Starting phenix.real_space_refine on Mon Dec 30 23:52:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8su9_40762/12_2024/8su9_40762.cif Found real_map, /net/cci-nas-00/data/ceres_data/8su9_40762/12_2024/8su9_40762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8su9_40762/12_2024/8su9_40762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8su9_40762/12_2024/8su9_40762.map" model { file = "/net/cci-nas-00/data/ceres_data/8su9_40762/12_2024/8su9_40762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8su9_40762/12_2024/8su9_40762.cif" } resolution = 2.83 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= 0.002 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 5 5.21 5 S 145 5.16 5 C 41764 2.51 5 N 11119 2.21 5 O 12318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 65385 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "B" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3186 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 1 Chain: "C" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "D" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3192 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 2 Chain: "E" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 388} Chain breaks: 1 Chain: "F" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3198 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 1 Chain: "G" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3119 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 379} Chain breaks: 2 Chain: "H" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3203 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 11, 'TRANS': 389} Chain breaks: 1 Chain: "I" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3145 Classifications: {'peptide': 394} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Chain breaks: 2 Chain: "J" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3199 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 1 Chain: "K" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3182 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 2 Chain: "L" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3199 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 1 Chain: "M" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4536 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 550} Chain breaks: 2 Chain: "N" Number of atoms: 4548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4548 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 551} Chain breaks: 2 Chain: "O" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4637 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain breaks: 1 Chain: "P" Number of atoms: 4346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4346 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 526} Chain breaks: 4 Chain: "Q" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4389 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 530} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4170 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 19, 'TRANS': 504} Chain breaks: 3 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 28.95, per 1000 atoms: 0.44 Number of scatterers: 65385 At special positions: 0 Unit cell: (196.47, 184.26, 220.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 145 16.00 P 34 15.00 Mg 5 11.99 O 12318 8.00 N 11119 7.00 C 41764 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: 12.16 Conformation dependent library (CDL) restraints added in 6.2 seconds 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15054 Finding SS restraints... Secondary structure from input PDB file: 382 helices and 68 sheets defined 46.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.49 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.809A pdb=" N SER A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.722A pdb=" N SER A 37 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 38 " --> pdb=" O GLY A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 38' Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 82 through 99 removed outlier: 3.699A pdb=" N ASP A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 122 removed outlier: 3.665A pdb=" N GLU A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.538A pdb=" N PHE A 130 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.752A pdb=" N LYS A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASP A 139 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA A 140 " --> pdb=" O LYS A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 140' Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.607A pdb=" N LYS A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.613A pdb=" N TRP A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 201 removed outlier: 4.005A pdb=" N PHE A 201 " --> pdb=" O PRO A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.646A pdb=" N TYR A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.666A pdb=" N ASN A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 336 through 346 removed outlier: 3.595A pdb=" N THR A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.841A pdb=" N GLU A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.697A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.535A pdb=" N ARG B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 removed outlier: 3.616A pdb=" N SER B 37 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 38 " --> pdb=" O GLY B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 34 through 38' Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 56 through 65 removed outlier: 4.015A pdb=" N LEU B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 81 through 99 removed outlier: 3.966A pdb=" N ASP B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 121 removed outlier: 3.772A pdb=" N GLU B 105 " --> pdb=" O CYS B 101 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 126 through 132 removed outlier: 4.232A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.522A pdb=" N LYS B 137 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASP B 139 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA B 140 " --> pdb=" O LYS B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 134 through 140' Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.502A pdb=" N LYS B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 181 Processing helix chain 'B' and resid 198 through 201 removed outlier: 3.587A pdb=" N PHE B 201 " --> pdb=" O PRO B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 252 through 260 removed outlier: 4.250A pdb=" N ASP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 removed outlier: 4.074A pdb=" N GLU B 286 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.600A pdb=" N LEU B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 335 through 345 removed outlier: 3.972A pdb=" N ALA B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 360 removed outlier: 3.667A pdb=" N ALA B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.545A pdb=" N LYS B 374 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 375 " --> pdb=" O GLY B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 375' Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.822A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 removed outlier: 3.545A pdb=" N VAL B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 34 through 37 Processing helix chain 'C' and resid 44 through 56 removed outlier: 3.522A pdb=" N TRP C 49 " --> pdb=" O MET C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 removed outlier: 4.202A pdb=" N GLY C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 99 removed outlier: 3.760A pdb=" N LEU C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 122 removed outlier: 3.502A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 removed outlier: 4.218A pdb=" N ARG C 131 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 140 removed outlier: 3.810A pdb=" N LYS C 138 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP C 139 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA C 140 " --> pdb=" O LYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 154 removed outlier: 3.661A pdb=" N LYS C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 181 removed outlier: 3.732A pdb=" N ASP C 179 " --> pdb=" O TRP C 175 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.897A pdb=" N PHE C 201 " --> pdb=" O PRO C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 201' Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.740A pdb=" N ASP C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.573A pdb=" N ILE C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.984A pdb=" N TYR C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.645A pdb=" N ALA C 321 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 349 through 360 Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.732A pdb=" N VAL C 381 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 407 removed outlier: 3.808A pdb=" N ALA C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.620A pdb=" N CYS D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 38 removed outlier: 3.798A pdb=" N SER D 37 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 38 " --> pdb=" O GLY D 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 34 through 38' Processing helix chain 'D' and resid 44 through 55 Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.622A pdb=" N ALA D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 78 Processing helix chain 'D' and resid 81 through 99 removed outlier: 3.711A pdb=" N ASP D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.817A pdb=" N LYS D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 132 removed outlier: 3.792A pdb=" N PHE D 130 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG D 131 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 removed outlier: 3.628A pdb=" N LYS D 137 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 138 " --> pdb=" O GLN D 135 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASP D 139 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA D 140 " --> pdb=" O LYS D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 140' Processing helix chain 'D' and resid 141 through 154 removed outlier: 4.020A pdb=" N ASN D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 179 removed outlier: 3.509A pdb=" N ASP D 179 " --> pdb=" O TRP D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 removed outlier: 3.971A pdb=" N PHE D 201 " --> pdb=" O PRO D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.877A pdb=" N TYR D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.561A pdb=" N ARG D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU D 293 " --> pdb=" O ARG D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 321 removed outlier: 3.969A pdb=" N ILE D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 318 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 335 through 344 removed outlier: 4.083A pdb=" N ALA D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 360 removed outlier: 3.964A pdb=" N ALA D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 375 removed outlier: 3.547A pdb=" N LYS D 374 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.701A pdb=" N LEU D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 removed outlier: 3.886A pdb=" N VAL D 400 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 405 removed outlier: 4.205A pdb=" N ASN D 405 " --> pdb=" O ALA D 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'E' and resid 11 through 23 Processing helix chain 'E' and resid 34 through 38 removed outlier: 3.596A pdb=" N SER E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL E 38 " --> pdb=" O GLY E 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 34 through 38' Processing helix chain 'E' and resid 45 through 56 removed outlier: 4.094A pdb=" N TRP E 49 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 66 removed outlier: 4.135A pdb=" N ALA E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 Processing helix chain 'E' and resid 82 through 100 removed outlier: 3.703A pdb=" N ILE E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 122 removed outlier: 4.006A pdb=" N GLU E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 140 removed outlier: 3.833A pdb=" N LYS E 137 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASP E 139 " --> pdb=" O GLY E 136 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA E 140 " --> pdb=" O LYS E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 140' Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.740A pdb=" N LYS E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 181 removed outlier: 3.594A pdb=" N ASP E 179 " --> pdb=" O TRP E 175 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU E 180 " --> pdb=" O ALA E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 201 removed outlier: 4.122A pdb=" N PHE E 201 " --> pdb=" O PRO E 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 201' Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 252 through 259 removed outlier: 3.502A pdb=" N ILE E 256 " --> pdb=" O TYR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.664A pdb=" N TYR E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU E 286 " --> pdb=" O PHE E 282 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE E 295 " --> pdb=" O PHE E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 321 Processing helix chain 'E' and resid 335 through 346 removed outlier: 3.765A pdb=" N LYS E 342 " --> pdb=" O GLU E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 360 Processing helix chain 'E' and resid 371 through 375 Processing helix chain 'E' and resid 376 through 383 removed outlier: 3.645A pdb=" N VAL E 381 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU E 382 " --> pdb=" O ASN E 378 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 406 removed outlier: 3.895A pdb=" N LEU E 399 " --> pdb=" O ILE E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 23 removed outlier: 3.517A pdb=" N CYS F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 56 through 66 removed outlier: 3.993A pdb=" N LEU F 60 " --> pdb=" O TYR F 56 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 77 Processing helix chain 'F' and resid 82 through 99 removed outlier: 3.971A pdb=" N ASP F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG F 99 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 122 removed outlier: 3.517A pdb=" N GLU F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 132 removed outlier: 4.150A pdb=" N ARG F 131 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 removed outlier: 3.775A pdb=" N LYS F 137 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 134 through 138' Processing helix chain 'F' and resid 141 through 154 removed outlier: 4.131A pdb=" N LYS F 145 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN F 154 " --> pdb=" O LYS F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 181 removed outlier: 3.640A pdb=" N TRP F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP F 179 " --> pdb=" O TRP F 175 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.838A pdb=" N PHE F 201 " --> pdb=" O PRO F 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 198 through 201' Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.892A pdb=" N GLU F 286 " --> pdb=" O PHE F 282 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.559A pdb=" N LEU F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY F 320 " --> pdb=" O ARG F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.531A pdb=" N ALA F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 360 removed outlier: 3.803A pdb=" N ALA F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 375 removed outlier: 3.677A pdb=" N LYS F 374 " --> pdb=" O GLY F 371 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA F 375 " --> pdb=" O GLY F 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 371 through 375' Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.606A pdb=" N GLU F 382 " --> pdb=" O ASN F 378 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU F 384 " --> pdb=" O PHE F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 407 Processing helix chain 'G' and resid 11 through 23 removed outlier: 3.541A pdb=" N PHE G 15 " --> pdb=" O ASN G 11 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 41 removed outlier: 3.544A pdb=" N ALA G 36 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER G 37 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL G 38 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 41 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 54 Processing helix chain 'G' and resid 61 through 66 Processing helix chain 'G' and resid 71 through 78 Processing helix chain 'G' and resid 83 through 100 removed outlier: 3.770A pdb=" N ASP G 87 " --> pdb=" O GLU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 122 removed outlier: 3.634A pdb=" N GLU G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS G 121 " --> pdb=" O LYS G 117 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 132 removed outlier: 3.758A pdb=" N PHE G 130 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 141 removed outlier: 3.542A pdb=" N LYS G 137 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS G 138 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP G 139 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA G 140 " --> pdb=" O LYS G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 153 removed outlier: 4.072A pdb=" N GLU G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU G 147 " --> pdb=" O TYR G 143 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE G 148 " --> pdb=" O HIS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 181 removed outlier: 4.060A pdb=" N TRP G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 203 removed outlier: 3.644A pdb=" N PHE G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP G 202 " --> pdb=" O GLN G 199 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 203 " --> pdb=" O ASN G 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 203' Processing helix chain 'G' and resid 244 through 252 Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.672A pdb=" N ILE G 257 " --> pdb=" O ILE G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 296 removed outlier: 3.692A pdb=" N TYR G 284 " --> pdb=" O ILE G 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU G 286 " --> pdb=" O PHE G 282 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET G 287 " --> pdb=" O VAL G 283 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER G 296 " --> pdb=" O GLY G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 321 removed outlier: 3.640A pdb=" N ASN G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 324 No H-bonds generated for 'chain 'G' and resid 322 through 324' Processing helix chain 'G' and resid 336 through 345 removed outlier: 3.529A pdb=" N LYS G 342 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS G 345 " --> pdb=" O THR G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 360 removed outlier: 3.536A pdb=" N LEU G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS G 359 " --> pdb=" O ILE G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 384 removed outlier: 3.645A pdb=" N GLU G 382 " --> pdb=" O ASN G 378 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS G 383 " --> pdb=" O SER G 379 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU G 384 " --> pdb=" O PHE G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 406 Processing helix chain 'H' and resid 11 through 23 removed outlier: 3.563A pdb=" N CYS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 38 removed outlier: 3.920A pdb=" N SER H 37 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL H 38 " --> pdb=" O GLY H 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 34 through 38' Processing helix chain 'H' and resid 44 through 54 Processing helix chain 'H' and resid 56 through 66 removed outlier: 3.527A pdb=" N LYS H 66 " --> pdb=" O ALA H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 78 removed outlier: 3.579A pdb=" N SER H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP H 76 " --> pdb=" O GLN H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 99 Processing helix chain 'H' and resid 102 through 122 removed outlier: 3.573A pdb=" N ARG H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 122 " --> pdb=" O GLU H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 132 removed outlier: 4.137A pdb=" N ARG H 131 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU H 132 " --> pdb=" O GLN H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 140 removed outlier: 3.769A pdb=" N LYS H 137 " --> pdb=" O ASN H 134 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS H 138 " --> pdb=" O GLN H 135 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ASP H 139 " --> pdb=" O GLY H 136 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA H 140 " --> pdb=" O LYS H 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 134 through 140' Processing helix chain 'H' and resid 141 through 154 removed outlier: 3.514A pdb=" N LYS H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN H 154 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 179 removed outlier: 3.752A pdb=" N ALA H 176 " --> pdb=" O ALA H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.923A pdb=" N PHE H 201 " --> pdb=" O PRO H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 244 through 252 Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.790A pdb=" N ILE H 295 " --> pdb=" O PHE H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 321 Processing helix chain 'H' and resid 322 through 324 No H-bonds generated for 'chain 'H' and resid 322 through 324' Processing helix chain 'H' and resid 335 through 344 removed outlier: 3.791A pdb=" N ALA H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 360 removed outlier: 3.657A pdb=" N ALA H 354 " --> pdb=" O GLU H 350 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE H 355 " --> pdb=" O ALA H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 375 removed outlier: 3.661A pdb=" N ALA H 375 " --> pdb=" O GLY H 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 372 through 375' Processing helix chain 'H' and resid 376 through 384 removed outlier: 3.709A pdb=" N LEU H 384 " --> pdb=" O PHE H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 405 removed outlier: 4.572A pdb=" N ASN H 405 " --> pdb=" O GLU H 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 23 removed outlier: 3.530A pdb=" N CYS I 23 " --> pdb=" O VAL I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 41 removed outlier: 3.911A pdb=" N SER I 37 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL I 38 " --> pdb=" O GLY I 35 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLY I 39 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY I 41 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 56 removed outlier: 3.991A pdb=" N GLN I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 66 removed outlier: 4.464A pdb=" N ALA I 62 " --> pdb=" O GLU I 58 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 78 Processing helix chain 'I' and resid 81 through 100 removed outlier: 3.855A pdb=" N LYS I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 122 removed outlier: 3.848A pdb=" N LYS I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU I 112 " --> pdb=" O PHE I 108 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS I 121 " --> pdb=" O LYS I 117 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 132 removed outlier: 3.648A pdb=" N PHE I 130 " --> pdb=" O GLY I 127 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG I 131 " --> pdb=" O GLU I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 140 removed outlier: 4.008A pdb=" N LYS I 137 " --> pdb=" O ASN I 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS I 138 " --> pdb=" O GLN I 135 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP I 139 " --> pdb=" O GLY I 136 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA I 140 " --> pdb=" O LYS I 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 134 through 140' Processing helix chain 'I' and resid 141 through 154 removed outlier: 3.701A pdb=" N LYS I 145 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU I 147 " --> pdb=" O TYR I 143 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE I 148 " --> pdb=" O HIS I 144 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN I 154 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 181 removed outlier: 3.608A pdb=" N TRP I 175 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA I 176 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA I 177 " --> pdb=" O LEU I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 201 removed outlier: 3.644A pdb=" N PHE I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 198 through 201' Processing helix chain 'I' and resid 244 through 252 Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 280 through 295 removed outlier: 3.946A pdb=" N TYR I 284 " --> pdb=" O ILE I 280 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE I 295 " --> pdb=" O PHE I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 321 Processing helix chain 'I' and resid 322 through 324 No H-bonds generated for 'chain 'I' and resid 322 through 324' Processing helix chain 'I' and resid 335 through 344 removed outlier: 3.620A pdb=" N ALA I 339 " --> pdb=" O GLU I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 358 Processing helix chain 'I' and resid 376 through 384 removed outlier: 3.579A pdb=" N GLU I 382 " --> pdb=" O ASN I 378 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 406 removed outlier: 3.961A pdb=" N LEU I 406 " --> pdb=" O ALA I 402 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 23 removed outlier: 3.679A pdb=" N SER J 17 " --> pdb=" O ASP J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 41 removed outlier: 3.611A pdb=" N SER J 37 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY J 39 " --> pdb=" O ALA J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 56 removed outlier: 3.759A pdb=" N VAL J 48 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 63 removed outlier: 3.565A pdb=" N ALA J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 78 Processing helix chain 'J' and resid 81 through 100 removed outlier: 3.801A pdb=" N LEU J 85 " --> pdb=" O ASN J 81 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE J 86 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 124 removed outlier: 3.688A pdb=" N GLU J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU J 107 " --> pdb=" O ASP J 103 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU J 112 " --> pdb=" O PHE J 108 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR J 120 " --> pdb=" O TYR J 116 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU J 124 " --> pdb=" O THR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 132 removed outlier: 3.975A pdb=" N GLN J 129 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG J 131 " --> pdb=" O GLU J 128 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU J 132 " --> pdb=" O GLN J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 140 removed outlier: 3.564A pdb=" N LYS J 137 " --> pdb=" O ASN J 134 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS J 138 " --> pdb=" O GLN J 135 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP J 139 " --> pdb=" O GLY J 136 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA J 140 " --> pdb=" O LYS J 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 134 through 140' Processing helix chain 'J' and resid 141 through 154 removed outlier: 3.608A pdb=" N LYS J 145 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 181 removed outlier: 3.583A pdb=" N ASP J 179 " --> pdb=" O TRP J 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 201 removed outlier: 3.929A pdb=" N PHE J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 198 through 201' Processing helix chain 'J' and resid 244 through 252 removed outlier: 3.700A pdb=" N TYR J 249 " --> pdb=" O ALA J 245 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP J 250 " --> pdb=" O SER J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 Processing helix chain 'J' and resid 281 through 296 removed outlier: 4.416A pdb=" N GLY J 285 " --> pdb=" O GLY J 281 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU J 286 " --> pdb=" O PHE J 282 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE J 295 " --> pdb=" O PHE J 291 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER J 296 " --> pdb=" O GLY J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 321 removed outlier: 3.535A pdb=" N ASN J 315 " --> pdb=" O ASP J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 324 No H-bonds generated for 'chain 'J' and resid 322 through 324' Processing helix chain 'J' and resid 336 through 345 removed outlier: 3.888A pdb=" N THR J 341 " --> pdb=" O LYS J 337 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS J 342 " --> pdb=" O GLU J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 360 Processing helix chain 'J' and resid 371 through 375 removed outlier: 3.588A pdb=" N LYS J 374 " --> pdb=" O GLY J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 376 through 384 removed outlier: 3.862A pdb=" N LEU J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 394 through 408 removed outlier: 3.709A pdb=" N VAL J 400 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA J 404 " --> pdb=" O VAL J 400 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN J 405 " --> pdb=" O GLU J 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 22 Processing helix chain 'K' and resid 23 through 25 No H-bonds generated for 'chain 'K' and resid 23 through 25' Processing helix chain 'K' and resid 37 through 41 Processing helix chain 'K' and resid 44 through 56 Processing helix chain 'K' and resid 59 through 66 removed outlier: 3.647A pdb=" N LEU K 63 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 78 Processing helix chain 'K' and resid 81 through 100 removed outlier: 3.545A pdb=" N LEU K 85 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER K 94 " --> pdb=" O THR K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 121 removed outlier: 3.591A pdb=" N ARG K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.600A pdb=" N PHE K 130 " --> pdb=" O GLY K 127 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG K 131 " --> pdb=" O GLU K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 140 removed outlier: 3.617A pdb=" N LYS K 137 " --> pdb=" O ASN K 134 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS K 138 " --> pdb=" O GLN K 135 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP K 139 " --> pdb=" O GLY K 136 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA K 140 " --> pdb=" O LYS K 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 134 through 140' Processing helix chain 'K' and resid 141 through 153 removed outlier: 3.965A pdb=" N LYS K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU K 146 " --> pdb=" O LYS K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 181 Processing helix chain 'K' and resid 199 through 201 No H-bonds generated for 'chain 'K' and resid 199 through 201' Processing helix chain 'K' and resid 244 through 252 Processing helix chain 'K' and resid 252 through 258 removed outlier: 3.579A pdb=" N ILE K 257 " --> pdb=" O ILE K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 295 removed outlier: 3.840A pdb=" N TYR K 284 " --> pdb=" O ILE K 280 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE K 291 " --> pdb=" O MET K 287 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY K 292 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU K 293 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE K 295 " --> pdb=" O PHE K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 321 removed outlier: 3.517A pdb=" N ALA K 321 " --> pdb=" O ILE K 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 322 through 324 No H-bonds generated for 'chain 'K' and resid 322 through 324' Processing helix chain 'K' and resid 335 through 344 removed outlier: 3.530A pdb=" N ALA K 339 " --> pdb=" O GLU K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 361 Processing helix chain 'K' and resid 372 through 375 removed outlier: 3.656A pdb=" N ALA K 375 " --> pdb=" O GLY K 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 372 through 375' Processing helix chain 'K' and resid 376 through 383 removed outlier: 3.720A pdb=" N GLU K 382 " --> pdb=" O ASN K 378 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS K 383 " --> pdb=" O SER K 379 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 406 Processing helix chain 'L' and resid 11 through 23 removed outlier: 3.667A pdb=" N SER L 17 " --> pdb=" O ASP L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 38 removed outlier: 3.811A pdb=" N SER L 37 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL L 38 " --> pdb=" O GLY L 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 34 through 38' Processing helix chain 'L' and resid 44 through 56 removed outlier: 3.803A pdb=" N VAL L 48 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP L 49 " --> pdb=" O MET L 45 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS L 50 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 66 Processing helix chain 'L' and resid 71 through 77 removed outlier: 3.801A pdb=" N ASN L 77 " --> pdb=" O ILE L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 99 removed outlier: 3.504A pdb=" N ARG L 99 " --> pdb=" O VAL L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 122 removed outlier: 3.799A pdb=" N GLU L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.818A pdb=" N GLN L 129 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE L 130 " --> pdb=" O GLY L 127 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 140 removed outlier: 3.699A pdb=" N LYS L 137 " --> pdb=" O ASN L 134 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS L 138 " --> pdb=" O GLN L 135 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP L 139 " --> pdb=" O GLY L 136 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA L 140 " --> pdb=" O LYS L 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 134 through 140' Processing helix chain 'L' and resid 141 through 153 removed outlier: 3.699A pdb=" N LYS L 145 " --> pdb=" O PHE L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 179 Processing helix chain 'L' and resid 198 through 201 removed outlier: 3.712A pdb=" N PHE L 201 " --> pdb=" O PRO L 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 198 through 201' Processing helix chain 'L' and resid 244 through 252 Processing helix chain 'L' and resid 252 through 259 Processing helix chain 'L' and resid 282 through 296 removed outlier: 3.659A pdb=" N GLU L 286 " --> pdb=" O PHE L 282 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE L 288 " --> pdb=" O TYR L 284 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE L 295 " --> pdb=" O PHE L 291 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER L 296 " --> pdb=" O GLY L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 321 Processing helix chain 'L' and resid 322 through 324 No H-bonds generated for 'chain 'L' and resid 322 through 324' Processing helix chain 'L' and resid 336 through 345 removed outlier: 3.597A pdb=" N LYS L 345 " --> pdb=" O THR L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 349 through 360 Processing helix chain 'L' and resid 371 through 375 Processing helix chain 'L' and resid 376 through 384 removed outlier: 3.785A pdb=" N LEU L 384 " --> pdb=" O PHE L 380 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 402 removed outlier: 4.131A pdb=" N LEU L 399 " --> pdb=" O ILE L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 403 through 408 removed outlier: 3.659A pdb=" N SER L 407 " --> pdb=" O ILE L 403 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS L 408 " --> pdb=" O ALA L 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 403 through 408' Processing helix chain 'M' and resid 129 through 137 removed outlier: 3.637A pdb=" N ILE M 135 " --> pdb=" O ASP M 131 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE M 136 " --> pdb=" O PHE M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 145 Proline residue: M 145 - end of helix Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 182 through 196 removed outlier: 3.541A pdb=" N PHE M 186 " --> pdb=" O GLY M 182 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER M 195 " --> pdb=" O THR M 191 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU M 196 " --> pdb=" O ARG M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 271 removed outlier: 3.672A pdb=" N LEU M 266 " --> pdb=" O GLY M 262 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE M 267 " --> pdb=" O PHE M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 276 through 287 removed outlier: 3.885A pdb=" N ALA M 280 " --> pdb=" O THR M 276 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 291 removed outlier: 3.540A pdb=" N THR M 291 " --> pdb=" O ILE M 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 288 through 291' Processing helix chain 'M' and resid 322 through 331 Processing helix chain 'M' and resid 342 through 344 No H-bonds generated for 'chain 'M' and resid 342 through 344' Processing helix chain 'M' and resid 345 through 355 removed outlier: 3.571A pdb=" N LEU M 349 " --> pdb=" O SER M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 373 removed outlier: 3.844A pdb=" N SER M 372 " --> pdb=" O ALA M 368 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN M 373 " --> pdb=" O PHE M 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 368 through 373' Processing helix chain 'M' and resid 374 through 386 removed outlier: 3.829A pdb=" N VAL M 378 " --> pdb=" O VAL M 374 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA M 385 " --> pdb=" O ILE M 381 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU M 386 " --> pdb=" O GLN M 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 392 Processing helix chain 'M' and resid 407 through 422 removed outlier: 3.591A pdb=" N LYS M 411 " --> pdb=" O THR M 407 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA M 412 " --> pdb=" O HIS M 408 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET M 413 " --> pdb=" O TRP M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 465 removed outlier: 4.219A pdb=" N SER M 451 " --> pdb=" O PRO M 447 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA M 452 " --> pdb=" O MET M 448 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU M 453 " --> pdb=" O LEU M 449 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU M 454 " --> pdb=" O LEU M 450 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU M 455 " --> pdb=" O SER M 451 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG M 463 " --> pdb=" O GLU M 459 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY M 465 " --> pdb=" O LEU M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 466 through 469 removed outlier: 3.681A pdb=" N SER M 469 " --> pdb=" O GLN M 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 466 through 469' Processing helix chain 'M' and resid 479 through 482 Processing helix chain 'M' and resid 522 through 528 removed outlier: 3.615A pdb=" N LEU M 526 " --> pdb=" O SER M 522 " (cutoff:3.500A) Processing helix chain 'M' and resid 543 through 550 Processing helix chain 'M' and resid 559 through 564 removed outlier: 3.598A pdb=" N SER M 562 " --> pdb=" O LYS M 559 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU M 564 " --> pdb=" O ILE M 561 " (cutoff:3.500A) Processing helix chain 'M' and resid 597 through 603 removed outlier: 3.886A pdb=" N GLU M 601 " --> pdb=" O VAL M 597 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 33 removed outlier: 3.878A pdb=" N GLN N 32 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 137 removed outlier: 3.569A pdb=" N LEU N 133 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE N 135 " --> pdb=" O ASP N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 145 No H-bonds generated for 'chain 'N' and resid 143 through 145' Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 182 through 198 removed outlier: 3.909A pdb=" N LYS N 197 " --> pdb=" O LYS N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 217 Processing helix chain 'N' and resid 261 through 271 removed outlier: 3.833A pdb=" N GLY N 265 " --> pdb=" O LEU N 261 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE N 267 " --> pdb=" O PHE N 263 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU N 269 " --> pdb=" O GLY N 265 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU N 270 " --> pdb=" O LEU N 266 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 286 Processing helix chain 'N' and resid 287 through 291 removed outlier: 3.607A pdb=" N ARG N 290 " --> pdb=" O ALA N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 331 Processing helix chain 'N' and resid 344 through 355 removed outlier: 4.466A pdb=" N THR N 348 " --> pdb=" O LYS N 344 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU N 349 " --> pdb=" O SER N 345 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 385 removed outlier: 3.603A pdb=" N VAL N 378 " --> pdb=" O VAL N 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 422 removed outlier: 3.965A pdb=" N LYS N 411 " --> pdb=" O THR N 407 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA N 412 " --> pdb=" O HIS N 408 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU N 416 " --> pdb=" O ALA N 412 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL N 417 " --> pdb=" O MET N 413 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 465 removed outlier: 3.629A pdb=" N ALA N 458 " --> pdb=" O LEU N 454 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU N 459 " --> pdb=" O GLU N 455 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE N 460 " --> pdb=" O MET N 456 " (cutoff:3.500A) Processing helix chain 'N' and resid 479 through 482 removed outlier: 3.589A pdb=" N TYR N 482 " --> pdb=" O ALA N 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 479 through 482' Processing helix chain 'N' and resid 498 through 503 Processing helix chain 'N' and resid 517 through 521 Processing helix chain 'N' and resid 522 through 527 Processing helix chain 'N' and resid 539 through 550 removed outlier: 3.605A pdb=" N ALA N 545 " --> pdb=" O ARG N 541 " (cutoff:3.500A) Processing helix chain 'N' and resid 557 through 564 removed outlier: 3.574A pdb=" N ILE N 561 " --> pdb=" O LEU N 558 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER N 562 " --> pdb=" O LYS N 559 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU N 564 " --> pdb=" O ILE N 561 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 137 Processing helix chain 'O' and resid 140 through 145 removed outlier: 3.570A pdb=" N LEU O 144 " --> pdb=" O LYS O 141 " (cutoff:3.500A) Proline residue: O 145 - end of helix Processing helix chain 'O' and resid 165 through 170 Processing helix chain 'O' and resid 182 through 198 Processing helix chain 'O' and resid 213 through 217 removed outlier: 3.602A pdb=" N PHE O 216 " --> pdb=" O ALA O 213 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR O 217 " --> pdb=" O GLN O 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 213 through 217' Processing helix chain 'O' and resid 261 through 271 removed outlier: 3.555A pdb=" N GLY O 265 " --> pdb=" O LEU O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 277 through 287 removed outlier: 3.555A pdb=" N ALA O 287 " --> pdb=" O ASN O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 288 through 291 removed outlier: 4.034A pdb=" N THR O 291 " --> pdb=" O ILE O 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 288 through 291' Processing helix chain 'O' and resid 321 through 331 removed outlier: 3.625A pdb=" N TRP O 325 " --> pdb=" O LYS O 321 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 344 No H-bonds generated for 'chain 'O' and resid 342 through 344' Processing helix chain 'O' and resid 345 through 355 removed outlier: 4.096A pdb=" N LEU O 349 " --> pdb=" O SER O 345 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL O 350 " --> pdb=" O LEU O 346 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA O 351 " --> pdb=" O ALA O 347 " (cutoff:3.500A) Processing helix chain 'O' and resid 368 through 386 Proline residue: O 376 - end of helix Processing helix chain 'O' and resid 409 through 421 removed outlier: 3.894A pdb=" N MET O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE O 420 " --> pdb=" O GLU O 416 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 465 removed outlier: 3.644A pdb=" N SER O 451 " --> pdb=" O PRO O 447 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY O 465 " --> pdb=" O LEU O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 479 through 482 Processing helix chain 'O' and resid 490 through 494 removed outlier: 4.306A pdb=" N ILE O 494 " --> pdb=" O ASP O 491 " (cutoff:3.500A) Processing helix chain 'O' and resid 496 through 507 Processing helix chain 'O' and resid 517 through 521 Processing helix chain 'O' and resid 522 through 527 removed outlier: 3.598A pdb=" N LEU O 526 " --> pdb=" O SER O 522 " (cutoff:3.500A) Processing helix chain 'O' and resid 539 through 550 removed outlier: 3.829A pdb=" N LEU O 543 " --> pdb=" O ASN O 539 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA O 545 " --> pdb=" O ARG O 541 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA O 549 " --> pdb=" O ALA O 545 " (cutoff:3.500A) Processing helix chain 'O' and resid 554 through 559 removed outlier: 3.759A pdb=" N LEU O 558 " --> pdb=" O ASN O 554 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS O 559 " --> pdb=" O GLU O 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 554 through 559' Processing helix chain 'O' and resid 597 through 603 removed outlier: 3.782A pdb=" N GLU O 601 " --> pdb=" O VAL O 597 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 33 removed outlier: 4.078A pdb=" N GLN P 32 " --> pdb=" O GLU P 29 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY P 33 " --> pdb=" O GLY P 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 29 through 33' Processing helix chain 'P' and resid 129 through 137 Processing helix chain 'P' and resid 140 through 144 removed outlier: 3.660A pdb=" N GLU P 143 " --> pdb=" O ASP P 140 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU P 144 " --> pdb=" O LYS P 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 140 through 144' Processing helix chain 'P' and resid 165 through 169 Processing helix chain 'P' and resid 182 through 198 Processing helix chain 'P' and resid 213 through 217 removed outlier: 3.528A pdb=" N PHE P 216 " --> pdb=" O ALA P 213 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR P 217 " --> pdb=" O GLN P 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 213 through 217' Processing helix chain 'P' and resid 261 through 270 removed outlier: 3.581A pdb=" N LEU P 266 " --> pdb=" O GLY P 262 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE P 267 " --> pdb=" O PHE P 263 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU P 270 " --> pdb=" O LEU P 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 277 through 287 Processing helix chain 'P' and resid 344 through 353 removed outlier: 4.072A pdb=" N THR P 348 " --> pdb=" O LYS P 344 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA P 351 " --> pdb=" O ALA P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 375 through 386 removed outlier: 3.682A pdb=" N GLN P 382 " --> pdb=" O VAL P 378 " (cutoff:3.500A) Processing helix chain 'P' and resid 389 through 392 Processing helix chain 'P' and resid 407 through 418 Processing helix chain 'P' and resid 445 through 465 removed outlier: 3.874A pdb=" N PHE P 462 " --> pdb=" O ALA P 458 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG P 463 " --> pdb=" O GLU P 459 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG P 464 " --> pdb=" O ILE P 460 " (cutoff:3.500A) Processing helix chain 'P' and resid 478 through 482 Processing helix chain 'P' and resid 497 through 504 Processing helix chain 'P' and resid 505 through 507 No H-bonds generated for 'chain 'P' and resid 505 through 507' Processing helix chain 'P' and resid 517 through 521 Processing helix chain 'P' and resid 525 through 527 No H-bonds generated for 'chain 'P' and resid 525 through 527' Processing helix chain 'P' and resid 539 through 548 Processing helix chain 'P' and resid 560 through 564 removed outlier: 3.647A pdb=" N GLY P 563 " --> pdb=" O GLN P 560 " (cutoff:3.500A) Processing helix chain 'P' and resid 598 through 602 Processing helix chain 'Q' and resid 129 through 137 removed outlier: 3.639A pdb=" N LEU Q 133 " --> pdb=" O THR Q 129 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN Q 134 " --> pdb=" O SER Q 130 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE Q 135 " --> pdb=" O ASP Q 131 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 145 No H-bonds generated for 'chain 'Q' and resid 143 through 145' Processing helix chain 'Q' and resid 182 through 198 Processing helix chain 'Q' and resid 259 through 261 No H-bonds generated for 'chain 'Q' and resid 259 through 261' Processing helix chain 'Q' and resid 262 through 270 removed outlier: 3.580A pdb=" N LEU Q 270 " --> pdb=" O LEU Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 287 Processing helix chain 'Q' and resid 321 through 332 Processing helix chain 'Q' and resid 344 through 355 removed outlier: 4.317A pdb=" N THR Q 348 " --> pdb=" O LYS Q 344 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU Q 349 " --> pdb=" O SER Q 345 " (cutoff:3.500A) Processing helix chain 'Q' and resid 367 through 372 removed outlier: 3.620A pdb=" N PHE Q 371 " --> pdb=" O ASP Q 367 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER Q 372 " --> pdb=" O ALA Q 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 367 through 372' Processing helix chain 'Q' and resid 374 through 386 removed outlier: 4.377A pdb=" N GLU Q 386 " --> pdb=" O GLN Q 382 " (cutoff:3.500A) Processing helix chain 'Q' and resid 387 through 393 removed outlier: 3.970A pdb=" N ILE Q 393 " --> pdb=" O ARG Q 389 " (cutoff:3.500A) Processing helix chain 'Q' and resid 409 through 421 removed outlier: 3.503A pdb=" N MET Q 413 " --> pdb=" O TRP Q 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 445 through 463 removed outlier: 3.856A pdb=" N ARG Q 463 " --> pdb=" O GLU Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 479 through 482 Processing helix chain 'Q' and resid 498 through 504 removed outlier: 3.858A pdb=" N LYS Q 502 " --> pdb=" O GLU Q 498 " (cutoff:3.500A) Processing helix chain 'Q' and resid 517 through 521 Processing helix chain 'Q' and resid 522 through 527 Processing helix chain 'Q' and resid 539 through 550 removed outlier: 3.735A pdb=" N ALA Q 545 " --> pdb=" O ARG Q 541 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA Q 549 " --> pdb=" O ALA Q 545 " (cutoff:3.500A) Processing helix chain 'Q' and resid 556 through 564 removed outlier: 3.820A pdb=" N LYS Q 559 " --> pdb=" O GLN Q 556 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE Q 561 " --> pdb=" O LEU Q 558 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER Q 562 " --> pdb=" O LYS Q 559 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU Q 564 " --> pdb=" O ILE Q 561 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 137 removed outlier: 3.663A pdb=" N ILE R 135 " --> pdb=" O ASP R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Proline residue: R 145 - end of helix Processing helix chain 'R' and resid 165 through 170 Processing helix chain 'R' and resid 182 through 196 Processing helix chain 'R' and resid 261 through 271 removed outlier: 3.900A pdb=" N GLY R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU R 266 " --> pdb=" O GLY R 262 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE R 267 " --> pdb=" O PHE R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 286 Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 331 removed outlier: 3.654A pdb=" N TRP R 325 " --> pdb=" O LYS R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 353 removed outlier: 4.310A pdb=" N THR R 348 " --> pdb=" O LYS R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 374 removed outlier: 3.518A pdb=" N PHE R 371 " --> pdb=" O ASP R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 374 through 386 removed outlier: 3.653A pdb=" N VAL R 378 " --> pdb=" O VAL R 374 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN R 383 " --> pdb=" O LYS R 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU R 384 " --> pdb=" O ILE R 380 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA R 385 " --> pdb=" O ILE R 381 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 422 removed outlier: 4.118A pdb=" N LYS R 411 " --> pdb=" O THR R 407 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA R 412 " --> pdb=" O HIS R 408 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET R 413 " --> pdb=" O TRP R 409 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU R 416 " --> pdb=" O ALA R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 465 removed outlier: 3.622A pdb=" N SER R 451 " --> pdb=" O PRO R 447 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA R 452 " --> pdb=" O MET R 448 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU R 453 " --> pdb=" O LEU R 449 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU R 454 " --> pdb=" O LEU R 450 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU R 455 " --> pdb=" O SER R 451 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET R 456 " --> pdb=" O ALA R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 478 through 483 removed outlier: 4.162A pdb=" N TYR R 482 " --> pdb=" O GLU R 478 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 507 removed outlier: 3.518A pdb=" N GLY R 504 " --> pdb=" O LEU R 500 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG R 505 " --> pdb=" O ALA R 501 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS R 506 " --> pdb=" O LYS R 502 " (cutoff:3.500A) Processing helix chain 'R' and resid 522 through 528 removed outlier: 3.691A pdb=" N MET R 528 " --> pdb=" O THR R 524 " (cutoff:3.500A) Processing helix chain 'R' and resid 539 through 550 removed outlier: 3.935A pdb=" N ALA R 549 " --> pdb=" O ALA R 545 " (cutoff:3.500A) Processing helix chain 'R' and resid 554 through 560 removed outlier: 3.545A pdb=" N GLN R 560 " --> pdb=" O GLN R 556 " (cutoff:3.500A) Processing helix chain 'R' and resid 561 through 564 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.605A pdb=" N ASN A 8 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 5 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 163 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 164 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN A 183 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU A 223 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE A 185 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LYS A 225 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.611A pdb=" N SER A 189 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 195 " --> pdb=" O SER A 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 207 Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.936A pdb=" N VAL B 28 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE B 165 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 30 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 164 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN B 183 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 223 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE B 185 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LYS B 225 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 188 through 189 Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 207 Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AA9, first strand: chain 'C' and resid 8 through 9 removed outlier: 8.687A pdb=" N THR C 367 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 329 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL C 369 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 331 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 28 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N PHE C 165 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL C 30 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE C 164 " --> pdb=" O TYR C 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB2, first strand: chain 'C' and resid 232 through 234 Processing sheet with id=AB3, first strand: chain 'D' and resid 8 through 10 removed outlier: 3.560A pdb=" N ASN D 8 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE D 3 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR D 367 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL D 329 " --> pdb=" O THR D 367 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL D 369 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE D 331 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR D 300 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N VAL D 330 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU D 302 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N TYR D 332 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE D 304 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL D 28 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N PHE D 165 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL D 30 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 164 " --> pdb=" O TYR D 224 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN D 183 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU D 223 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE D 185 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LYS D 225 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 188 through 189 Processing sheet with id=AB5, first strand: chain 'D' and resid 203 through 207 Processing sheet with id=AB6, first strand: chain 'D' and resid 232 through 234 Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 5 removed outlier: 7.065A pdb=" N VAL E 28 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N PHE E 165 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL E 30 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE E 164 " --> pdb=" O TYR E 224 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN E 183 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU E 223 " --> pdb=" O GLN E 183 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE E 185 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LYS E 225 " --> pdb=" O PHE E 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 188 through 189 Processing sheet with id=AB9, first strand: chain 'E' and resid 232 through 234 Processing sheet with id=AC1, first strand: chain 'F' and resid 8 through 9 removed outlier: 8.524A pdb=" N THR F 367 " --> pdb=" O PHE F 327 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL F 329 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL F 369 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE F 331 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN F 27 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE F 303 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY F 29 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN F 305 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU F 31 " --> pdb=" O ASN F 305 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL F 28 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N PHE F 165 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 30 " --> pdb=" O PHE F 165 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE F 164 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN F 183 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU F 223 " --> pdb=" O GLN F 183 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE F 185 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LYS F 225 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 188 through 189 Processing sheet with id=AC3, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AC4, first strand: chain 'F' and resid 232 through 234 Processing sheet with id=AC5, first strand: chain 'G' and resid 8 through 9 removed outlier: 3.623A pdb=" N GLN G 5 " --> pdb=" O ASN G 8 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL G 28 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N PHE G 165 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL G 30 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE G 164 " --> pdb=" O TYR G 224 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN G 183 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU G 223 " --> pdb=" O GLN G 183 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE G 185 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LYS G 225 " --> pdb=" O PHE G 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 188 through 189 removed outlier: 3.506A pdb=" N SER G 189 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN G 195 " --> pdb=" O SER G 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 232 through 234 Processing sheet with id=AC8, first strand: chain 'H' and resid 8 through 9 removed outlier: 3.720A pdb=" N ASN H 8 " --> pdb=" O GLN H 5 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR H 367 " --> pdb=" O PHE H 327 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL H 329 " --> pdb=" O THR H 367 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL H 369 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE H 331 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL H 28 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N PHE H 165 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL H 30 " --> pdb=" O PHE H 165 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE H 164 " --> pdb=" O TYR H 224 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN H 183 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU H 223 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE H 185 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LYS H 225 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 188 through 189 removed outlier: 4.432A pdb=" N ARG H 194 " --> pdb=" O GLU H 242 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU H 242 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE H 196 " --> pdb=" O VAL H 240 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL H 240 " --> pdb=" O PHE H 196 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 203 through 207 Processing sheet with id=AD2, first strand: chain 'I' and resid 8 through 10 removed outlier: 3.829A pdb=" N ASN I 8 " --> pdb=" O GLN I 5 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE I 3 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE I 164 " --> pdb=" O TYR I 224 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 188 through 189 Processing sheet with id=AD4, first strand: chain 'I' and resid 233 through 234 Processing sheet with id=AD5, first strand: chain 'J' and resid 8 through 9 removed outlier: 3.771A pdb=" N ASN J 8 " --> pdb=" O GLN J 5 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN J 5 " --> pdb=" O ASN J 8 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR J 300 " --> pdb=" O HIS J 328 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N VAL J 330 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU J 302 " --> pdb=" O VAL J 330 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N TYR J 332 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE J 304 " --> pdb=" O TYR J 332 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL J 28 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N PHE J 165 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL J 30 " --> pdb=" O PHE J 165 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE J 164 " --> pdb=" O TYR J 224 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN J 183 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU J 223 " --> pdb=" O GLN J 183 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE J 185 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LYS J 225 " --> pdb=" O PHE J 185 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 188 through 189 Processing sheet with id=AD7, first strand: chain 'J' and resid 203 through 207 Processing sheet with id=AD8, first strand: chain 'J' and resid 232 through 234 Processing sheet with id=AD9, first strand: chain 'K' and resid 8 through 9 removed outlier: 6.668A pdb=" N THR K 300 " --> pdb=" O HIS K 328 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N VAL K 330 " --> pdb=" O THR K 300 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU K 302 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N TYR K 332 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE K 304 " --> pdb=" O TYR K 332 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL K 28 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N PHE K 165 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL K 30 " --> pdb=" O PHE K 165 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE K 164 " --> pdb=" O TYR K 224 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN K 183 " --> pdb=" O ALA K 221 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU K 223 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE K 185 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LYS K 225 " --> pdb=" O PHE K 185 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 188 through 189 Processing sheet with id=AE2, first strand: chain 'K' and resid 232 through 234 Processing sheet with id=AE3, first strand: chain 'L' and resid 8 through 10 removed outlier: 3.618A pdb=" N ASN L 8 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE L 3 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR L 367 " --> pdb=" O PHE L 327 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL L 329 " --> pdb=" O THR L 367 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL L 369 " --> pdb=" O VAL L 329 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE L 331 " --> pdb=" O VAL L 369 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN L 27 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N PHE L 303 " --> pdb=" O ASN L 27 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY L 29 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASN L 305 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU L 31 " --> pdb=" O ASN L 305 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA L 163 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE L 164 " --> pdb=" O TYR L 224 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN L 183 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU L 223 " --> pdb=" O GLN L 183 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE L 185 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LYS L 225 " --> pdb=" O PHE L 185 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 188 through 189 Processing sheet with id=AE5, first strand: chain 'L' and resid 232 through 234 Processing sheet with id=AE6, first strand: chain 'M' and resid 13 through 18 removed outlier: 7.082A pdb=" N ARG M 24 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU M 18 " --> pdb=" O ARG M 22 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG M 22 " --> pdb=" O LEU M 18 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 22 through 27 current: chain 'M' and resid 59 through 70 removed outlier: 6.615A pdb=" N LEU M 60 " --> pdb=" O PHE M 101 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE M 101 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL M 62 " --> pdb=" O ILE M 99 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE M 95 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET M 68 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN M 93 " --> pdb=" O MET M 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 110 through 112 current: chain 'N' and resid 23 through 27 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 23 through 27 current: chain 'N' and resid 59 through 70 removed outlier: 6.138A pdb=" N LEU N 60 " --> pdb=" O PHE N 101 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE N 101 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL N 62 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE N 95 " --> pdb=" O THR N 66 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET N 68 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN N 93 " --> pdb=" O MET N 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 110 through 112 current: chain 'O' and resid 22 through 27 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 22 through 27 current: chain 'O' and resid 60 through 70 removed outlier: 3.561A pdb=" N GLY O 100 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG O 64 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA O 98 " --> pdb=" O ARG O 64 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR O 66 " --> pdb=" O ALA O 96 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ALA O 96 " --> pdb=" O THR O 66 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N MET O 68 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE O 94 " --> pdb=" O MET O 68 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE O 70 " --> pdb=" O ARG O 92 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG O 92 " --> pdb=" O PHE O 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 109 through 112 current: chain 'P' and resid 22 through 27 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 22 through 27 current: chain 'P' and resid 59 through 70 removed outlier: 6.331A pdb=" N LEU P 60 " --> pdb=" O PHE P 101 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE P 101 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL P 62 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE P 95 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N MET P 68 " --> pdb=" O GLN P 93 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLN P 93 " --> pdb=" O MET P 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 109 through 112 current: chain 'Q' and resid 23 through 27 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 23 through 27 current: chain 'Q' and resid 60 through 70 removed outlier: 6.584A pdb=" N LEU Q 60 " --> pdb=" O PHE Q 101 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE Q 101 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL Q 62 " --> pdb=" O ILE Q 99 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE Q 95 " --> pdb=" O THR Q 66 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N MET Q 68 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLN Q 93 " --> pdb=" O MET Q 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 109 through 112 current: chain 'R' and resid 22 through 27 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 22 through 27 current: chain 'R' and resid 60 through 65 removed outlier: 3.952A pdb=" N GLY R 100 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ARG R 64 " --> pdb=" O ALA R 98 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ALA R 98 " --> pdb=" O ARG R 64 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 35 through 38 Processing sheet with id=AE8, first strand: chain 'M' and resid 160 through 164 removed outlier: 4.320A pdb=" N GLY M 151 " --> pdb=" O ILE M 161 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA M 163 " --> pdb=" O GLU M 149 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLU M 149 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N HIS M 172 " --> pdb=" O CYS M 529 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN M 531 " --> pdb=" O HIS M 172 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA M 174 " --> pdb=" O ASN M 531 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER M 510 " --> pdb=" O THR M 472 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG M 202 " --> pdb=" O VAL M 473 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU M 475 " --> pdb=" O ARG M 202 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL M 204 " --> pdb=" O LEU M 475 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU M 477 " --> pdb=" O VAL M 204 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE M 206 " --> pdb=" O GLU M 477 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE M 203 " --> pdb=" O HIS M 434 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL M 436 " --> pdb=" O ILE M 203 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE M 205 " --> pdb=" O VAL M 436 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU M 227 " --> pdb=" O ASN M 437 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 256 through 257 removed outlier: 5.930A pdb=" N ILE M 256 " --> pdb=" O ASN M 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'M' and resid 292 through 293 Processing sheet with id=AF2, first strand: chain 'M' and resid 356 through 359 removed outlier: 3.959A pdb=" N GLY M 363 " --> pdb=" O ASP M 359 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 35 through 38 Processing sheet with id=AF4, first strand: chain 'N' and resid 160 through 164 removed outlier: 7.153A pdb=" N ILE N 161 " --> pdb=" O LEU N 150 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N HIS N 172 " --> pdb=" O CYS N 529 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN N 531 " --> pdb=" O HIS N 172 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA N 174 " --> pdb=" O ASN N 531 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR N 515 " --> pdb=" O VAL N 175 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU N 477 " --> pdb=" O PHE N 206 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS N 223 " --> pdb=" O ILE N 435 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ASN N 437 " --> pdb=" O LYS N 223 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR N 225 " --> pdb=" O ASN N 437 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LYS N 254 " --> pdb=" O HIS N 224 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE N 226 " --> pdb=" O LYS N 254 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 256 through 257 removed outlier: 6.578A pdb=" N ILE N 256 " --> pdb=" O ASN N 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'N' and resid 292 through 293 removed outlier: 3.661A pdb=" N PHE N 308 " --> pdb=" O LEU N 300 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 356 through 358 removed outlier: 3.718A pdb=" N LYS N 365 " --> pdb=" O ALA N 357 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 35 through 37 Processing sheet with id=AF9, first strand: chain 'O' and resid 160 through 164 removed outlier: 3.961A pdb=" N GLY O 151 " --> pdb=" O ILE O 161 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA O 163 " --> pdb=" O GLU O 149 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU O 149 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA O 174 " --> pdb=" O PHE O 533 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR O 472 " --> pdb=" O SER O 510 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE O 512 " --> pdb=" O THR O 472 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU O 474 " --> pdb=" O ILE O 512 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER O 514 " --> pdb=" O LEU O 474 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU O 476 " --> pdb=" O SER O 514 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU O 477 " --> pdb=" O PHE O 206 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE O 203 " --> pdb=" O HIS O 434 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL O 436 " --> pdb=" O ILE O 203 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE O 205 " --> pdb=" O VAL O 436 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS O 223 " --> pdb=" O ILE O 435 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASN O 437 " --> pdb=" O LYS O 223 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR O 225 " --> pdb=" O ASN O 437 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS O 254 " --> pdb=" O HIS O 224 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE O 226 " --> pdb=" O LYS O 254 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 256 through 257 removed outlier: 6.853A pdb=" N ILE O 256 " --> pdb=" O ASN O 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'O' and resid 292 through 293 removed outlier: 3.678A pdb=" N PHE O 308 " --> pdb=" O LEU O 300 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 35 through 38 removed outlier: 3.642A pdb=" N GLY P 41 " --> pdb=" O HIS P 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 160 through 164 removed outlier: 7.108A pdb=" N ILE P 161 " --> pdb=" O LEU P 150 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N HIS P 172 " --> pdb=" O CYS P 529 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN P 531 " --> pdb=" O HIS P 172 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL P 473 " --> pdb=" O ARG P 202 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS P 223 " --> pdb=" O ILE P 435 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASN P 437 " --> pdb=" O LYS P 223 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR P 225 " --> pdb=" O ASN P 437 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N LYS P 254 " --> pdb=" O HIS P 224 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE P 226 " --> pdb=" O LYS P 254 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 256 through 257 removed outlier: 6.503A pdb=" N ILE P 256 " --> pdb=" O ASN P 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'P' and resid 292 through 293 Processing sheet with id=AG7, first strand: chain 'Q' and resid 160 through 164 removed outlier: 7.146A pdb=" N ILE Q 161 " --> pdb=" O LEU Q 150 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N HIS Q 172 " --> pdb=" O ASN Q 531 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N PHE Q 533 " --> pdb=" O HIS Q 172 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA Q 174 " --> pdb=" O PHE Q 533 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU Q 477 " --> pdb=" O PHE Q 206 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS Q 223 " --> pdb=" O ILE Q 435 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASN Q 437 " --> pdb=" O LYS Q 223 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR Q 225 " --> pdb=" O ASN Q 437 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LYS Q 254 " --> pdb=" O HIS Q 224 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE Q 226 " --> pdb=" O LYS Q 254 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 256 through 257 removed outlier: 7.171A pdb=" N ILE Q 256 " --> pdb=" O ASN Q 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'Q' and resid 292 through 293 Processing sheet with id=AH1, first strand: chain 'R' and resid 160 through 164 removed outlier: 7.182A pdb=" N ILE R 161 " --> pdb=" O LEU R 150 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU R 578 " --> pdb=" O GLY R 573 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY R 573 " --> pdb=" O LEU R 578 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'R' and resid 203 through 206 removed outlier: 3.734A pdb=" N THR R 225 " --> pdb=" O ILE R 435 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN R 437 " --> pdb=" O THR R 225 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 256 through 257 removed outlier: 6.694A pdb=" N ILE R 256 " --> pdb=" O ASN R 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'R' and resid 292 through 293 removed outlier: 3.664A pdb=" N HIS R 292 " --> pdb=" O TYR R 299 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR R 299 " --> pdb=" O HIS R 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'R' and resid 356 through 358 2232 hydrogen bonds defined for protein. 6360 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: 25.81 Time building geometry restraints manager: 14.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 10852 1.30 - 1.43: 17971 1.43 - 1.56: 37712 1.56 - 1.68: 66 1.68 - 1.81: 223 Bond restraints: 66824 Sorted by residual: bond pdb=" N TYR A 270 " pdb=" CA TYR A 270 " ideal model delta sigma weight residual 1.456 1.490 -0.033 9.40e-03 1.13e+04 1.25e+01 bond pdb=" N ASP P 316 " pdb=" CA ASP P 316 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" CA ALA A 273 " pdb=" CB ALA A 273 " ideal model delta sigma weight residual 1.532 1.479 0.053 1.59e-02 3.96e+03 1.10e+01 bond pdb=" N ILE A 269 " pdb=" CA ILE A 269 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" C PRO A 271 " pdb=" O PRO A 271 " ideal model delta sigma weight residual 1.228 1.176 0.052 2.00e-02 2.50e+03 6.87e+00 ... (remaining 66819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 89564 2.27 - 4.54: 712 4.54 - 6.81: 97 6.81 - 9.07: 14 9.07 - 11.34: 6 Bond angle restraints: 90393 Sorted by residual: angle pdb=" CA TYR A 270 " pdb=" C TYR A 270 " pdb=" N PRO A 271 " ideal model delta sigma weight residual 117.82 124.92 -7.10 7.80e-01 1.64e+00 8.28e+01 angle pdb=" N SER P 320 " pdb=" CA SER P 320 " pdb=" C SER P 320 " ideal model delta sigma weight residual 112.88 101.54 11.34 1.29e+00 6.01e-01 7.73e+01 angle pdb=" N ALA P 323 " pdb=" CA ALA P 323 " pdb=" C ALA P 323 " ideal model delta sigma weight residual 110.53 99.73 10.80 1.29e+00 6.01e-01 7.02e+01 angle pdb=" N LEU P 322 " pdb=" CA LEU P 322 " pdb=" C LEU P 322 " ideal model delta sigma weight residual 113.41 104.23 9.18 1.22e+00 6.72e-01 5.67e+01 angle pdb=" N TYR A 270 " pdb=" CA TYR A 270 " pdb=" C TYR A 270 " ideal model delta sigma weight residual 108.07 102.27 5.80 8.90e-01 1.26e+00 4.25e+01 ... (remaining 90388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.91: 38787 31.91 - 63.82: 1077 63.82 - 95.73: 124 95.73 - 127.65: 6 127.65 - 159.56: 2 Dihedral angle restraints: 39996 sinusoidal: 16468 harmonic: 23528 Sorted by residual: dihedral pdb=" CA TYR A 270 " pdb=" C TYR A 270 " pdb=" N PRO A 271 " pdb=" CA PRO A 271 " ideal model delta harmonic sigma weight residual 0.00 -41.91 41.91 0 5.00e+00 4.00e-02 7.03e+01 dihedral pdb=" O1B ADP N 701 " pdb=" O3A ADP N 701 " pdb=" PB ADP N 701 " pdb=" PA ADP N 701 " ideal model delta sinusoidal sigma weight residual -60.00 -166.04 106.03 1 2.00e+01 2.50e-03 3.06e+01 dihedral pdb=" C5' ADP P 701 " pdb=" O5' ADP P 701 " pdb=" PA ADP P 701 " pdb=" O2A ADP P 701 " ideal model delta sinusoidal sigma weight residual -60.00 -159.48 99.49 1 2.00e+01 2.50e-03 2.80e+01 ... (remaining 39993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 9114 0.076 - 0.152: 716 0.152 - 0.228: 6 0.228 - 0.304: 0 0.304 - 0.380: 1 Chirality restraints: 9837 Sorted by residual: chirality pdb=" CA ARG P 315 " pdb=" N ARG P 315 " pdb=" C ARG P 315 " pdb=" CB ARG P 315 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ALA P 323 " pdb=" N ALA P 323 " pdb=" C ALA P 323 " pdb=" CB ALA P 323 " both_signs ideal model delta sigma weight residual False 2.48 2.71 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ASN P 318 " pdb=" N ASN P 318 " pdb=" C ASN P 318 " pdb=" CB ASN P 318 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 9834 not shown) Planarity restraints: 11590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 290 " 0.632 9.50e-02 1.11e+02 2.83e-01 4.90e+01 pdb=" NE ARG P 290 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG P 290 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG P 290 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG P 290 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 322 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C LEU P 322 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU P 322 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA P 323 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS P 314 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C CYS P 314 " 0.044 2.00e-02 2.50e+03 pdb=" O CYS P 314 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG P 315 " -0.014 2.00e-02 2.50e+03 ... (remaining 11587 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 257 2.59 - 3.17: 48862 3.17 - 3.75: 87374 3.75 - 4.32: 122369 4.32 - 4.90: 214726 Nonbonded interactions: 473588 Sorted by model distance: nonbonded pdb=" O3B ADP N 701 " pdb="MG MG N 702 " model vdw 2.013 2.170 nonbonded pdb=" O3B ADP M 701 " pdb="MG MG M 702 " model vdw 2.014 2.170 nonbonded pdb=" O2B ADP Q 701 " pdb="MG MG Q 702 " model vdw 2.019 2.170 nonbonded pdb=" O ARG Q 296 " pdb=" OD1 ASN Q 297 " model vdw 2.086 3.040 nonbonded pdb=" O3B ADP O 701 " pdb="MG MG O 702 " model vdw 2.120 2.170 ... (remaining 473583 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 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'B' and (resid 2 through 387 or resid 395 through 406 or resid 501)) selection = (chain 'C' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'D' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'E' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'F' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'G' and (resid 2 through 208 or resid 218 through 406 or resid 501)) selection = (chain 'H' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'I' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'J' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'K' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'L' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) } ncs_group { reference = (chain 'M' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 584)) selection = (chain 'N' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'O' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'P' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 355 or resid 375 through 484 or resid 498 through 584)) selection = (chain 'Q' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'R' and (resid 10 through 227 or resid 238 through 328 or resid 336 throu \ gh 355 or resid 375 through 484 or resid 498 through 584)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 0.050 Extract box with map and model: 1.960 Check model and map are aligned: 0.400 Set scattering table: 0.450 Process input model: 112.020 Find NCS groups from input model: 3.400 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.053 66824 Z= 0.176 Angle : 0.558 11.343 90393 Z= 0.313 Chirality : 0.041 0.380 9837 Planarity : 0.004 0.283 11590 Dihedral : 14.790 159.557 24942 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.86 % Cis-general : 0.00 % Twisted Proline : 0.39 % 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: -0.97 (0.09), residues: 8032 helix: 0.12 (0.10), residues: 3157 sheet: 0.40 (0.16), residues: 1018 loop : -1.59 (0.09), residues: 3857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 409 HIS 0.006 0.001 HIS B 313 PHE 0.022 0.001 PHE I 363 TYR 0.022 0.001 TYR R 497 ARG 0.004 0.000 ARG P 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 957 time to evaluate : 5.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 LYS cc_start: 0.8340 (mttt) cc_final: 0.8126 (mtmm) REVERT: B 342 LYS cc_start: 0.8001 (mttm) cc_final: 0.7722 (mtpm) REVERT: B 378 ASN cc_start: 0.7767 (m-40) cc_final: 0.7490 (m-40) REVERT: B 382 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7611 (tt0) REVERT: C 24 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7730 (mt0) REVERT: C 90 THR cc_start: 0.8707 (m) cc_final: 0.8371 (p) REVERT: C 102 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7831 (mm-30) REVERT: D 378 ASN cc_start: 0.8330 (m-40) cc_final: 0.8060 (m-40) REVERT: E 13 ASP cc_start: 0.6800 (m-30) cc_final: 0.6238 (t0) REVERT: F 206 ARG cc_start: 0.6728 (tmm-80) cc_final: 0.6429 (ttm170) REVERT: F 316 ARG cc_start: 0.7983 (tpp-160) cc_final: 0.7439 (mmm160) REVERT: G 239 THR cc_start: 0.8068 (p) cc_final: 0.7764 (t) REVERT: H 110 LYS cc_start: 0.8312 (mtmm) cc_final: 0.8112 (ttmm) REVERT: H 207 ASN cc_start: 0.7160 (m-40) cc_final: 0.6891 (m-40) REVERT: H 270 TYR cc_start: 0.6855 (m-80) cc_final: 0.6398 (m-80) REVERT: H 316 ARG cc_start: 0.8331 (mmm160) cc_final: 0.7878 (mmp-170) REVERT: I 79 LEU cc_start: 0.8770 (mt) cc_final: 0.8524 (mt) REVERT: I 231 THR cc_start: 0.8443 (m) cc_final: 0.8008 (p) REVERT: I 337 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6996 (mmtt) REVERT: J 74 ASP cc_start: 0.7658 (m-30) cc_final: 0.7261 (m-30) REVERT: J 103 ASP cc_start: 0.8340 (m-30) cc_final: 0.8077 (m-30) REVERT: J 106 GLU cc_start: 0.7720 (tp30) cc_final: 0.7358 (mm-30) REVERT: J 263 TYR cc_start: 0.7154 (t80) cc_final: 0.6777 (t80) REVERT: K 26 ASP cc_start: 0.8547 (m-30) cc_final: 0.8331 (m-30) REVERT: K 146 GLU cc_start: 0.8235 (tt0) cc_final: 0.8018 (tt0) REVERT: K 338 GLU cc_start: 0.7936 (mp0) cc_final: 0.7720 (mp0) REVERT: N 141 LYS cc_start: 0.6938 (ptmm) cc_final: 0.6707 (ptpt) REVERT: N 383 GLN cc_start: 0.8448 (mt0) cc_final: 0.8205 (mt0) REVERT: N 528 MET cc_start: 0.8820 (mtp) cc_final: 0.8610 (mtp) REVERT: N 540 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7263 (mm-30) REVERT: N 592 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7490 (tppp) REVERT: O 34 ARG cc_start: 0.6891 (ttp-170) cc_final: 0.6676 (ttm-80) REVERT: O 238 LYS cc_start: 0.7215 (tptp) cc_final: 0.6575 (tppt) REVERT: P 144 LEU cc_start: 0.8124 (mt) cc_final: 0.7877 (mp) REVERT: P 503 GLU cc_start: 0.8177 (pp20) cc_final: 0.7923 (pp20) REVERT: Q 5 LYS cc_start: 0.6031 (mmmt) cc_final: 0.5760 (ttmt) REVERT: Q 8 GLU cc_start: 0.5559 (mm-30) cc_final: 0.4809 (pm20) REVERT: Q 550 MET cc_start: 0.8444 (ptp) cc_final: 0.8157 (ptm) REVERT: Q 592 LYS cc_start: 0.7211 (mtmt) cc_final: 0.6969 (tttp) REVERT: R 300 LEU cc_start: 0.7438 (mp) cc_final: 0.7084 (tm) outliers start: 0 outliers final: 2 residues processed: 957 average time/residue: 1.5674 time to fit residues: 1900.1545 Evaluate side-chains 531 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 529 time to evaluate : 5.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain O residue 578 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 681 optimal weight: 6.9990 chunk 611 optimal weight: 0.0470 chunk 339 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 412 optimal weight: 7.9990 chunk 326 optimal weight: 9.9990 chunk 632 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 384 optimal weight: 6.9990 chunk 470 optimal weight: 6.9990 chunk 732 optimal weight: 7.9990 overall best weight: 5.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 227 HIS B 405 ASN C 129 GLN C 156 GLN D 72 GLN D 199 GLN D 247 GLN D 324 ASN D 365 GLN D 405 ASN E 81 ASN F 5 GLN F 81 ASN F 405 ASN G 218 HIS H 55 ASN H 364 ASN I 227 HIS I 378 ASN J 227 HIS J 315 ASN J 383 HIS K 254 ASN M 556 GLN O 383 GLN O 440 ASN O 539 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 66824 Z= 0.442 Angle : 0.774 15.594 90393 Z= 0.395 Chirality : 0.051 0.220 9837 Planarity : 0.005 0.121 11590 Dihedral : 9.849 164.126 9502 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.13 % Allowed : 9.31 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -1.23 (0.09), residues: 8032 helix: -0.09 (0.09), residues: 3289 sheet: 0.22 (0.16), residues: 977 loop : -1.76 (0.09), residues: 3766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 409 HIS 0.014 0.002 HIS G 218 PHE 0.024 0.003 PHE O 206 TYR 0.027 0.002 TYR C 376 ARG 0.009 0.001 ARG R 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 540 time to evaluate : 5.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7539 (mmp) cc_final: 0.6973 (mmp) REVERT: A 363 PHE cc_start: 0.7357 (m-80) cc_final: 0.7086 (m-80) REVERT: A 374 LYS cc_start: 0.8513 (mttt) cc_final: 0.8267 (mtmm) REVERT: B 378 ASN cc_start: 0.7656 (m-40) cc_final: 0.7369 (m110) REVERT: C 24 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7377 (mt0) REVERT: C 100 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7598 (mtp85) REVERT: C 102 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7804 (mm-30) REVERT: C 352 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: D 9 LYS cc_start: 0.8232 (tptm) cc_final: 0.8023 (tptm) REVERT: D 13 ASP cc_start: 0.7408 (m-30) cc_final: 0.7199 (m-30) REVERT: D 242 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.8994 (tt0) REVERT: D 270 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.7066 (m-10) REVERT: D 378 ASN cc_start: 0.8457 (m-40) cc_final: 0.8128 (m-40) REVERT: F 54 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7608 (mp10) REVERT: G 146 GLU cc_start: 0.7602 (tp30) cc_final: 0.7361 (tp30) REVERT: G 262 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.5903 (p90) REVERT: H 207 ASN cc_start: 0.7136 (m-40) cc_final: 0.6868 (m-40) REVERT: H 270 TYR cc_start: 0.7020 (m-80) cc_final: 0.6493 (m-80) REVERT: I 79 LEU cc_start: 0.8863 (mt) cc_final: 0.8650 (mt) REVERT: I 107 GLU cc_start: 0.8347 (tp30) cc_final: 0.8055 (tp30) REVERT: I 337 LYS cc_start: 0.7434 (mmtt) cc_final: 0.7127 (mmtt) REVERT: J 24 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: J 74 ASP cc_start: 0.7729 (m-30) cc_final: 0.7318 (m-30) REVERT: J 263 TYR cc_start: 0.7138 (t80) cc_final: 0.6803 (t80) REVERT: K 24 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7096 (mp-120) REVERT: K 156 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8459 (tp40) REVERT: K 342 LYS cc_start: 0.7871 (mttm) cc_final: 0.7531 (ttmt) REVERT: L 46 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7921 (ttmt) REVERT: L 121 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8461 (ttmt) REVERT: L 342 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7991 (ttmm) REVERT: M 21 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6885 (tp30) REVERT: M 294 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8190 (ptpt) REVERT: M 386 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6677 (mm-30) REVERT: M 466 GLN cc_start: 0.6785 (pt0) cc_final: 0.6437 (pp30) REVERT: M 470 TYR cc_start: 0.7644 (t80) cc_final: 0.6989 (t80) REVERT: M 498 GLU cc_start: 0.5154 (OUTLIER) cc_final: 0.4400 (pt0) REVERT: M 601 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: N 5 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7328 (mttm) REVERT: N 141 LYS cc_start: 0.7158 (ptmm) cc_final: 0.6875 (ptpt) REVERT: N 540 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7340 (mm-30) REVERT: O 34 ARG cc_start: 0.7184 (ttp-170) cc_final: 0.6858 (ttm-80) REVERT: O 141 LYS cc_start: 0.7599 (pmtt) cc_final: 0.7211 (tptp) REVERT: O 237 GLU cc_start: 0.5961 (mp0) cc_final: 0.5126 (pm20) REVERT: O 495 LYS cc_start: 0.6854 (mptt) cc_final: 0.6631 (mmtt) REVERT: O 550 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8350 (ptm) REVERT: O 555 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: P 141 LYS cc_start: 0.7728 (mmtm) cc_final: 0.7372 (ptmt) REVERT: P 250 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.6502 (m-10) REVERT: P 281 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7956 (tt) REVERT: P 478 GLU cc_start: 0.8312 (mp0) cc_final: 0.8106 (mp0) REVERT: P 550 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.5904 (tmt) REVERT: Q 1 MET cc_start: 0.3383 (OUTLIER) cc_final: 0.2608 (mmt) REVERT: Q 8 GLU cc_start: 0.6061 (mm-30) cc_final: 0.4978 (pm20) REVERT: Q 143 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7640 (mm-30) REVERT: Q 270 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7679 (pp) REVERT: Q 418 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: Q 550 MET cc_start: 0.8698 (ptp) cc_final: 0.8429 (ptm) REVERT: R 508 LYS cc_start: 0.7025 (mtmt) cc_final: 0.6767 (ptpt) outliers start: 148 outliers final: 59 residues processed: 646 average time/residue: 1.5352 time to fit residues: 1262.7789 Evaluate side-chains 544 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 463 time to evaluate : 5.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 374 LYS Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 374 LYS Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 262 PHE Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 156 GLN Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 386 GLU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 601 GLU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 443 GLN Chi-restraints excluded: chain N residue 559 LYS Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 440 ASN Chi-restraints excluded: chain O residue 550 MET Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 250 TYR Chi-restraints excluded: chain P residue 251 TYR Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 394 VAL Chi-restraints excluded: chain P residue 525 VAL Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 418 ASP Chi-restraints excluded: chain Q residue 582 ILE Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 407 optimal weight: 0.4980 chunk 227 optimal weight: 6.9990 chunk 609 optimal weight: 20.0000 chunk 499 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 734 optimal weight: 20.0000 chunk 793 optimal weight: 0.4980 chunk 653 optimal weight: 3.9990 chunk 728 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 588 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 227 HIS B 313 HIS C 156 GLN D 135 GLN D 199 GLN D 247 GLN D 324 ASN G 218 HIS G 227 HIS I 227 HIS J 227 HIS N 107 ASN N 466 GLN O 383 GLN O 440 ASN O 539 ASN R 107 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 66824 Z= 0.153 Angle : 0.536 13.309 90393 Z= 0.275 Chirality : 0.042 0.176 9837 Planarity : 0.004 0.048 11590 Dihedral : 8.999 165.895 9498 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.80 % Allowed : 11.59 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.82 (0.09), residues: 8032 helix: 0.33 (0.09), residues: 3293 sheet: 0.34 (0.16), residues: 1008 loop : -1.61 (0.09), residues: 3731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 116 HIS 0.011 0.001 HIS G 218 PHE 0.022 0.001 PHE A 262 TYR 0.035 0.001 TYR R 497 ARG 0.008 0.000 ARG F 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 525 time to evaluate : 5.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7369 (mmp) cc_final: 0.6851 (mmp) REVERT: A 156 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: A 374 LYS cc_start: 0.8370 (mttt) cc_final: 0.8129 (mtmm) REVERT: B 378 ASN cc_start: 0.7560 (m-40) cc_final: 0.7260 (m110) REVERT: C 24 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7342 (mt0) REVERT: C 90 THR cc_start: 0.8801 (m) cc_final: 0.8338 (p) REVERT: C 102 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7679 (mm-30) REVERT: D 83 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.6465 (mt-10) REVERT: D 99 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7683 (mtp180) REVERT: D 242 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.8863 (tt0) REVERT: D 317 ILE cc_start: 0.8561 (mt) cc_final: 0.8352 (mp) REVERT: D 378 ASN cc_start: 0.8357 (m-40) cc_final: 0.8065 (m-40) REVERT: F 316 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.7436 (mmm160) REVERT: G 146 GLU cc_start: 0.7345 (tp30) cc_final: 0.7057 (tp30) REVERT: G 219 TYR cc_start: 0.6970 (m-80) cc_final: 0.6515 (m-80) REVERT: G 361 MET cc_start: 0.6924 (tpp) cc_final: 0.6645 (tpp) REVERT: H 207 ASN cc_start: 0.7130 (m-40) cc_final: 0.6868 (m-40) REVERT: H 270 TYR cc_start: 0.6834 (m-80) cc_final: 0.6397 (m-80) REVERT: I 79 LEU cc_start: 0.8799 (mt) cc_final: 0.8589 (mt) REVERT: I 199 GLN cc_start: 0.8275 (mp10) cc_final: 0.7755 (mp10) REVERT: I 337 LYS cc_start: 0.7369 (mmtt) cc_final: 0.7060 (mmtt) REVERT: J 24 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8077 (mt0) REVERT: J 74 ASP cc_start: 0.7714 (m-30) cc_final: 0.7303 (m-30) REVERT: J 263 TYR cc_start: 0.7050 (t80) cc_final: 0.6635 (t80) REVERT: K 342 LYS cc_start: 0.7842 (mttm) cc_final: 0.7492 (ttmt) REVERT: L 361 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8125 (mtt) REVERT: M 21 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6597 (tp30) REVERT: M 34 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6549 (ptm160) REVERT: M 294 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8114 (ptpt) REVERT: M 466 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.6442 (pp30) REVERT: M 470 TYR cc_start: 0.7671 (t80) cc_final: 0.7222 (t80) REVERT: M 601 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: N 141 LYS cc_start: 0.7156 (ptmm) cc_final: 0.6891 (ptpt) REVERT: N 503 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6704 (mp0) REVERT: N 540 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7159 (mm-30) REVERT: N 550 MET cc_start: 0.8365 (ptt) cc_final: 0.8103 (ptp) REVERT: N 592 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7714 (tppp) REVERT: O 34 ARG cc_start: 0.7076 (ttp-170) cc_final: 0.6752 (ttm-80) REVERT: O 141 LYS cc_start: 0.7533 (pmtt) cc_final: 0.7144 (tptp) REVERT: O 237 GLU cc_start: 0.6114 (mp0) cc_final: 0.5158 (pm20) REVERT: O 300 LEU cc_start: 0.8580 (mt) cc_final: 0.8220 (tp) REVERT: P 141 LYS cc_start: 0.7844 (mmtm) cc_final: 0.7361 (ptmt) REVERT: P 251 TYR cc_start: 0.8224 (p90) cc_final: 0.8020 (p90) REVERT: P 293 PHE cc_start: 0.6534 (t80) cc_final: 0.6183 (t80) REVERT: P 478 GLU cc_start: 0.8351 (mp0) cc_final: 0.8030 (mp0) REVERT: P 550 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.5930 (tmt) REVERT: Q 1 MET cc_start: 0.3378 (OUTLIER) cc_final: 0.2512 (mmt) REVERT: Q 8 GLU cc_start: 0.5730 (mm-30) cc_final: 0.4760 (pm20) REVERT: Q 270 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7652 (pp) REVERT: Q 418 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7240 (m-30) REVERT: Q 520 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: Q 550 MET cc_start: 0.8559 (ptp) cc_final: 0.8297 (ptm) REVERT: R 248 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5936 (mt-10) REVERT: R 300 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6132 (mp) REVERT: R 536 ARG cc_start: 0.6624 (tpp80) cc_final: 0.6264 (tpp80) outliers start: 125 outliers final: 43 residues processed: 621 average time/residue: 1.5065 time to fit residues: 1198.2942 Evaluate side-chains 526 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 465 time to evaluate : 5.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 361 MET Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 601 GLU Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 592 LYS Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 440 ASN Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 276 THR Chi-restraints excluded: chain Q residue 418 ASP Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain R residue 248 GLU Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 725 optimal weight: 2.9990 chunk 551 optimal weight: 6.9990 chunk 381 optimal weight: 0.0050 chunk 81 optimal weight: 10.0000 chunk 350 optimal weight: 7.9990 chunk 492 optimal weight: 2.9990 chunk 736 optimal weight: 40.0000 chunk 780 optimal weight: 0.2980 chunk 384 optimal weight: 1.9990 chunk 698 optimal weight: 0.7980 chunk 210 optimal weight: 9.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 GLN D 247 GLN D 324 ASN E 266 GLN G 154 ASN G 278 HIS J 315 ASN N 297 ASN N 466 GLN N 554 ASN O 383 GLN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 66824 Z= 0.139 Angle : 0.507 12.280 90393 Z= 0.259 Chirality : 0.041 0.169 9837 Planarity : 0.003 0.049 11590 Dihedral : 8.653 167.953 9498 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.96 % Allowed : 12.86 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.58 (0.09), residues: 8032 helix: 0.57 (0.10), residues: 3288 sheet: 0.44 (0.16), residues: 1004 loop : -1.51 (0.09), residues: 3740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 116 HIS 0.004 0.001 HIS K 218 PHE 0.022 0.001 PHE A 262 TYR 0.027 0.001 TYR R 497 ARG 0.008 0.000 ARG K 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 501 time to evaluate : 5.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7447 (mmp) cc_final: 0.6915 (mmp) REVERT: A 156 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: A 374 LYS cc_start: 0.8338 (mttt) cc_final: 0.8074 (mtmm) REVERT: B 128 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7174 (mm-30) REVERT: B 183 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: B 378 ASN cc_start: 0.7542 (m-40) cc_final: 0.7248 (m110) REVERT: C 24 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7616 (mt0) REVERT: D 242 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.8813 (tt0) REVERT: D 378 ASN cc_start: 0.8351 (m-40) cc_final: 0.8070 (m-40) REVERT: E 9 LYS cc_start: 0.7538 (mtpp) cc_final: 0.6849 (ttmm) REVERT: E 97 LYS cc_start: 0.8681 (ttmm) cc_final: 0.8432 (ttmt) REVERT: E 107 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7689 (tp30) REVERT: F 316 ARG cc_start: 0.7941 (tpp-160) cc_final: 0.7483 (mmm160) REVERT: G 219 TYR cc_start: 0.6878 (m-80) cc_final: 0.6390 (m-80) REVERT: G 287 MET cc_start: 0.8592 (mmt) cc_final: 0.8123 (mmt) REVERT: G 361 MET cc_start: 0.7086 (tpp) cc_final: 0.6795 (tpp) REVERT: H 128 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7107 (pp20) REVERT: H 207 ASN cc_start: 0.7109 (m-40) cc_final: 0.6839 (m-40) REVERT: H 270 TYR cc_start: 0.6819 (m-80) cc_final: 0.6373 (m-80) REVERT: I 199 GLN cc_start: 0.8228 (mp10) cc_final: 0.7718 (mp10) REVERT: J 24 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: J 74 ASP cc_start: 0.7710 (m-30) cc_final: 0.7282 (m-30) REVERT: J 199 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8118 (pm20) REVERT: K 24 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.6916 (mp-120) REVERT: K 342 LYS cc_start: 0.7799 (mttm) cc_final: 0.7437 (ttmt) REVERT: L 342 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7947 (ttmm) REVERT: L 361 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8069 (mtt) REVERT: M 21 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6508 (tp30) REVERT: M 294 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8067 (ptpt) REVERT: M 313 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6623 (m-30) REVERT: M 454 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6965 (mt) REVERT: M 466 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6495 (pp30) REVERT: M 478 GLU cc_start: 0.8653 (mp0) cc_final: 0.8394 (mp0) REVERT: M 498 GLU cc_start: 0.5511 (OUTLIER) cc_final: 0.4849 (pt0) REVERT: N 338 ASN cc_start: 0.8299 (m-40) cc_final: 0.8079 (m110) REVERT: N 503 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6651 (mp0) REVERT: N 550 MET cc_start: 0.8270 (ptt) cc_final: 0.8063 (ptp) REVERT: N 592 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7739 (tppp) REVERT: O 34 ARG cc_start: 0.7199 (ttp-170) cc_final: 0.6821 (ttm-80) REVERT: O 141 LYS cc_start: 0.7489 (pmtt) cc_final: 0.7191 (tptp) REVERT: O 237 GLU cc_start: 0.6150 (mp0) cc_final: 0.5135 (pm20) REVERT: O 238 LYS cc_start: 0.7058 (tptp) cc_final: 0.6694 (tppt) REVERT: O 300 LEU cc_start: 0.8516 (mt) cc_final: 0.8172 (tp) REVERT: O 389 ARG cc_start: 0.6838 (mtp85) cc_final: 0.6323 (mtp180) REVERT: O 544 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7043 (tm130) REVERT: P 293 PHE cc_start: 0.6404 (t80) cc_final: 0.6169 (t80) REVERT: P 462 PHE cc_start: 0.7315 (m-10) cc_final: 0.7090 (m-10) REVERT: P 478 GLU cc_start: 0.8417 (mp0) cc_final: 0.8163 (mp0) REVERT: Q 1 MET cc_start: 0.3335 (OUTLIER) cc_final: 0.2480 (mmt) REVERT: Q 8 GLU cc_start: 0.5736 (mm-30) cc_final: 0.4779 (pm20) REVERT: Q 270 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7719 (pp) REVERT: Q 520 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: R 300 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6143 (mp) REVERT: R 476 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7444 (mp) REVERT: R 536 ARG cc_start: 0.6506 (tpp80) cc_final: 0.6235 (tpp80) outliers start: 136 outliers final: 54 residues processed: 603 average time/residue: 1.4818 time to fit residues: 1149.4896 Evaluate side-chains 537 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 460 time to evaluate : 5.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 199 GLN Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 361 MET Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 454 LEU Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 592 LYS Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain O residue 584 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 276 THR Chi-restraints excluded: chain Q residue 304 ASP Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 649 optimal weight: 3.9990 chunk 442 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 580 optimal weight: 3.9990 chunk 321 optimal weight: 0.0970 chunk 665 optimal weight: 8.9990 chunk 539 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 398 optimal weight: 7.9990 chunk 700 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 227 HIS C 156 GLN D 199 GLN E 81 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN G 278 HIS J 227 HIS J 315 ASN N 297 ASN N 466 GLN N 554 ASN O 383 GLN O 440 ASN Q 373 ASN R 107 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 66824 Z= 0.244 Angle : 0.596 11.689 90393 Z= 0.304 Chirality : 0.044 0.183 9837 Planarity : 0.004 0.047 11590 Dihedral : 8.899 168.206 9498 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.59 % Allowed : 13.33 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.71 (0.09), residues: 8032 helix: 0.46 (0.09), residues: 3293 sheet: 0.37 (0.16), residues: 1001 loop : -1.58 (0.09), residues: 3738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 116 HIS 0.008 0.001 HIS L 267 PHE 0.025 0.002 PHE G 380 TYR 0.021 0.002 TYR G 312 ARG 0.007 0.000 ARG P 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 455 time to evaluate : 5.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7630 (mmp) cc_final: 0.7200 (mmt) REVERT: A 156 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: A 374 LYS cc_start: 0.8376 (mttt) cc_final: 0.8141 (mtmm) REVERT: B 128 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: B 378 ASN cc_start: 0.7503 (m-40) cc_final: 0.7227 (m110) REVERT: C 24 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7404 (mt0) REVERT: D 83 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: D 242 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.8919 (tt0) REVERT: D 317 ILE cc_start: 0.8732 (mt) cc_final: 0.8483 (mp) REVERT: D 378 ASN cc_start: 0.8385 (m-40) cc_final: 0.8098 (m-40) REVERT: E 9 LYS cc_start: 0.7571 (mtpp) cc_final: 0.6890 (ttmm) REVERT: F 316 ARG cc_start: 0.7930 (tpp-160) cc_final: 0.7387 (mmm160) REVERT: G 219 TYR cc_start: 0.6865 (m-80) cc_final: 0.6363 (m-80) REVERT: G 262 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7029 (p90) REVERT: G 287 MET cc_start: 0.8609 (mmt) cc_final: 0.8130 (mmt) REVERT: H 128 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7213 (pp20) REVERT: H 207 ASN cc_start: 0.7190 (m-40) cc_final: 0.6864 (m-40) REVERT: H 270 TYR cc_start: 0.6903 (m-80) cc_final: 0.6546 (m-80) REVERT: I 199 GLN cc_start: 0.8205 (mp10) cc_final: 0.7747 (mp10) REVERT: I 337 LYS cc_start: 0.7456 (mmtt) cc_final: 0.7077 (pttp) REVERT: I 353 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7711 (mtmm) REVERT: J 24 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: J 74 ASP cc_start: 0.7736 (m-30) cc_final: 0.7308 (m-30) REVERT: J 199 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8109 (pm20) REVERT: K 156 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8391 (tp40) REVERT: K 342 LYS cc_start: 0.7856 (mttm) cc_final: 0.7489 (ttmt) REVERT: L 46 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7902 (ttmt) REVERT: L 342 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7961 (ttmm) REVERT: M 21 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6670 (tp30) REVERT: M 34 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6577 (ptm160) REVERT: M 95 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8582 (mm) REVERT: M 294 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8006 (ptpt) REVERT: M 313 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6811 (m-30) REVERT: M 454 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.7030 (mt) REVERT: M 466 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6512 (pp30) REVERT: M 478 GLU cc_start: 0.8715 (mp0) cc_final: 0.8441 (mp0) REVERT: M 498 GLU cc_start: 0.5582 (OUTLIER) cc_final: 0.4926 (pt0) REVERT: M 601 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: N 5 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7350 (mttm) REVERT: N 326 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7566 (mp) REVERT: N 338 ASN cc_start: 0.8305 (m-40) cc_final: 0.8100 (m110) REVERT: N 503 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6671 (mp0) REVERT: N 550 MET cc_start: 0.8392 (ptt) cc_final: 0.8137 (ptp) REVERT: O 34 ARG cc_start: 0.7329 (ttp-170) cc_final: 0.6852 (ttm-80) REVERT: O 134 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8751 (m-40) REVERT: O 141 LYS cc_start: 0.7581 (pmtt) cc_final: 0.7137 (tptp) REVERT: O 238 LYS cc_start: 0.7036 (tptp) cc_final: 0.6631 (tppt) REVERT: O 389 ARG cc_start: 0.6895 (mtp85) cc_final: 0.6422 (mtp180) REVERT: O 505 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7607 (tpp-160) REVERT: O 544 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7100 (tm130) REVERT: O 555 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: P 3 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.4606 (tt) REVERT: P 281 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7917 (tt) REVERT: P 293 PHE cc_start: 0.6697 (t80) cc_final: 0.6265 (t80) REVERT: P 462 PHE cc_start: 0.7341 (m-10) cc_final: 0.7137 (m-10) REVERT: P 478 GLU cc_start: 0.8446 (mp0) cc_final: 0.8166 (mp0) REVERT: P 502 LYS cc_start: 0.7368 (mtpm) cc_final: 0.7114 (mtpm) REVERT: P 520 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: P 550 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.6056 (tmt) REVERT: Q 1 MET cc_start: 0.3539 (OUTLIER) cc_final: 0.2524 (mmt) REVERT: Q 8 GLU cc_start: 0.6132 (mm-30) cc_final: 0.5069 (pm20) REVERT: Q 270 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7734 (pp) REVERT: Q 520 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: R 144 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6192 (tm) REVERT: R 300 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6153 (mp) REVERT: R 476 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7538 (mp) REVERT: R 494 ILE cc_start: 0.2898 (OUTLIER) cc_final: 0.2694 (mm) REVERT: R 536 ARG cc_start: 0.6643 (tpp80) cc_final: 0.6372 (tpp80) outliers start: 180 outliers final: 78 residues processed: 592 average time/residue: 1.5214 time to fit residues: 1170.6979 Evaluate side-chains 557 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 442 time to evaluate : 5.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 262 PHE Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 353 LYS Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 199 GLN Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 156 GLN Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 454 LEU Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 601 GLU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 259 GLN Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 592 LYS Chi-restraints excluded: chain N residue 601 GLU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 440 ASN Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 520 GLU Chi-restraints excluded: chain P residue 524 THR Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 276 THR Chi-restraints excluded: chain Q residue 304 ASP Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain Q residue 538 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 494 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 262 optimal weight: 10.0000 chunk 702 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 457 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 780 optimal weight: 4.9990 chunk 648 optimal weight: 0.4980 chunk 361 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 409 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN C 156 GLN D 199 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 ASN G 278 HIS H 55 ASN J 227 HIS L 54 GLN N 297 ASN N 466 GLN O 383 GLN P 319 GLN R 107 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 66824 Z= 0.158 Angle : 0.529 12.253 90393 Z= 0.271 Chirality : 0.041 0.182 9837 Planarity : 0.004 0.047 11590 Dihedral : 8.703 168.763 9498 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.26 % Allowed : 14.26 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.58 (0.09), residues: 8032 helix: 0.59 (0.10), residues: 3298 sheet: 0.40 (0.16), residues: 1007 loop : -1.51 (0.09), residues: 3727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 116 HIS 0.004 0.001 HIS L 267 PHE 0.026 0.001 PHE R 293 TYR 0.044 0.001 TYR R 497 ARG 0.009 0.000 ARG P 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 471 time to evaluate : 5.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7604 (mmp) cc_final: 0.7219 (mmt) REVERT: A 156 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7535 (mp10) REVERT: A 374 LYS cc_start: 0.8351 (mttt) cc_final: 0.8127 (mtmm) REVERT: B 128 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7200 (mm-30) REVERT: B 378 ASN cc_start: 0.7566 (m-40) cc_final: 0.7283 (m110) REVERT: C 24 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7344 (mt0) REVERT: D 83 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: D 152 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8010 (tt) REVERT: D 156 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: D 242 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.8879 (tt0) REVERT: D 317 ILE cc_start: 0.8608 (mt) cc_final: 0.8347 (mp) REVERT: D 378 ASN cc_start: 0.8368 (m-40) cc_final: 0.8072 (m-40) REVERT: E 9 LYS cc_start: 0.7555 (mtpp) cc_final: 0.6912 (ttmm) REVERT: F 316 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7389 (mmm160) REVERT: G 219 TYR cc_start: 0.6821 (m-80) cc_final: 0.6315 (m-80) REVERT: G 361 MET cc_start: 0.7004 (tpp) cc_final: 0.6668 (tpp) REVERT: H 128 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7107 (pp20) REVERT: H 207 ASN cc_start: 0.7151 (m-40) cc_final: 0.6819 (m-40) REVERT: H 270 TYR cc_start: 0.6875 (m-80) cc_final: 0.6439 (m-80) REVERT: I 199 GLN cc_start: 0.8153 (mp10) cc_final: 0.7719 (mp10) REVERT: I 337 LYS cc_start: 0.7395 (mmtt) cc_final: 0.7061 (pttp) REVERT: I 353 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7680 (mtmm) REVERT: J 24 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: J 74 ASP cc_start: 0.7731 (m-30) cc_final: 0.7300 (m-30) REVERT: K 156 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8357 (tp40) REVERT: K 342 LYS cc_start: 0.7828 (mttm) cc_final: 0.7452 (ttmt) REVERT: L 46 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7825 (ttmt) REVERT: L 342 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7917 (ttmm) REVERT: M 21 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6348 (tp30) REVERT: M 34 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6557 (ptm160) REVERT: M 95 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8505 (mm) REVERT: M 281 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7741 (tt) REVERT: M 294 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7998 (ptpt) REVERT: M 313 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6666 (m-30) REVERT: M 466 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.6480 (pp30) REVERT: M 478 GLU cc_start: 0.8650 (mp0) cc_final: 0.8373 (mp0) REVERT: M 498 GLU cc_start: 0.5379 (OUTLIER) cc_final: 0.4727 (pt0) REVERT: N 5 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7346 (mttm) REVERT: N 121 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8528 (mp) REVERT: N 326 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7478 (mp) REVERT: N 503 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6639 (mp0) REVERT: N 550 MET cc_start: 0.8330 (ptt) cc_final: 0.8117 (ptp) REVERT: O 34 ARG cc_start: 0.7304 (ttp-170) cc_final: 0.6871 (ttm-80) REVERT: O 134 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8697 (m-40) REVERT: O 141 LYS cc_start: 0.7605 (pmtt) cc_final: 0.7158 (tptp) REVERT: O 238 LYS cc_start: 0.7036 (tptp) cc_final: 0.6631 (tppt) REVERT: O 300 LEU cc_start: 0.8534 (mt) cc_final: 0.8177 (tp) REVERT: O 389 ARG cc_start: 0.6845 (mtp85) cc_final: 0.6398 (mtp180) REVERT: O 505 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7574 (tpp-160) REVERT: O 544 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7050 (tm130) REVERT: O 555 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: P 293 PHE cc_start: 0.6674 (t80) cc_final: 0.6278 (t80) REVERT: P 325 TRP cc_start: 0.6216 (t60) cc_final: 0.5976 (m100) REVERT: P 462 PHE cc_start: 0.7263 (m-10) cc_final: 0.7059 (m-10) REVERT: P 478 GLU cc_start: 0.8416 (mp0) cc_final: 0.8133 (mp0) REVERT: P 550 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6070 (tmt) REVERT: Q 1 MET cc_start: 0.3548 (OUTLIER) cc_final: 0.2520 (mmt) REVERT: Q 5 LYS cc_start: 0.5155 (mmtt) cc_final: 0.4338 (ttmt) REVERT: Q 8 GLU cc_start: 0.5772 (mm-30) cc_final: 0.4867 (pm20) REVERT: Q 270 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7764 (pp) REVERT: Q 520 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: R 144 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6268 (tm) REVERT: R 293 PHE cc_start: 0.4999 (t80) cc_final: 0.4551 (t80) REVERT: R 300 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6076 (mp) REVERT: R 476 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7647 (mp) REVERT: R 494 ILE cc_start: 0.2919 (OUTLIER) cc_final: 0.2670 (mm) REVERT: R 536 ARG cc_start: 0.6612 (tpp80) cc_final: 0.6333 (tpp80) outliers start: 157 outliers final: 71 residues processed: 591 average time/residue: 1.4922 time to fit residues: 1135.9298 Evaluate side-chains 547 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 442 time to evaluate : 5.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain I residue 353 LYS Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 156 GLN Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 121 LEU Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 259 GLN Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 592 LYS Chi-restraints excluded: chain N residue 601 GLU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 420 PHE Chi-restraints excluded: chain P residue 524 THR Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 276 THR Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain Q residue 538 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 494 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 752 optimal weight: 0.4980 chunk 88 optimal weight: 0.9990 chunk 444 optimal weight: 1.9990 chunk 570 optimal weight: 0.8980 chunk 441 optimal weight: 9.9990 chunk 657 optimal weight: 0.0070 chunk 436 optimal weight: 0.0980 chunk 777 optimal weight: 30.0000 chunk 486 optimal weight: 0.1980 chunk 474 optimal weight: 9.9990 chunk 359 optimal weight: 7.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN G 218 HIS G 278 HIS J 199 GLN J 315 ASN N 297 ASN N 466 GLN O 383 GLN P 539 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 66824 Z= 0.110 Angle : 0.466 12.210 90393 Z= 0.237 Chirality : 0.040 0.178 9837 Planarity : 0.003 0.046 11590 Dihedral : 8.259 172.827 9498 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.70 % Allowed : 15.06 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.29 (0.09), residues: 8032 helix: 0.86 (0.10), residues: 3281 sheet: 0.55 (0.16), residues: 1011 loop : -1.38 (0.09), residues: 3740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 116 HIS 0.002 0.000 HIS I 267 PHE 0.025 0.001 PHE A 262 TYR 0.041 0.001 TYR R 497 ARG 0.008 0.000 ARG P 463 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 491 time to evaluate : 5.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7484 (mmp) cc_final: 0.7175 (mmt) REVERT: A 156 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: A 374 LYS cc_start: 0.8180 (mttt) cc_final: 0.7943 (mtmm) REVERT: B 156 GLN cc_start: 0.7794 (mt0) cc_final: 0.7554 (tp40) REVERT: B 378 ASN cc_start: 0.7459 (m-40) cc_final: 0.7167 (m110) REVERT: C 352 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7173 (mt-10) REVERT: D 83 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.6733 (mm-30) REVERT: D 152 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7883 (tt) REVERT: D 242 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8762 (tt0) REVERT: D 378 ASN cc_start: 0.8312 (m-40) cc_final: 0.8023 (m-40) REVERT: E 9 LYS cc_start: 0.7528 (mtpp) cc_final: 0.6867 (ttmm) REVERT: F 316 ARG cc_start: 0.7826 (tpp-160) cc_final: 0.7485 (mmm160) REVERT: G 219 TYR cc_start: 0.6823 (m-80) cc_final: 0.6323 (m-80) REVERT: G 361 MET cc_start: 0.6769 (tpp) cc_final: 0.6564 (tpp) REVERT: G 364 ASN cc_start: 0.6382 (p0) cc_final: 0.6153 (t0) REVERT: H 207 ASN cc_start: 0.7115 (m-40) cc_final: 0.6760 (m-40) REVERT: H 270 TYR cc_start: 0.6817 (m-80) cc_final: 0.6439 (m-80) REVERT: I 199 GLN cc_start: 0.8114 (mp10) cc_final: 0.7626 (mp10) REVERT: I 231 THR cc_start: 0.7987 (m) cc_final: 0.7388 (p) REVERT: I 257 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7809 (mm) REVERT: I 337 LYS cc_start: 0.7376 (mmtt) cc_final: 0.7011 (pttp) REVERT: J 24 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: J 74 ASP cc_start: 0.7716 (m-30) cc_final: 0.7277 (m-30) REVERT: K 312 TYR cc_start: 0.8141 (t80) cc_final: 0.7874 (t80) REVERT: K 342 LYS cc_start: 0.7766 (mttm) cc_final: 0.7399 (ttmt) REVERT: M 21 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6649 (tp30) REVERT: M 466 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6430 (pp30) REVERT: M 478 GLU cc_start: 0.8600 (mp0) cc_final: 0.8351 (mp0) REVERT: N 5 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7346 (mttm) REVERT: N 592 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7769 (tppp) REVERT: O 34 ARG cc_start: 0.7215 (ttp-170) cc_final: 0.6754 (ttm-80) REVERT: O 238 LYS cc_start: 0.6990 (tptp) cc_final: 0.6622 (ttpt) REVERT: O 300 LEU cc_start: 0.8498 (mt) cc_final: 0.8163 (tp) REVERT: O 321 LYS cc_start: 0.6735 (mppt) cc_final: 0.6183 (mmmt) REVERT: O 389 ARG cc_start: 0.6646 (mtp85) cc_final: 0.6258 (mtp180) REVERT: O 505 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7526 (tpp-160) REVERT: P 3 LEU cc_start: 0.5758 (OUTLIER) cc_final: 0.4724 (tt) REVERT: P 293 PHE cc_start: 0.6362 (t80) cc_final: 0.6131 (t80) REVERT: P 463 ARG cc_start: 0.7172 (mtt-85) cc_final: 0.6939 (mpt-90) REVERT: P 478 GLU cc_start: 0.8360 (mp0) cc_final: 0.8094 (mp0) REVERT: Q 1 MET cc_start: 0.3618 (OUTLIER) cc_final: 0.2644 (mmt) REVERT: Q 8 GLU cc_start: 0.5553 (mm-30) cc_final: 0.4669 (pm20) REVERT: Q 21 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6755 (tp30) REVERT: Q 143 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7604 (mt-10) REVERT: Q 270 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7798 (pp) REVERT: R 494 ILE cc_start: 0.2876 (OUTLIER) cc_final: 0.2604 (mm) REVERT: R 536 ARG cc_start: 0.6509 (tpp80) cc_final: 0.6250 (tpp80) outliers start: 118 outliers final: 46 residues processed: 583 average time/residue: 1.5047 time to fit residues: 1137.8323 Evaluate side-chains 507 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 446 time to evaluate : 5.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain I residue 257 ILE Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 199 GLN Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 72 GLN Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 592 LYS Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain O residue 584 ILE Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 420 PHE Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 304 ASP Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 494 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 481 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 464 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 494 optimal weight: 5.9990 chunk 529 optimal weight: 4.9990 chunk 384 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 611 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN C 24 GLN C 156 GLN D 199 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS G 218 HIS G 278 HIS J 199 GLN J 227 HIS J 315 ASN L 394 ASN N 297 ASN N 466 GLN N 554 ASN O 383 GLN O 440 ASN Q 373 ASN R 107 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 66824 Z= 0.281 Angle : 0.626 12.399 90393 Z= 0.319 Chirality : 0.045 0.197 9837 Planarity : 0.004 0.049 11590 Dihedral : 8.850 173.084 9498 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.99 % Allowed : 15.44 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.61 (0.09), residues: 8032 helix: 0.53 (0.09), residues: 3314 sheet: 0.39 (0.16), residues: 1014 loop : -1.52 (0.09), residues: 3704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 325 HIS 0.008 0.001 HIS H 313 PHE 0.028 0.002 PHE A 262 TYR 0.036 0.002 TYR R 497 ARG 0.008 0.000 ARG P 468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 445 time to evaluate : 5.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7630 (mmp) cc_final: 0.7163 (mmt) REVERT: A 156 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: A 374 LYS cc_start: 0.8373 (mttt) cc_final: 0.8138 (mtmm) REVERT: B 128 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: B 378 ASN cc_start: 0.7540 (m-40) cc_final: 0.7288 (m110) REVERT: D 83 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: D 242 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.8924 (tt0) REVERT: D 317 ILE cc_start: 0.8710 (mt) cc_final: 0.8443 (mp) REVERT: D 378 ASN cc_start: 0.8387 (m-40) cc_final: 0.8096 (m-40) REVERT: E 9 LYS cc_start: 0.7558 (mtpp) cc_final: 0.6892 (ttmm) REVERT: G 219 TYR cc_start: 0.6923 (m-80) cc_final: 0.6398 (m-10) REVERT: G 364 ASN cc_start: 0.6474 (p0) cc_final: 0.6190 (t0) REVERT: H 128 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7139 (pp20) REVERT: H 207 ASN cc_start: 0.7150 (m-40) cc_final: 0.6821 (m-40) REVERT: H 270 TYR cc_start: 0.6888 (m-80) cc_final: 0.6467 (m-80) REVERT: I 199 GLN cc_start: 0.8205 (mp10) cc_final: 0.7742 (mp10) REVERT: I 337 LYS cc_start: 0.7511 (mmtt) cc_final: 0.7094 (pttp) REVERT: I 353 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7726 (mtmm) REVERT: J 24 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: J 74 ASP cc_start: 0.7723 (m-30) cc_final: 0.7282 (m-30) REVERT: K 342 LYS cc_start: 0.7855 (mttm) cc_final: 0.7488 (ttmt) REVERT: L 46 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7910 (ttmt) REVERT: L 54 GLN cc_start: 0.7533 (tp-100) cc_final: 0.7310 (tt0) REVERT: L 342 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7930 (ttmm) REVERT: M 21 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6374 (tp30) REVERT: M 34 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6468 (ptm160) REVERT: M 95 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8561 (mm) REVERT: M 466 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6628 (pp30) REVERT: M 478 GLU cc_start: 0.8736 (mp0) cc_final: 0.8463 (mp0) REVERT: M 498 GLU cc_start: 0.5070 (OUTLIER) cc_final: 0.4334 (pt0) REVERT: N 5 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7354 (mttm) REVERT: N 121 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8590 (mp) REVERT: O 34 ARG cc_start: 0.7367 (ttp-170) cc_final: 0.6850 (ttm-80) REVERT: O 134 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8767 (m-40) REVERT: O 238 LYS cc_start: 0.7054 (tptp) cc_final: 0.6626 (ttpt) REVERT: O 389 ARG cc_start: 0.6696 (mtp85) cc_final: 0.6276 (mtp180) REVERT: O 505 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7541 (tpp-160) REVERT: O 528 MET cc_start: 0.9021 (mtp) cc_final: 0.8680 (mtt) REVERT: P 3 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.4552 (tt) REVERT: P 293 PHE cc_start: 0.6775 (t80) cc_final: 0.6339 (t80) REVERT: P 462 PHE cc_start: 0.7209 (m-10) cc_final: 0.6945 (m-10) REVERT: P 478 GLU cc_start: 0.8463 (mp0) cc_final: 0.8186 (mp0) REVERT: Q 1 MET cc_start: 0.3535 (OUTLIER) cc_final: 0.2435 (mmt) REVERT: Q 8 GLU cc_start: 0.5546 (mm-30) cc_final: 0.4613 (pm20) REVERT: Q 270 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7803 (pp) REVERT: Q 520 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: R 293 PHE cc_start: 0.4799 (t80) cc_final: 0.4542 (t80) REVERT: R 494 ILE cc_start: 0.2962 (OUTLIER) cc_final: 0.2687 (mm) REVERT: R 536 ARG cc_start: 0.6669 (tpp80) cc_final: 0.6390 (tpp80) outliers start: 138 outliers final: 71 residues processed: 553 average time/residue: 1.4508 time to fit residues: 1040.7771 Evaluate side-chains 525 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 432 time to evaluate : 5.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 353 LYS Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 121 LEU Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 592 LYS Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 440 ASN Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 524 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 276 THR Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain Q residue 538 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 494 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 707 optimal weight: 1.9990 chunk 745 optimal weight: 6.9990 chunk 679 optimal weight: 9.9990 chunk 724 optimal weight: 8.9990 chunk 744 optimal weight: 1.9990 chunk 436 optimal weight: 2.9990 chunk 315 optimal weight: 6.9990 chunk 569 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 654 optimal weight: 5.9990 chunk 685 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN C 156 GLN D 199 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 HIS G 278 HIS H 209 ASN N 297 ASN N 466 GLN N 554 ASN O 383 GLN O 440 ASN P 224 HIS Q 373 ASN R 107 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 66824 Z= 0.312 Angle : 0.656 12.919 90393 Z= 0.335 Chirality : 0.046 0.210 9837 Planarity : 0.004 0.050 11590 Dihedral : 9.089 170.263 9498 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.03 % Allowed : 15.58 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.87 (0.09), residues: 8032 helix: 0.30 (0.09), residues: 3314 sheet: 0.25 (0.16), residues: 1009 loop : -1.64 (0.09), residues: 3709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 325 HIS 0.009 0.001 HIS B 227 PHE 0.030 0.002 PHE A 262 TYR 0.036 0.002 TYR R 497 ARG 0.008 0.001 ARG P 468 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 443 time to evaluate : 5.731 Fit side-chains revert: symmetry clash REVERT: A 45 MET cc_start: 0.7703 (mmp) cc_final: 0.7244 (mmt) REVERT: A 156 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: A 374 LYS cc_start: 0.8428 (mttt) cc_final: 0.8186 (mtmm) REVERT: B 128 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: B 378 ASN cc_start: 0.7521 (m-40) cc_final: 0.7241 (m110) REVERT: C 24 GLN cc_start: 0.8024 (mt0) cc_final: 0.7675 (mt0) REVERT: D 83 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.6806 (mm-30) REVERT: D 242 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.8947 (tt0) REVERT: D 317 ILE cc_start: 0.8835 (mt) cc_final: 0.8594 (mp) REVERT: D 378 ASN cc_start: 0.8454 (m-40) cc_final: 0.8118 (m-40) REVERT: E 9 LYS cc_start: 0.7524 (mtpp) cc_final: 0.6852 (ttmm) REVERT: E 13 ASP cc_start: 0.6786 (m-30) cc_final: 0.6104 (t0) REVERT: G 219 TYR cc_start: 0.6978 (m-80) cc_final: 0.6435 (m-10) REVERT: G 361 MET cc_start: 0.6913 (tpp) cc_final: 0.6627 (tpp) REVERT: G 364 ASN cc_start: 0.6436 (p0) cc_final: 0.6157 (t0) REVERT: H 128 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7129 (pp20) REVERT: H 207 ASN cc_start: 0.7161 (m-40) cc_final: 0.6847 (m-40) REVERT: H 270 TYR cc_start: 0.6858 (m-80) cc_final: 0.6483 (m-80) REVERT: I 199 GLN cc_start: 0.8210 (mp10) cc_final: 0.7748 (mp10) REVERT: I 337 LYS cc_start: 0.7482 (mmtt) cc_final: 0.7112 (pttp) REVERT: I 353 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7731 (mtmm) REVERT: J 24 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8126 (mt0) REVERT: J 74 ASP cc_start: 0.7716 (m-30) cc_final: 0.7275 (m-30) REVERT: J 287 MET cc_start: 0.8755 (mmt) cc_final: 0.8096 (mmt) REVERT: K 5 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: K 342 LYS cc_start: 0.7892 (mttm) cc_final: 0.7529 (ttmt) REVERT: K 345 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7171 (mmtp) REVERT: L 46 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7904 (ttmt) REVERT: L 342 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7878 (ttmm) REVERT: M 21 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6605 (tp30) REVERT: M 34 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6581 (ptm160) REVERT: M 95 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8671 (mm) REVERT: M 386 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6837 (mm-30) REVERT: M 466 GLN cc_start: 0.6828 (OUTLIER) cc_final: 0.6575 (pp30) REVERT: M 478 GLU cc_start: 0.8755 (mp0) cc_final: 0.8485 (mp0) REVERT: M 498 GLU cc_start: 0.5088 (OUTLIER) cc_final: 0.4348 (pt0) REVERT: N 5 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7349 (mttm) REVERT: N 121 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8643 (mp) REVERT: O 34 ARG cc_start: 0.7418 (ttp-170) cc_final: 0.6786 (ttm-80) REVERT: O 107 ASN cc_start: 0.6946 (p0) cc_final: 0.6251 (t0) REVERT: O 134 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8714 (m-40) REVERT: O 238 LYS cc_start: 0.7053 (tptp) cc_final: 0.6583 (ttpt) REVERT: O 389 ARG cc_start: 0.6820 (mtp85) cc_final: 0.6324 (mtp180) REVERT: O 505 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7478 (tpp-160) REVERT: P 3 LEU cc_start: 0.5670 (OUTLIER) cc_final: 0.4549 (tt) REVERT: P 293 PHE cc_start: 0.6801 (t80) cc_final: 0.6360 (t80) REVERT: P 438 MET cc_start: 0.8903 (ptp) cc_final: 0.8594 (mtt) REVERT: P 462 PHE cc_start: 0.7326 (m-10) cc_final: 0.7088 (m-10) REVERT: P 478 GLU cc_start: 0.8480 (mp0) cc_final: 0.8196 (mp0) REVERT: Q 1 MET cc_start: 0.3723 (OUTLIER) cc_final: 0.2592 (mmt) REVERT: Q 8 GLU cc_start: 0.5864 (mm-30) cc_final: 0.4857 (pm20) REVERT: Q 411 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7370 (mmpt) REVERT: Q 520 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: R 293 PHE cc_start: 0.4920 (t80) cc_final: 0.4690 (t80) REVERT: R 330 ARG cc_start: 0.4574 (mtt180) cc_final: 0.4250 (ttp-110) REVERT: R 476 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7716 (mp) REVERT: R 494 ILE cc_start: 0.2940 (OUTLIER) cc_final: 0.2656 (mm) REVERT: R 536 ARG cc_start: 0.6686 (tpp80) cc_final: 0.6351 (tpp80) outliers start: 141 outliers final: 75 residues processed: 552 average time/residue: 1.4991 time to fit residues: 1073.8236 Evaluate side-chains 535 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 434 time to evaluate : 5.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 353 LYS Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 345 LYS Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 386 GLU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 121 LEU Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 259 GLN Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 592 LYS Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 388 ILE Chi-restraints excluded: chain P residue 394 VAL Chi-restraints excluded: chain P residue 524 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 276 THR Chi-restraints excluded: chain Q residue 411 LYS Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain Q residue 538 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 494 ILE Chi-restraints excluded: chain R residue 582 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 722 optimal weight: 10.0000 chunk 475 optimal weight: 0.0770 chunk 766 optimal weight: 4.9990 chunk 467 optimal weight: 1.9990 chunk 363 optimal weight: 0.9980 chunk 532 optimal weight: 7.9990 chunk 803 optimal weight: 5.9990 chunk 739 optimal weight: 0.7980 chunk 640 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 494 optimal weight: 5.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN D 199 GLN G 218 HIS G 278 HIS J 315 ASN N 297 ASN N 466 GLN O 383 GLN O 440 ASN P 319 GLN Q 373 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 66824 Z= 0.133 Angle : 0.519 13.085 90393 Z= 0.265 Chirality : 0.041 0.204 9837 Planarity : 0.003 0.048 11590 Dihedral : 8.596 171.329 9498 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.17 % Allowed : 16.55 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.47 (0.09), residues: 8032 helix: 0.69 (0.10), residues: 3278 sheet: 0.44 (0.16), residues: 997 loop : -1.45 (0.09), residues: 3757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 325 HIS 0.004 0.001 HIS L 267 PHE 0.027 0.001 PHE A 262 TYR 0.041 0.001 TYR R 497 ARG 0.009 0.000 ARG P 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 447 time to evaluate : 5.835 Fit side-chains revert: symmetry clash REVERT: A 45 MET cc_start: 0.7549 (mmp) cc_final: 0.7198 (mmt) REVERT: A 156 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7512 (mp10) REVERT: A 374 LYS cc_start: 0.8336 (mttt) cc_final: 0.8111 (mtmm) REVERT: B 156 GLN cc_start: 0.7839 (mt0) cc_final: 0.7552 (tp40) REVERT: B 378 ASN cc_start: 0.7544 (m-40) cc_final: 0.7252 (m110) REVERT: C 24 GLN cc_start: 0.7835 (mt0) cc_final: 0.7561 (mt0) REVERT: D 83 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.6735 (mm-30) REVERT: D 152 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7902 (tt) REVERT: D 242 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8822 (tt0) REVERT: D 378 ASN cc_start: 0.8381 (m-40) cc_final: 0.8081 (m-40) REVERT: E 9 LYS cc_start: 0.7518 (mtpp) cc_final: 0.6835 (ttmm) REVERT: E 106 GLU cc_start: 0.7339 (mp0) cc_final: 0.7133 (mp0) REVERT: E 199 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7494 (mp10) REVERT: F 316 ARG cc_start: 0.7885 (tpp-160) cc_final: 0.7413 (mmm160) REVERT: G 219 TYR cc_start: 0.6931 (m-80) cc_final: 0.6411 (m-80) REVERT: G 364 ASN cc_start: 0.6477 (p0) cc_final: 0.6177 (t0) REVERT: H 128 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7153 (pp20) REVERT: H 207 ASN cc_start: 0.7134 (m-40) cc_final: 0.6808 (m-40) REVERT: H 270 TYR cc_start: 0.6766 (m-80) cc_final: 0.6357 (m-80) REVERT: I 199 GLN cc_start: 0.8076 (mp10) cc_final: 0.7636 (mp10) REVERT: I 337 LYS cc_start: 0.7460 (mmtt) cc_final: 0.7140 (pttp) REVERT: I 353 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7649 (mtmm) REVERT: J 24 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: J 74 ASP cc_start: 0.7713 (m-30) cc_final: 0.7282 (m-30) REVERT: K 5 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: K 312 TYR cc_start: 0.8246 (t80) cc_final: 0.7999 (t80) REVERT: K 342 LYS cc_start: 0.7823 (mttm) cc_final: 0.7481 (ttmm) REVERT: L 46 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7860 (ttmt) REVERT: L 54 GLN cc_start: 0.7470 (tp-100) cc_final: 0.7152 (tt0) REVERT: L 342 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7900 (ttmm) REVERT: M 21 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6407 (tp30) REVERT: M 466 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6440 (pp30) REVERT: M 478 GLU cc_start: 0.8638 (mp0) cc_final: 0.8373 (mp0) REVERT: N 5 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7345 (mttm) REVERT: O 34 ARG cc_start: 0.7275 (ttp-170) cc_final: 0.6741 (ttm-80) REVERT: O 134 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8674 (m-40) REVERT: O 238 LYS cc_start: 0.7017 (tptp) cc_final: 0.6620 (ttpt) REVERT: O 300 LEU cc_start: 0.8539 (mt) cc_final: 0.8213 (tp) REVERT: O 389 ARG cc_start: 0.6847 (mtp85) cc_final: 0.6406 (mtp180) REVERT: O 505 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7472 (tpp-160) REVERT: P 3 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.4563 (tt) REVERT: P 293 PHE cc_start: 0.6689 (t80) cc_final: 0.6304 (t80) REVERT: P 456 MET cc_start: 0.8108 (mtp) cc_final: 0.7798 (mtp) REVERT: P 462 PHE cc_start: 0.7251 (m-10) cc_final: 0.6984 (m-10) REVERT: P 478 GLU cc_start: 0.8401 (mp0) cc_final: 0.8125 (mp0) REVERT: Q 1 MET cc_start: 0.3956 (OUTLIER) cc_final: 0.2940 (mmt) REVERT: Q 8 GLU cc_start: 0.5519 (mm-30) cc_final: 0.4695 (pm20) REVERT: Q 21 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6760 (tp30) REVERT: Q 411 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7281 (mmpt) REVERT: Q 455 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8087 (tt0) REVERT: Q 520 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: R 330 ARG cc_start: 0.4562 (mtt180) cc_final: 0.4237 (ttp-110) REVERT: R 536 ARG cc_start: 0.6624 (tpp80) cc_final: 0.6341 (tpp80) outliers start: 81 outliers final: 51 residues processed: 510 average time/residue: 1.5202 time to fit residues: 998.1297 Evaluate side-chains 505 residues out of total 6937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 435 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 199 GLN Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 353 LYS Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 592 LYS Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 388 ILE Chi-restraints excluded: chain P residue 524 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 276 THR Chi-restraints excluded: chain Q residue 411 LYS Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 392 optimal weight: 0.9980 chunk 508 optimal weight: 4.9990 chunk 681 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 590 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 641 optimal weight: 0.0170 chunk 268 optimal weight: 8.9990 chunk 658 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN D 199 GLN G 218 HIS G 278 HIS J 315 ASN N 297 ASN N 466 GLN N 554 ASN O 383 GLN P 383 GLN Q 373 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112338 restraints weight = 82025.402| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.16 r_work: 0.3068 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 66824 Z= 0.161 Angle : 0.538 14.530 90393 Z= 0.274 Chirality : 0.041 0.200 9837 Planarity : 0.003 0.047 11590 Dihedral : 8.586 173.010 9498 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.34 % Allowed : 16.45 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.43 (0.09), residues: 8032 helix: 0.71 (0.10), residues: 3299 sheet: 0.44 (0.16), residues: 1006 loop : -1.42 (0.09), residues: 3727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 116 HIS 0.005 0.001 HIS I 267 PHE 0.027 0.001 PHE A 262 TYR 0.039 0.001 TYR R 497 ARG 0.009 0.000 ARG P 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18784.27 seconds wall clock time: 326 minutes 54.90 seconds (19614.90 seconds total)