtm110) cc_final: 0.8598 (mtm110) REVERT: I 5 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8656 (ttmt) REVERT: I 143 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: I 475 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: C 199 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.7164 (t80) REVERT: C 223 TYR cc_start: 0.8044 (t80) cc_final: 0.7640 (t80) REVERT: C 295 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8090 (pt) REVERT: J 143 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: J 201 SER cc_start: 0.1175 (OUTLIER) cc_final: 0.0963 (p) REVERT: J 211 MET cc_start: 0.6333 (mpt) cc_final: 0.5778 (tpt) REVERT: J 475 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: c 5 ARG cc_start: 0.8460 (ptt90) cc_final: 0.8104 (ptm160) REVERT: c 14 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8523 (tptp) REVERT: D 223 TYR cc_start: 0.8453 (t80) cc_final: 0.8137 (t80) REVERT: D 226 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8471 (mmmm) REVERT: D 255 GLU cc_start: 0.7683 (mp0) cc_final: 0.7381 (mp0) REVERT: K 395 ARG cc_start: 0.8515 (ttp80) cc_final: 0.7972 (ttp80) REVERT: d 69 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: d 84 TYR cc_start: 0.7974 (m-80) cc_final: 0.7673 (m-80) REVERT: d 87 MET cc_start: 0.7158 (tpt) cc_final: 0.6815 (tpt) REVERT: E 199 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6622 (t80) REVERT: E 229 ASN cc_start: 0.8158 (m110) cc_final: 0.7781 (p0) REVERT: E 272 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8038 (pmt100) REVERT: L 143 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7621 (mt-10) REVERT: L 211 MET cc_start: 0.4734 (OUTLIER) cc_final: 0.4486 (tmt) REVERT: e 38 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: e 65 ASP cc_start: 0.6069 (p0) cc_final: 0.5849 (p0) REVERT: e 79 LEU cc_start: 0.8849 (tm) cc_final: 0.8640 (tm) REVERT: e 84 TYR cc_start: 0.7139 (m-80) cc_final: 0.6844 (m-10) REVERT: F 225 LYS cc_start: 0.8828 (mtmm) cc_final: 0.8597 (mppt) REVERT: F 272 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8053 (ptt-90) REVERT: F 287 ASP cc_start: 0.8663 (m-30) cc_final: 0.8411 (p0) REVERT: M 143 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: M 211 MET cc_start: 0.3689 (tmt) cc_final: 0.3372 (tmm) REVERT: f 5 ARG cc_start: 0.8603 (ptm160) cc_final: 0.8402 (ptm-80) REVERT: f 87 MET cc_start: 0.6410 (tpt) cc_final: 0.6163 (tpt) REVERT: G 59 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8813 (mp0) REVERT: G 199 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6714 (t80) REVERT: G 214 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.8994 (t) REVERT: G 229 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8085 (t0) REVERT: G 295 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8440 (pp) REVERT: G 303 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8168 (mp0) REVERT: G 345 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8557 (mtp85) REVERT: N 143 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: N 193 MET cc_start: 0.5084 (mpt) cc_final: 0.4181 (ppp) REVERT: N 379 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8409 (mm) REVERT: N 475 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8008 (mp0) outliers start: 182 outliers final: 88 residues processed: 613 average time/residue: 1.3003 time to fit residues: 1042.3690 Evaluate side-chains 571 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 450 time to evaluate : 5.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain a residue 82 GLU Chi-restraints excluded: chain a residue 84 TYR Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 68 VAL Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 14 LYS Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain c residue 72 TYR Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 38 GLN Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain e residue 92 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 272 ARG Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 69 PHE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 85 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 436 optimal weight: 1.9990 chunk 558 optimal weight: 0.4980 chunk 433 optimal weight: 4.9990 chunk 644 optimal weight: 2.9990 chunk 427 optimal weight: 10.0000 chunk 762 optimal weight: 40.0000 chunk 477 optimal weight: 8.9990 chunk 464 optimal weight: 1.9990 chunk 351 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN a 70 ASN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 55 GLN ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 GLN f 53 ASN ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 61607 Z= 0.239 Angle : 0.602 11.600 83258 Z= 0.298 Chirality : 0.044 0.170 10010 Planarity : 0.003 0.064 10668 Dihedral : 7.929 59.707 9001 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.27 % Rotamer: Outliers : 2.91 % Allowed : 16.56 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.09), residues: 8008 helix: 1.83 (0.08), residues: 3953 sheet: -0.20 (0.16), residues: 1013 loop : -0.11 (0.11), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 44 HIS 0.002 0.000 HIS J 266 PHE 0.012 0.001 PHE C 195 TYR 0.023 0.001 TYR A 288 ARG 0.010 0.000 ARG c 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 459 time to evaluate : 5.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7663 (p0) cc_final: 0.7421 (p0) REVERT: A 193 MET cc_start: 0.8838 (tpp) cc_final: 0.8624 (tpp) REVERT: A 225 LYS cc_start: 0.9298 (mmmm) cc_final: 0.9007 (mppt) REVERT: A 226 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8097 (mtpp) REVERT: A 231 LYS cc_start: 0.9347 (mptt) cc_final: 0.9145 (tptt) REVERT: A 272 ARG cc_start: 0.8257 (mtm110) cc_final: 0.7949 (mtm110) REVERT: A 345 ARG cc_start: 0.8889 (mtp-110) cc_final: 0.8520 (ttm110) REVERT: H 143 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: H 189 THR cc_start: 0.9019 (p) cc_final: 0.8643 (m) REVERT: H 193 MET cc_start: 0.3721 (mmt) cc_final: 0.1569 (pmm) REVERT: a 82 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: a 87 MET cc_start: 0.6728 (tpt) cc_final: 0.6446 (tpt) REVERT: a 91 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: B 225 LYS cc_start: 0.8902 (mtmm) cc_final: 0.7571 (mppt) REVERT: B 226 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8021 (mmmt) REVERT: B 272 ARG cc_start: 0.8612 (mtm180) cc_final: 0.8252 (mtm180) REVERT: B 303 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: B 330 THR cc_start: 0.8987 (m) cc_final: 0.8594 (p) REVERT: B 368 ARG cc_start: 0.8838 (mtm110) cc_final: 0.8510 (mtm180) REVERT: I 5 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8655 (ttmt) REVERT: I 143 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: I 475 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: C 199 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.7165 (t80) REVERT: C 223 TYR cc_start: 0.8139 (t80) cc_final: 0.7463 (t80) REVERT: J 143 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7622 (mt-10) REVERT: J 201 SER cc_start: 0.1234 (OUTLIER) cc_final: 0.1024 (p) REVERT: J 211 MET cc_start: 0.6108 (mpt) cc_final: 0.5523 (tpt) REVERT: J 475 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: c 3 ARG cc_start: 0.6208 (mmm160) cc_final: 0.5917 (mmm-85) REVERT: c 5 ARG cc_start: 0.8483 (ptt90) cc_final: 0.8148 (ptm160) REVERT: D 223 TYR cc_start: 0.8501 (t80) cc_final: 0.8158 (t80) REVERT: D 226 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8456 (mmmm) REVERT: D 255 GLU cc_start: 0.7842 (mp0) cc_final: 0.7603 (mp0) REVERT: K 395 ARG cc_start: 0.8523 (ttp80) cc_final: 0.7992 (ttp80) REVERT: d 69 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: d 87 MET cc_start: 0.7092 (tpt) cc_final: 0.6705 (tpt) REVERT: E 229 ASN cc_start: 0.8166 (m110) cc_final: 0.7795 (p0) REVERT: E 272 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8028 (pmt100) REVERT: L 143 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: L 193 MET cc_start: 0.4361 (ppp) cc_final: 0.4012 (mmm) REVERT: L 211 MET cc_start: 0.4705 (OUTLIER) cc_final: 0.4463 (tmt) REVERT: e 38 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7950 (mt0) REVERT: e 79 LEU cc_start: 0.8820 (tm) cc_final: 0.8617 (tm) REVERT: e 84 TYR cc_start: 0.7195 (m-80) cc_final: 0.6976 (m-10) REVERT: F 199 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6568 (t80) REVERT: F 225 LYS cc_start: 0.8839 (mtmm) cc_final: 0.8626 (mppt) REVERT: F 285 ARG cc_start: 0.9164 (tpp80) cc_final: 0.8958 (tpp80) REVERT: F 287 ASP cc_start: 0.8745 (m-30) cc_final: 0.8419 (p0) REVERT: M 143 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: M 211 MET cc_start: 0.3760 (tmt) cc_final: 0.3512 (tmm) REVERT: f 4 LEU cc_start: 0.8331 (mm) cc_final: 0.8044 (mt) REVERT: f 5 ARG cc_start: 0.8657 (ptm160) cc_final: 0.8422 (ptm-80) REVERT: f 19 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6756 (mp10) REVERT: f 84 TYR cc_start: 0.8132 (m-80) cc_final: 0.7724 (m-80) REVERT: f 87 MET cc_start: 0.6416 (tpt) cc_final: 0.6167 (tpt) REVERT: G 59 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8809 (mp0) REVERT: G 214 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.8997 (t) REVERT: G 295 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8393 (pp) REVERT: G 303 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8163 (mp0) REVERT: G 345 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8674 (mmm160) REVERT: N 143 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: N 193 MET cc_start: 0.4992 (mpt) cc_final: 0.4060 (ppp) REVERT: N 379 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8400 (mm) REVERT: N 475 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: g 51 LEU cc_start: 0.7239 (mp) cc_final: 0.6991 (mt) outliers start: 187 outliers final: 91 residues processed: 605 average time/residue: 1.3447 time to fit residues: 1059.6447 Evaluate side-chains 567 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 448 time to evaluate : 5.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain a residue 82 GLU Chi-restraints excluded: chain a residue 91 GLU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain c residue 72 TYR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 38 GLN Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain e residue 92 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 19 GLN Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 69 PHE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 85 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 455 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 484 optimal weight: 8.9990 chunk 519 optimal weight: 2.9990 chunk 376 optimal weight: 4.9990 chunk 71 optimal weight: 30.0000 chunk 599 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN a 55 GLN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 GLN ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 61607 Z= 0.375 Angle : 0.649 10.622 83258 Z= 0.322 Chirality : 0.046 0.193 10010 Planarity : 0.004 0.063 10668 Dihedral : 7.580 58.573 9001 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 2.88 % Allowed : 16.70 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.09), residues: 8008 helix: 1.76 (0.08), residues: 3953 sheet: -0.23 (0.17), residues: 978 loop : -0.15 (0.11), residues: 3077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 44 HIS 0.003 0.001 HIS J 401 PHE 0.013 0.001 PHE C 195 TYR 0.024 0.002 TYR c 84 ARG 0.009 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 464 time to evaluate : 5.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7536 (p0) cc_final: 0.7282 (p0) REVERT: A 193 MET cc_start: 0.8813 (tpp) cc_final: 0.8580 (tpp) REVERT: A 199 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6828 (t80) REVERT: A 225 LYS cc_start: 0.9278 (mmmm) cc_final: 0.9001 (mppt) REVERT: A 226 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8390 (mtpp) REVERT: A 272 ARG cc_start: 0.8255 (mtm110) cc_final: 0.7937 (mtm110) REVERT: A 345 ARG cc_start: 0.8933 (mtp-110) cc_final: 0.8504 (ttm110) REVERT: H 143 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: H 189 THR cc_start: 0.8997 (p) cc_final: 0.8594 (m) REVERT: a 82 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: a 87 MET cc_start: 0.6784 (tpt) cc_final: 0.6487 (tpt) REVERT: B 223 TYR cc_start: 0.8587 (t80) cc_final: 0.8257 (t80) REVERT: B 225 LYS cc_start: 0.8918 (mtmm) cc_final: 0.7570 (mppt) REVERT: B 226 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8070 (mmmt) REVERT: B 272 ARG cc_start: 0.8610 (mtm180) cc_final: 0.8259 (mtm180) REVERT: B 303 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8341 (mp0) REVERT: B 330 THR cc_start: 0.8963 (m) cc_final: 0.8572 (p) REVERT: B 368 ARG cc_start: 0.8840 (mtm110) cc_final: 0.8511 (mtm180) REVERT: I 5 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8669 (ttmt) REVERT: I 143 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: I 475 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: C 199 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.7147 (t80) REVERT: C 223 TYR cc_start: 0.8213 (t80) cc_final: 0.7439 (t80) REVERT: C 255 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: C 295 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8295 (pp) REVERT: J 143 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: J 201 SER cc_start: 0.1123 (OUTLIER) cc_final: 0.0889 (p) REVERT: J 475 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: c 5 ARG cc_start: 0.8495 (ptt90) cc_final: 0.8166 (ptm160) REVERT: c 14 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8266 (tptp) REVERT: c 87 MET cc_start: 0.6717 (tpt) cc_final: 0.5731 (tpt) REVERT: c 91 GLU cc_start: 0.9034 (pt0) cc_final: 0.8740 (pp20) REVERT: D 223 TYR cc_start: 0.8495 (t80) cc_final: 0.8231 (t80) REVERT: D 226 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8433 (mmmm) REVERT: D 255 GLU cc_start: 0.7882 (mp0) cc_final: 0.7612 (mp0) REVERT: d 69 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: d 87 MET cc_start: 0.7088 (tpt) cc_final: 0.6728 (tpt) REVERT: E 229 ASN cc_start: 0.8158 (m110) cc_final: 0.7778 (p0) REVERT: E 272 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8061 (pmt100) REVERT: E 285 ARG cc_start: 0.9009 (mmm-85) cc_final: 0.8379 (mmm-85) REVERT: L 143 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: L 193 MET cc_start: 0.4300 (ppp) cc_final: 0.3948 (mmm) REVERT: L 211 MET cc_start: 0.4538 (OUTLIER) cc_final: 0.4316 (tmt) REVERT: e 79 LEU cc_start: 0.8850 (tm) cc_final: 0.8641 (tm) REVERT: e 84 TYR cc_start: 0.7276 (m-80) cc_final: 0.7056 (m-10) REVERT: F 199 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6705 (t80) REVERT: F 225 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8598 (mppt) REVERT: F 226 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8481 (mtpp) REVERT: F 287 ASP cc_start: 0.8723 (m-30) cc_final: 0.8492 (p0) REVERT: F 345 ARG cc_start: 0.9219 (mmm160) cc_final: 0.8892 (mtp180) REVERT: M 143 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: M 211 MET cc_start: 0.3778 (tmt) cc_final: 0.3528 (tmm) REVERT: f 4 LEU cc_start: 0.8347 (mm) cc_final: 0.8031 (mt) REVERT: f 5 ARG cc_start: 0.8621 (ptm160) cc_final: 0.8396 (ptm-80) REVERT: f 84 TYR cc_start: 0.8237 (m-80) cc_final: 0.7964 (m-80) REVERT: f 87 MET cc_start: 0.6482 (tpt) cc_final: 0.6185 (tpt) REVERT: G 59 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8764 (mp0) REVERT: G 214 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8962 (t) REVERT: G 229 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.8125 (t0) REVERT: G 295 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8401 (pp) REVERT: G 303 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8147 (mp0) REVERT: G 345 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8655 (mmm160) REVERT: N 143 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: N 193 MET cc_start: 0.5027 (mpt) cc_final: 0.4043 (ppp) REVERT: N 379 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8388 (mm) REVERT: N 475 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: g 51 LEU cc_start: 0.7335 (mp) cc_final: 0.7097 (mt) outliers start: 185 outliers final: 93 residues processed: 606 average time/residue: 1.3232 time to fit residues: 1044.9740 Evaluate side-chains 581 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 457 time to evaluate : 5.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 82 GLU Chi-restraints excluded: chain a residue 84 TYR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 14 LYS Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain c residue 72 TYR Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 166 MET Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain e residue 92 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 226 LYS Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 69 PHE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 1.9990 chunk 730 optimal weight: 1.9990 chunk 666 optimal weight: 0.8980 chunk 710 optimal weight: 8.9990 chunk 427 optimal weight: 30.0000 chunk 309 optimal weight: 5.9990 chunk 557 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 641 optimal weight: 9.9990 chunk 671 optimal weight: 0.7980 chunk 707 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN a 55 GLN a 70 ASN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 38 GLN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 61607 Z= 0.279 Angle : 0.630 12.681 83258 Z= 0.312 Chirality : 0.045 0.249 10010 Planarity : 0.004 0.063 10668 Dihedral : 6.986 58.982 9001 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.65 % Favored : 97.28 % Rotamer: Outliers : 2.62 % Allowed : 17.17 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 8008 helix: 1.81 (0.08), residues: 3947 sheet: -0.19 (0.17), residues: 978 loop : -0.17 (0.11), residues: 3083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 44 HIS 0.002 0.000 HIS J 401 PHE 0.012 0.001 PHE C 195 TYR 0.023 0.001 TYR A 288 ARG 0.010 0.000 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 468 time to evaluate : 5.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7474 (p0) cc_final: 0.7215 (p0) REVERT: A 193 MET cc_start: 0.8844 (tpp) cc_final: 0.8612 (tpp) REVERT: A 223 TYR cc_start: 0.8072 (t80) cc_final: 0.7516 (t80) REVERT: A 225 LYS cc_start: 0.9285 (mmmm) cc_final: 0.9010 (mppt) REVERT: A 226 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8429 (mtpp) REVERT: A 319 ARG cc_start: 0.7434 (ppt170) cc_final: 0.7170 (ppt170) REVERT: A 345 ARG cc_start: 0.8944 (mtp-110) cc_final: 0.8660 (mtm180) REVERT: H 189 THR cc_start: 0.9001 (p) cc_final: 0.8598 (m) REVERT: H 193 MET cc_start: 0.3693 (mmt) cc_final: 0.1495 (pmm) REVERT: a 82 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: a 91 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: B 226 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8107 (mmmt) REVERT: B 272 ARG cc_start: 0.8618 (mtm180) cc_final: 0.8274 (mtm180) REVERT: B 330 THR cc_start: 0.8968 (m) cc_final: 0.8577 (p) REVERT: I 5 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8655 (ttmt) REVERT: I 143 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: I 211 MET cc_start: 0.3086 (ppp) cc_final: 0.2801 (ppp) REVERT: I 475 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: b 15 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6233 (mtp-110) REVERT: C 199 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.7068 (t80) REVERT: C 223 TYR cc_start: 0.8225 (t80) cc_final: 0.7354 (t80) REVERT: J 143 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: J 201 SER cc_start: 0.1125 (OUTLIER) cc_final: 0.0924 (p) REVERT: J 211 MET cc_start: 0.6327 (mpt) cc_final: 0.5606 (tpt) REVERT: J 475 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: c 3 ARG cc_start: 0.6140 (mmm160) cc_final: 0.5855 (mmm-85) REVERT: c 5 ARG cc_start: 0.8497 (ptt90) cc_final: 0.8185 (ptm160) REVERT: c 14 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8320 (tptp) REVERT: c 84 TYR cc_start: 0.8252 (m-80) cc_final: 0.7988 (m-80) REVERT: c 87 MET cc_start: 0.6794 (tpt) cc_final: 0.6506 (tpt) REVERT: D 223 TYR cc_start: 0.8545 (t80) cc_final: 0.8233 (t80) REVERT: D 226 LYS cc_start: 0.8831 (mmmm) cc_final: 0.8430 (mmmm) REVERT: D 255 GLU cc_start: 0.7861 (mp0) cc_final: 0.7586 (mp0) REVERT: D 272 ARG cc_start: 0.8702 (mtm180) cc_final: 0.7889 (ptt-90) REVERT: d 69 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: d 87 MET cc_start: 0.6983 (tpt) cc_final: 0.6635 (tpt) REVERT: E 229 ASN cc_start: 0.8187 (m110) cc_final: 0.7818 (p0) REVERT: E 272 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8078 (pmt100) REVERT: E 285 ARG cc_start: 0.9033 (mmm-85) cc_final: 0.8470 (mmm-85) REVERT: L 143 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: L 193 MET cc_start: 0.4333 (ppp) cc_final: 0.3970 (mmm) REVERT: L 211 MET cc_start: 0.4574 (OUTLIER) cc_final: 0.4336 (tmt) REVERT: F 199 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6743 (t80) REVERT: F 223 TYR cc_start: 0.8118 (t80) cc_final: 0.7706 (t80) REVERT: F 225 LYS cc_start: 0.8828 (mtmm) cc_final: 0.8625 (mppt) REVERT: F 226 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8508 (mtpp) REVERT: F 272 ARG cc_start: 0.8798 (mtm180) cc_final: 0.8093 (ptt-90) REVERT: F 287 ASP cc_start: 0.8709 (m-30) cc_final: 0.8456 (p0) REVERT: M 143 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: M 211 MET cc_start: 0.3806 (tmt) cc_final: 0.3554 (tmm) REVERT: f 4 LEU cc_start: 0.8336 (mm) cc_final: 0.8043 (mt) REVERT: f 5 ARG cc_start: 0.8662 (ptm160) cc_final: 0.8407 (ptm-80) REVERT: f 21 GLN cc_start: 0.8804 (pt0) cc_final: 0.8579 (pm20) REVERT: f 87 MET cc_start: 0.6490 (tpt) cc_final: 0.6262 (tpt) REVERT: G 59 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8767 (mp0) REVERT: G 214 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8971 (t) REVERT: G 229 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.8058 (t0) REVERT: G 272 ARG cc_start: 0.8700 (mtm180) cc_final: 0.7951 (ptt-90) REVERT: G 303 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8146 (mp0) REVERT: G 345 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8684 (mmm160) REVERT: N 143 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: N 193 MET cc_start: 0.5077 (mpt) cc_final: 0.4051 (ppp) REVERT: N 379 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8393 (mm) REVERT: N 475 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: g 51 LEU cc_start: 0.7295 (mp) cc_final: 0.7062 (mt) outliers start: 168 outliers final: 87 residues processed: 599 average time/residue: 1.3626 time to fit residues: 1060.2225 Evaluate side-chains 570 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 456 time to evaluate : 5.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 82 GLU Chi-restraints excluded: chain a residue 84 TYR Chi-restraints excluded: chain a residue 91 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 14 LYS Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain c residue 72 TYR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 166 MET Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain e residue 92 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 226 LYS Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 69 PHE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 1.9990 chunk 751 optimal weight: 3.9990 chunk 458 optimal weight: 3.9990 chunk 356 optimal weight: 0.0050 chunk 522 optimal weight: 20.0000 chunk 788 optimal weight: 10.0000 chunk 725 optimal weight: 4.9990 chunk 627 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 484 optimal weight: 9.9990 chunk 384 optimal weight: 0.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN a 55 GLN a 70 ASN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 38 GLN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 61607 Z= 0.173 Angle : 0.625 12.830 83258 Z= 0.306 Chirality : 0.044 0.201 10010 Planarity : 0.004 0.067 10668 Dihedral : 6.502 62.627 9000 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.30 % Rotamer: Outliers : 2.03 % Allowed : 18.01 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.09), residues: 8008 helix: 1.90 (0.08), residues: 3959 sheet: -0.04 (0.17), residues: 938 loop : -0.20 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 44 HIS 0.002 0.000 HIS J 266 PHE 0.014 0.001 PHE F 195 TYR 0.029 0.001 TYR A 288 ARG 0.016 0.000 ARG F 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 470 time to evaluate : 5.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7508 (p0) cc_final: 0.7242 (p0) REVERT: A 193 MET cc_start: 0.8858 (tpp) cc_final: 0.8603 (tpp) REVERT: A 223 TYR cc_start: 0.8129 (t80) cc_final: 0.7646 (t80) REVERT: A 225 LYS cc_start: 0.9325 (mmmm) cc_final: 0.9046 (mppt) REVERT: A 226 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8147 (mtpp) REVERT: A 272 ARG cc_start: 0.8530 (mtm180) cc_final: 0.7668 (ptt-90) REVERT: A 345 ARG cc_start: 0.8942 (mtp-110) cc_final: 0.8683 (ttm170) REVERT: H 143 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: H 193 MET cc_start: 0.3918 (mmt) cc_final: 0.1667 (pmm) REVERT: a 82 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: B 226 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8165 (mmmt) REVERT: B 272 ARG cc_start: 0.8594 (mtm180) cc_final: 0.8240 (mtm180) REVERT: B 285 ARG cc_start: 0.8913 (tpp80) cc_final: 0.8578 (tpp80) REVERT: I 143 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: I 211 MET cc_start: 0.2999 (ppp) cc_final: 0.2705 (ppp) REVERT: I 475 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: b 84 TYR cc_start: 0.7090 (m-10) cc_final: 0.6808 (m-10) REVERT: C 199 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.7118 (t80) REVERT: C 223 TYR cc_start: 0.8405 (t80) cc_final: 0.7616 (t80) REVERT: C 345 ARG cc_start: 0.8973 (mmm160) cc_final: 0.8648 (mtp85) REVERT: J 143 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: J 211 MET cc_start: 0.6331 (mpt) cc_final: 0.5601 (tpt) REVERT: J 475 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: c 5 ARG cc_start: 0.8466 (ptt90) cc_final: 0.8146 (ptm160) REVERT: c 14 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8255 (tptp) REVERT: c 87 MET cc_start: 0.6667 (tpt) cc_final: 0.5714 (tpt) REVERT: c 91 GLU cc_start: 0.9005 (pt0) cc_final: 0.8669 (pp20) REVERT: D 223 TYR cc_start: 0.8512 (t80) cc_final: 0.8274 (t80) REVERT: D 226 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8421 (mmmm) REVERT: D 255 GLU cc_start: 0.7838 (mp0) cc_final: 0.7549 (mp0) REVERT: D 272 ARG cc_start: 0.8652 (mtm180) cc_final: 0.7894 (ptt-90) REVERT: d 69 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: d 87 MET cc_start: 0.6933 (tpt) cc_final: 0.6607 (tpt) REVERT: E 229 ASN cc_start: 0.8218 (m110) cc_final: 0.7885 (p0) REVERT: E 272 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8044 (pmt100) REVERT: E 285 ARG cc_start: 0.9033 (mmm-85) cc_final: 0.8471 (mmm-85) REVERT: L 143 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: L 193 MET cc_start: 0.4318 (ppp) cc_final: 0.3960 (mmm) REVERT: L 211 MET cc_start: 0.4629 (OUTLIER) cc_final: 0.4371 (tmt) REVERT: L 316 MET cc_start: 0.4464 (ppp) cc_final: 0.4160 (pmm) REVERT: F 199 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6717 (t80) REVERT: F 223 TYR cc_start: 0.8197 (t80) cc_final: 0.7724 (t80) REVERT: F 225 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8635 (mppt) REVERT: F 226 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8552 (mtpp) REVERT: F 272 ARG cc_start: 0.8777 (mtm180) cc_final: 0.8056 (ptt-90) REVERT: F 287 ASP cc_start: 0.8711 (m-30) cc_final: 0.8384 (p0) REVERT: F 288 TYR cc_start: 0.8863 (t80) cc_final: 0.8606 (m-80) REVERT: M 143 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: M 211 MET cc_start: 0.3805 (tmt) cc_final: 0.3549 (tmm) REVERT: f 4 LEU cc_start: 0.8300 (mm) cc_final: 0.8046 (pp) REVERT: f 5 ARG cc_start: 0.8671 (ptm160) cc_final: 0.8440 (ptm-80) REVERT: f 72 TYR cc_start: 0.8034 (m-80) cc_final: 0.7766 (m-80) REVERT: f 84 TYR cc_start: 0.8231 (m-80) cc_final: 0.7833 (m-80) REVERT: f 87 MET cc_start: 0.6565 (tpt) cc_final: 0.6260 (tpt) REVERT: G 59 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8765 (mp0) REVERT: G 214 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8999 (t) REVERT: G 229 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8037 (t0) REVERT: G 272 ARG cc_start: 0.8697 (mtm180) cc_final: 0.7999 (ptt-90) REVERT: G 303 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8116 (mp0) REVERT: G 345 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8684 (mmm160) REVERT: N 143 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: N 193 MET cc_start: 0.5006 (mpt) cc_final: 0.4055 (ppp) REVERT: N 379 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8376 (mm) REVERT: N 475 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: g 51 LEU cc_start: 0.7142 (mp) cc_final: 0.6913 (mt) outliers start: 130 outliers final: 77 residues processed: 575 average time/residue: 1.3252 time to fit residues: 990.1635 Evaluate side-chains 552 residues out of total 6419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 451 time to evaluate : 5.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 82 GLU Chi-restraints excluded: chain a residue 84 TYR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 14 LYS Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain c residue 72 TYR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 166 MET Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 47 ASP Chi-restraints excluded: chain e residue 92 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 226 LYS Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 41 GLU Chi-restraints excluded: chain f residue 69 PHE Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 0.9980 chunk 668 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 578 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 628 optimal weight: 0.9980 chunk 263 optimal weight: 0.1980 chunk 645 optimal weight: 0.0670 chunk 79 optimal weight: 30.0000 chunk 115 optimal weight: 1.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN a 70 ASN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 38 GLN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.130541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.071371 restraints weight = 117002.690| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.67 r_work: 0.2800 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 61607 Z= 0.176 Angle : 0.625 12.671 83258 Z= 0.306 Chirality : 0.044 0.248 10010 Planarity : 0.003 0.056 10668 Dihedral : 6.349 58.800 9000 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.24 % Rotamer: Outliers : 1.90 % Allowed : 18.07 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.09), residues: 8008 helix: 1.96 (0.08), residues: 3959 sheet: -0.04 (0.17), residues: 949 loop : -0.21 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 44 HIS 0.002 0.000 HIS J 266 PHE 0.028 0.001 PHE a 69 TYR 0.051 0.001 TYR e 84 ARG 0.011 0.000 ARG F 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18668.49 seconds wall clock time: 324 minutes 48.53 seconds (19488.53 seconds total)