Starting phenix.real_space_refine on Sun Dec 29 09:06:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8suw_40778/12_2024/8suw_40778.cif Found real_map, /net/cci-nas-00/data/ceres_data/8suw_40778/12_2024/8suw_40778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8suw_40778/12_2024/8suw_40778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8suw_40778/12_2024/8suw_40778.map" model { file = "/net/cci-nas-00/data/ceres_data/8suw_40778/12_2024/8suw_40778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8suw_40778/12_2024/8suw_40778.cif" } resolution = 3.15 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= 0.060 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 30 5.49 5 Mg 3 5.21 5 S 121 5.16 5 C 36162 2.51 5 N 9572 2.21 5 O 10689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 56577 Number of models: 1 Model: "" Number of chains: 31 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: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3175 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 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: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3187 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 11, 'TRANS': 387} Chain breaks: 2 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: 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: "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: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 11, 'TRANS': 387} Chain breaks: 2 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: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 11, 'TRANS': 387} Chain breaks: 2 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: 4208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4208 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 20, 'TRANS': 510} Chain breaks: 4 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} Time building chain proxies: 24.87, per 1000 atoms: 0.44 Number of scatterers: 56577 At special positions: 0 Unit cell: (187.59, 185.37, 218.67, 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 121 16.00 P 30 15.00 Mg 3 11.99 O 10689 8.00 N 9572 7.00 C 36162 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: 10.53 Conformation dependent library (CDL) restraints added in 5.4 seconds 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13004 Finding SS restraints... Secondary structure from input PDB file: 346 helices and 59 sheets defined 48.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.48 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.616A pdb=" N CYS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 59 through 66 removed outlier: 3.526A pdb=" N LEU A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 81 through 99 removed outlier: 3.794A pdb=" N LEU A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 122 removed outlier: 3.764A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 removed outlier: 3.536A pdb=" N GLN A 129 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 132 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.879A pdb=" N LYS A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASP A 139 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 6.329A 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: 3.866A pdb=" N LYS A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.506A 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 258 Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.066A pdb=" N TYR A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.678A pdb=" N ASN A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.917A pdb=" N ALA A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.542A pdb=" N HIS A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.673A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 23 removed outlier: 3.632A pdb=" N SER B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.534A pdb=" N VAL B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.049A pdb=" N GLY B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 3.791A 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: 3.514A pdb=" N LEU B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 122 removed outlier: 3.629A pdb=" N GLU B 105 " --> pdb=" O CYS B 101 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 removed outlier: 4.182A pdb=" N GLN B 129 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 130 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.706A pdb=" N LYS B 137 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 134 through 138' Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.546A 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: 3.926A 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: 4.253A pdb=" N ASP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.769A pdb=" N GLU B 286 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.538A pdb=" N LEU B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 345 removed outlier: 3.762A pdb=" N ALA B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 360 removed outlier: 3.815A pdb=" N ALA B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.641A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 removed outlier: 3.752A pdb=" N VAL B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 removed outlier: 3.570A pdb=" N SER C 21 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 37 removed outlier: 3.837A pdb=" N SER C 37 " --> pdb=" O ALA C 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 34 through 37' Processing helix chain 'C' and resid 44 through 56 removed outlier: 3.508A pdb=" N VAL C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 removed outlier: 3.852A pdb=" N LEU C 60 " --> pdb=" O TYR C 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 82 through 100 Processing helix chain 'C' and resid 101 through 122 removed outlier: 3.860A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 removed outlier: 4.172A pdb=" N ARG C 131 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 140 removed outlier: 3.982A pdb=" N LYS C 137 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS C 138 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASP C 139 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA C 140 " --> pdb=" O LYS C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 140' Processing helix chain 'C' and resid 141 through 154 removed outlier: 3.971A pdb=" N LYS C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 181 removed outlier: 3.706A pdb=" N ASP C 179 " --> pdb=" O TRP C 175 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.916A 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 Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.840A pdb=" N ILE C 256 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 4.007A pdb=" N TYR C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 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 345 Processing helix chain 'C' and resid 349 through 360 Processing helix chain 'C' and resid 376 through 384 removed outlier: 4.041A pdb=" N GLU C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 384 " --> pdb=" O PHE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 407 removed outlier: 3.588A pdb=" N SER C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.555A pdb=" N CYS D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 55 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 71 through 78 Processing helix chain 'D' and resid 81 through 99 removed outlier: 3.596A pdb=" N ASP D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.601A pdb=" N GLU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 132 removed outlier: 3.535A pdb=" N GLN D 129 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE D 130 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG D 131 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 removed outlier: 3.823A pdb=" N LYS D 137 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS D 138 " --> pdb=" O GLN D 135 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASP D 139 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 6.435A 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: 4.013A pdb=" N ASN D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.699A pdb=" N ASP D 179 " --> pdb=" O TRP D 175 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 removed outlier: 3.637A 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 253 removed outlier: 3.823A pdb=" N ILE D 253 " --> pdb=" O TYR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.718A pdb=" N ILE D 295 " --> pdb=" O PHE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 321 removed outlier: 4.120A pdb=" N ILE D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) removed outlier: 4.881A 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 336 through 345 removed outlier: 3.738A pdb=" N LYS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 360 removed outlier: 3.599A pdb=" N ILE D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 375 Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.730A pdb=" N LEU D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'E' and resid 11 through 23 removed outlier: 3.515A pdb=" N CYS E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 38 removed outlier: 3.740A pdb=" N SER E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL E 38 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.614A pdb=" N TRP E 49 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 65 removed outlier: 3.983A pdb=" N LEU E 60 " --> pdb=" O TYR E 56 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY E 61 " --> pdb=" O PRO E 57 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP E 65 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 Processing helix chain 'E' and resid 81 through 100 removed outlier: 3.526A pdb=" N ASP E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 122 removed outlier: 3.781A pdb=" N LYS E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 141 through 154 removed outlier: 3.785A pdb=" N LYS E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 181 removed outlier: 3.879A pdb=" N ASP E 179 " --> pdb=" O TRP E 175 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 180 " --> pdb=" O ALA E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.572A pdb=" N PHE E 201 " --> pdb=" O PRO E 198 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP E 202 " --> pdb=" O GLN E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.630A pdb=" N TYR E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 286 " --> pdb=" O PHE E 282 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 321 Processing helix chain 'E' and resid 335 through 346 removed outlier: 3.873A pdb=" N LYS E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY E 346 " --> pdb=" O LYS E 342 " (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 384 removed outlier: 3.625A pdb=" N VAL E 381 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU E 382 " --> pdb=" O ASN E 378 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU E 384 " --> pdb=" O PHE E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 406 removed outlier: 4.012A pdb=" N LEU E 399 " --> pdb=" O ILE E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 23 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 56 through 66 removed outlier: 4.163A pdb=" N LEU F 60 " --> pdb=" O TYR F 56 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 78 Processing helix chain 'F' and resid 81 through 99 removed outlier: 3.665A pdb=" N LEU F 85 " --> pdb=" O ASN F 81 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG F 99 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 122 removed outlier: 3.789A pdb=" N GLU F 105 " --> pdb=" O CYS F 101 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 132 removed outlier: 3.875A pdb=" N ARG F 131 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 removed outlier: 3.680A pdb=" N LYS F 137 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 3.667A 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 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 142 through 154 removed outlier: 3.649A pdb=" N GLU F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN F 154 " --> pdb=" O LYS F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 181 removed outlier: 3.512A pdb=" N TRP F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.956A 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 297 removed outlier: 3.746A pdb=" N GLU F 286 " --> pdb=" O PHE F 282 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.527A pdb=" N ASN F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY F 320 " --> pdb=" O ARG F 316 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 321 " --> pdb=" O ILE F 317 " (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: 3.978A pdb=" N ALA F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 360 removed outlier: 3.511A pdb=" N LYS F 353 " --> pdb=" O SER F 349 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 375 removed outlier: 3.511A pdb=" N LYS F 374 " --> pdb=" O GLY F 371 " (cutoff:3.500A) removed outlier: 3.570A 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: 3.679A pdb=" N LEU F 384 " --> pdb=" O PHE F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 399 Processing helix chain 'F' and resid 400 through 406 removed outlier: 3.975A pdb=" N ALA F 404 " --> pdb=" O VAL F 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 24 Processing helix chain 'G' and resid 34 through 40 removed outlier: 3.774A pdb=" N SER G 37 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL G 38 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 59 through 66 Processing helix chain 'G' and resid 71 through 78 Processing helix chain 'G' and resid 81 through 100 removed outlier: 3.846A pdb=" N LEU G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 106 removed outlier: 4.144A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 121 removed outlier: 4.188A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 132 removed outlier: 4.350A pdb=" N ARG G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU G 132 " --> pdb=" O GLN G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 141 removed outlier: 3.617A pdb=" N LYS G 138 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASP G 139 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA G 140 " --> pdb=" O LYS G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 155 removed outlier: 3.959A pdb=" N ARG G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 181 removed outlier: 3.825A pdb=" N ALA G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 201 removed outlier: 3.703A pdb=" N PHE G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 201' Processing helix chain 'G' and resid 244 through 252 Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.631A pdb=" N ILE G 257 " --> pdb=" O ILE G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 296 removed outlier: 5.048A pdb=" N VAL G 283 " --> pdb=" O THR G 279 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR G 284 " --> pdb=" O ILE G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 321 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: 3.637A pdb=" N LYS G 345 " --> pdb=" O THR G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 358 removed outlier: 3.830A pdb=" N LEU G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 372 through 375 removed outlier: 3.596A pdb=" N ALA G 375 " --> pdb=" O GLY G 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 372 through 375' Processing helix chain 'G' and resid 376 through 382 removed outlier: 3.551A pdb=" N GLU G 382 " --> pdb=" O ASN G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 405 Processing helix chain 'H' and resid 11 through 23 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 56 through 66 Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.915A pdb=" N ASP H 76 " --> pdb=" O GLN H 72 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN H 77 " --> pdb=" O ILE H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 99 Processing helix chain 'H' and resid 102 through 123 removed outlier: 3.500A pdb=" N GLU H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU H 115 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 4.656A 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) Processing helix chain 'H' and resid 126 through 131 removed outlier: 4.086A pdb=" N GLN H 129 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG H 131 " --> pdb=" O GLU H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.991A pdb=" N LYS H 138 " --> pdb=" O GLN H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 154 removed outlier: 3.567A pdb=" N ASN H 154 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 181 removed outlier: 3.718A pdb=" N ALA H 176 " --> pdb=" O ALA H 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP H 179 " --> pdb=" O TRP H 175 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY H 181 " --> pdb=" O ALA H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.830A 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 removed outlier: 3.578A pdb=" N TYR H 252 " --> pdb=" O ALA H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 259 removed outlier: 4.030A pdb=" N ILE H 257 " --> pdb=" O ILE H 253 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN H 258 " --> pdb=" O ASN H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.534A pdb=" N PHE H 288 " --> pdb=" O TYR H 284 " (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 345 removed outlier: 4.049A pdb=" N ALA H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS H 345 " --> pdb=" O THR H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 360 removed outlier: 3.590A pdb=" N ILE H 355 " --> pdb=" O ALA H 351 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN H 360 " --> pdb=" O VAL H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 375 removed outlier: 3.844A 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 383 removed outlier: 3.577A pdb=" N GLU H 382 " --> pdb=" O ASN H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 405 removed outlier: 4.275A pdb=" N ALA H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE H 403 " --> pdb=" O LEU H 399 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN H 405 " --> pdb=" O GLU H 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 23 Processing helix chain 'I' and resid 34 through 41 removed outlier: 3.767A pdb=" N VAL I 38 " --> pdb=" O GLY I 35 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY I 39 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS I 40 " --> pdb=" O SER I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 56 removed outlier: 3.608A pdb=" N GLN I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 66 removed outlier: 3.744A pdb=" N GLY I 61 " --> pdb=" O PRO I 57 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA I 62 " --> pdb=" O GLU I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 78 Processing helix chain 'I' and resid 81 through 100 removed outlier: 3.970A pdb=" N LYS I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 122 removed outlier: 3.882A pdb=" N LYS I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU I 112 " --> pdb=" O PHE I 108 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER I 114 " --> pdb=" O LYS I 110 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 132 removed outlier: 3.683A pdb=" N GLN I 129 " --> pdb=" O THR I 126 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG I 131 " --> pdb=" O GLU I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 140 removed outlier: 3.536A pdb=" N LYS I 138 " --> pdb=" O GLN I 135 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASP I 139 " --> pdb=" O GLY I 136 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA I 140 " --> pdb=" O LYS I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 154 removed outlier: 3.687A pdb=" N LYS I 145 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 181 removed outlier: 3.907A pdb=" N ALA I 176 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA I 177 " --> pdb=" O LEU I 173 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU I 178 " --> pdb=" O GLU I 174 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP I 179 " --> pdb=" O TRP I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 202 removed outlier: 3.672A pdb=" N PHE I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) 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: 4.064A pdb=" N TYR I 284 " --> pdb=" O ILE I 280 " (cutoff:3.500A) removed outlier: 3.804A 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 345 removed outlier: 3.523A pdb=" N ALA I 339 " --> pdb=" O GLU I 335 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS I 345 " --> pdb=" O THR I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 358 removed outlier: 3.683A pdb=" N LEU I 358 " --> pdb=" O ALA I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 384 removed outlier: 3.812A pdb=" N LEU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 397 Processing helix chain 'I' and resid 398 through 406 removed outlier: 3.900A pdb=" N ALA I 402 " --> pdb=" O GLU I 398 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU I 406 " --> pdb=" O ALA I 402 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 23 removed outlier: 3.618A pdb=" N CYS J 23 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 56 Processing helix chain 'J' and resid 56 through 66 removed outlier: 3.664A pdb=" N ALA J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 78 Processing helix chain 'J' and resid 83 through 100 removed outlier: 3.751A pdb=" N ASP J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 122 removed outlier: 3.627A pdb=" N GLU J 107 " --> pdb=" O ASP J 103 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU J 112 " --> pdb=" O PHE J 108 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR J 120 " --> pdb=" O TYR J 116 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 removed outlier: 3.600A pdb=" N PHE J 130 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG J 131 " --> pdb=" O GLU J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 140 removed outlier: 3.800A pdb=" N LYS J 137 " --> pdb=" O ASN J 134 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS J 138 " --> pdb=" O GLN J 135 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP J 139 " --> pdb=" O GLY J 136 " (cutoff:3.500A) removed outlier: 6.345A 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: 3.717A pdb=" N ASN J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 181 removed outlier: 3.589A pdb=" N ALA J 176 " --> pdb=" O ALA J 172 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP J 179 " --> pdb=" O TRP J 175 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 201 removed outlier: 3.573A 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: 3.649A pdb=" N TYR J 249 " --> pdb=" O ALA J 245 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP J 250 " --> pdb=" O SER J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 258 Processing helix chain 'J' and resid 281 through 295 removed outlier: 4.384A pdb=" N GLY J 285 " --> pdb=" O GLY J 281 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE J 295 " --> pdb=" O PHE J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 320 removed outlier: 3.624A pdb=" N ASN J 315 " --> pdb=" O ASP J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 345 removed outlier: 3.703A pdb=" N THR J 341 " --> pdb=" O LYS J 337 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS J 342 " --> pdb=" O GLU J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 360 removed outlier: 3.502A pdb=" N LYS J 353 " --> pdb=" O SER J 349 " (cutoff:3.500A) Processing helix chain 'J' and resid 371 through 375 Processing helix chain 'J' and resid 376 through 384 removed outlier: 3.739A pdb=" N LEU J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 402 Processing helix chain 'J' and resid 403 through 408 removed outlier: 4.048A pdb=" N SER J 407 " --> pdb=" O ILE J 403 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS J 408 " --> pdb=" O ALA J 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 403 through 408' Processing helix chain 'K' and resid 11 through 23 removed outlier: 3.556A pdb=" N CYS K 23 " --> pdb=" O VAL K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 41 removed outlier: 3.749A pdb=" N SER K 37 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLY K 39 " --> pdb=" O ALA K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 56 Processing helix chain 'K' and resid 58 through 65 removed outlier: 4.513A pdb=" N ALA K 62 " --> pdb=" O GLU K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 78 Processing helix chain 'K' and resid 81 through 100 removed outlier: 3.882A pdb=" N LYS K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER K 94 " --> pdb=" O THR K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 121 removed outlier: 3.516A pdb=" N ARG K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.950A pdb=" N GLN K 129 " --> pdb=" O THR K 126 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG K 131 " --> pdb=" O GLU K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 138 removed outlier: 3.821A pdb=" N LYS K 138 " --> pdb=" O GLN K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 153 removed outlier: 3.883A pdb=" N LYS K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU K 146 " --> pdb=" O LYS K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 181 removed outlier: 3.566A pdb=" N ASP K 179 " --> pdb=" O TRP K 175 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 203 removed outlier: 3.860A pdb=" N PHE K 201 " --> pdb=" O PRO K 198 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU K 203 " --> pdb=" O ASN K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 252 Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 280 through 295 removed outlier: 4.014A pdb=" N TYR K 284 " --> pdb=" O ILE K 280 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE K 291 " --> pdb=" O MET K 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE K 295 " --> pdb=" O PHE K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 321 removed outlier: 3.544A pdb=" N ASN K 315 " --> pdb=" O ASP K 311 " (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 345 removed outlier: 3.680A pdb=" N LYS K 345 " --> pdb=" O THR K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 361 Processing helix chain 'K' and resid 376 through 384 removed outlier: 3.761A pdb=" N GLU K 382 " --> pdb=" O ASN K 378 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS K 383 " --> pdb=" O SER K 379 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU K 384 " --> pdb=" O PHE K 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 406 Processing helix chain 'L' and resid 11 through 22 Processing helix chain 'L' and resid 44 through 56 removed outlier: 3.652A pdb=" N VAL L 48 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP L 49 " --> pdb=" O MET L 45 " (cutoff:3.500A) removed outlier: 3.679A 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 Processing helix chain 'L' and resid 81 through 99 removed outlier: 3.954A pdb=" N LEU L 85 " --> pdb=" O ASN L 81 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP L 87 " --> pdb=" O GLU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 122 removed outlier: 4.240A pdb=" N GLU L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 removed outlier: 4.427A pdb=" N ARG L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU L 132 " --> pdb=" O GLN L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 138 removed outlier: 3.925A pdb=" N LYS L 137 " --> pdb=" O ASN L 134 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS L 138 " --> pdb=" O GLN L 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 134 through 138' Processing helix chain 'L' and resid 141 through 153 removed outlier: 3.796A pdb=" N LYS L 145 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU L 146 " --> pdb=" O LYS L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 181 Processing helix chain 'L' and resid 198 through 201 removed outlier: 3.855A 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 250 Processing helix chain 'L' and resid 252 through 259 Processing helix chain 'L' and resid 283 through 296 removed outlier: 3.502A pdb=" N MET L 287 " --> pdb=" O VAL L 283 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE L 288 " --> pdb=" O TYR L 284 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG L 289 " --> pdb=" O GLY L 285 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER L 296 " --> pdb=" O GLY L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 321 removed outlier: 3.856A pdb=" N ASN L 315 " --> pdb=" O ASP L 311 " (cutoff:3.500A) 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: 3.763A 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 removed outlier: 3.574A pdb=" N LYS L 374 " --> pdb=" O GLY L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 384 removed outlier: 3.702A pdb=" N LEU L 384 " --> pdb=" O PHE L 380 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 401 removed outlier: 4.052A pdb=" N LEU L 399 " --> pdb=" O VAL L 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 137 removed outlier: 3.724A pdb=" N ILE M 135 " --> pdb=" O ASP M 131 " (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 removed outlier: 3.594A pdb=" N LEU M 169 " --> pdb=" O VAL M 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 165 through 169' Processing helix chain 'M' and resid 182 through 198 removed outlier: 3.603A pdb=" N LYS M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 261 removed outlier: 3.596A pdb=" N ALA M 260 " --> pdb=" O PRO M 257 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU M 261 " --> pdb=" O TYR M 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 257 through 261' Processing helix chain 'M' and resid 262 through 271 removed outlier: 3.701A pdb=" N ILE M 267 " --> pdb=" O PHE M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 287 Processing helix chain 'M' and resid 288 through 291 Processing helix chain 'M' and resid 318 through 320 No H-bonds generated for 'chain 'M' and resid 318 through 320' Processing helix chain 'M' and resid 321 through 332 removed outlier: 3.845A pdb=" N ARG M 331 " --> pdb=" O ASP M 327 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG M 332 " --> pdb=" O LEU M 328 " (cutoff:3.500A) 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 356 removed outlier: 3.933A pdb=" N LEU M 349 " --> pdb=" O SER M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 387 removed outlier: 3.684A pdb=" N VAL M 378 " --> pdb=" O VAL M 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 394 Processing helix chain 'M' and resid 407 through 421 removed outlier: 4.096A pdb=" N MET M 413 " --> pdb=" O TRP M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 450 Processing helix chain 'M' and resid 450 through 465 removed outlier: 4.114A pdb=" N LEU M 454 " --> pdb=" O LEU M 450 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU M 455 " --> pdb=" O SER M 451 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY M 465 " --> pdb=" O LEU M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 482 removed outlier: 3.622A pdb=" N HIS M 481 " --> pdb=" O GLU M 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 517 through 521 removed outlier: 3.683A pdb=" N GLU M 520 " --> pdb=" O ARG M 517 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 528 removed outlier: 3.947A pdb=" N LEU M 526 " --> pdb=" O SER M 522 " (cutoff:3.500A) Processing helix chain 'M' and resid 539 through 542 removed outlier: 3.684A pdb=" N ASP M 542 " --> pdb=" O ASN M 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 539 through 542' Processing helix chain 'M' and resid 543 through 550 removed outlier: 4.114A pdb=" N MET M 550 " --> pdb=" O LEU M 546 " (cutoff:3.500A) Processing helix chain 'M' and resid 555 through 563 removed outlier: 4.097A pdb=" N LEU M 558 " --> pdb=" O GLU M 555 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS M 559 " --> pdb=" O GLN M 556 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN M 560 " --> pdb=" O ILE M 557 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE M 561 " --> pdb=" O LEU M 558 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER M 562 " --> pdb=" O LYS M 559 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY M 563 " --> pdb=" O GLN M 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 555 through 563' Processing helix chain 'M' and resid 600 through 605 removed outlier: 4.093A pdb=" N ASN M 604 " --> pdb=" O GLU M 601 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS M 605 " --> pdb=" O TRP M 602 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 137 removed outlier: 3.866A pdb=" N ILE N 135 " --> pdb=" O ASP N 131 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE N 136 " --> pdb=" O PHE N 132 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR N 137 " --> pdb=" O LEU N 133 " (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 195 Processing helix chain 'N' and resid 210 through 215 removed outlier: 3.695A pdb=" N ALA N 213 " --> pdb=" O GLY N 210 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 262 Processing helix chain 'N' and resid 263 through 271 removed outlier: 3.800A pdb=" N ILE N 267 " --> pdb=" O PHE N 263 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS N 268 " --> pdb=" O ALA N 264 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU N 269 " --> pdb=" O GLY N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 287 removed outlier: 3.994A pdb=" N ALA N 280 " --> pdb=" O THR N 276 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG N 282 " --> pdb=" O LEU N 278 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN N 283 " --> pdb=" O PRO N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 288 through 291 removed outlier: 3.974A pdb=" N THR N 291 " --> pdb=" O ILE N 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 288 through 291' Processing helix chain 'N' and resid 321 through 331 removed outlier: 4.094A pdb=" N TRP N 325 " --> pdb=" O LYS N 321 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG N 331 " --> pdb=" O ASP N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 344 No H-bonds generated for 'chain 'N' and resid 342 through 344' Processing helix chain 'N' and resid 345 through 356 removed outlier: 4.203A pdb=" N LEU N 349 " --> pdb=" O SER N 345 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL N 350 " --> pdb=" O LEU N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 372 removed outlier: 3.937A pdb=" N PHE N 371 " --> pdb=" O ASP N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 385 removed outlier: 3.620A pdb=" N ILE N 380 " --> pdb=" O PRO N 376 " (cutoff:3.500A) Processing helix chain 'N' and resid 386 through 392 removed outlier: 6.957A pdb=" N ARG N 389 " --> pdb=" O GLU N 386 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS N 391 " --> pdb=" O ILE N 388 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 421 removed outlier: 4.486A pdb=" N GLU N 416 " --> pdb=" O ALA N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 438 through 441 Processing helix chain 'N' and resid 445 through 464 removed outlier: 3.625A pdb=" N GLU N 459 " --> pdb=" O GLU N 455 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE N 460 " --> pdb=" O MET N 456 " (cutoff:3.500A) Processing helix chain 'N' and resid 478 through 482 removed outlier: 3.519A pdb=" N TYR N 482 " --> pdb=" O ALA N 479 " (cutoff:3.500A) 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 549 Processing helix chain 'N' and resid 556 through 560 removed outlier: 3.804A pdb=" N LYS N 559 " --> pdb=" O GLN N 556 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN N 560 " --> pdb=" O ILE N 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 556 through 560' Processing helix chain 'O' and resid 129 through 137 removed outlier: 3.564A pdb=" N ILE O 135 " --> pdb=" O ASP O 131 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR O 137 " --> pdb=" O LEU O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 147 Proline residue: O 145 - end of helix Processing helix chain 'O' and resid 164 through 170 Processing helix chain 'O' and resid 182 through 198 removed outlier: 3.560A pdb=" N TYR O 198 " --> pdb=" O VAL O 194 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 216 removed outlier: 4.262A pdb=" N ALA O 215 " --> pdb=" O GLU O 211 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE O 216 " --> pdb=" O TYR O 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 211 through 216' Processing helix chain 'O' and resid 262 through 271 Processing helix chain 'O' and resid 277 through 288 Processing helix chain 'O' and resid 321 through 332 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 354 removed outlier: 3.513A pdb=" N VAL O 350 " --> pdb=" O LEU O 346 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA O 351 " --> pdb=" O ALA O 347 " (cutoff:3.500A) Processing helix chain 'O' and resid 367 through 386 Proline residue: O 376 - end of helix Processing helix chain 'O' and resid 389 through 394 Processing helix chain 'O' and resid 407 through 416 removed outlier: 3.960A pdb=" N MET O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU O 416 " --> pdb=" O ALA O 412 " (cutoff:3.500A) Processing helix chain 'O' and resid 417 through 422 Processing helix chain 'O' and resid 445 through 465 removed outlier: 3.793A pdb=" N GLU O 459 " --> pdb=" O GLU O 455 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE O 460 " --> pdb=" O MET O 456 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY O 465 " --> pdb=" O LEU O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 478 through 482 Processing helix chain 'O' and resid 490 through 494 removed outlier: 3.807A 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 Processing helix chain 'O' and resid 542 through 547 Processing helix chain 'O' and resid 557 through 561 removed outlier: 3.697A pdb=" N GLN O 560 " --> pdb=" O ILE O 557 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE O 561 " --> pdb=" O LEU O 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 557 through 561' Processing helix chain 'O' and resid 597 through 603 removed outlier: 3.628A pdb=" N GLU O 601 " --> pdb=" O VAL O 597 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 137 removed outlier: 3.503A pdb=" N TYR P 137 " --> pdb=" O LEU P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 144 removed outlier: 3.978A pdb=" N LEU P 144 " --> pdb=" O LYS P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 170 Processing helix chain 'P' and resid 183 through 198 Processing helix chain 'P' and resid 211 through 216 removed outlier: 3.600A pdb=" N GLN P 214 " --> pdb=" O GLU P 211 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE P 216 " --> pdb=" O ALA P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 262 removed outlier: 3.541A pdb=" N LEU P 261 " --> pdb=" O TYR P 258 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY P 262 " --> pdb=" O GLN P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 271 removed outlier: 4.089A pdb=" N LEU P 270 " --> pdb=" O LEU P 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 277 through 287 removed outlier: 3.609A pdb=" N LEU P 281 " --> pdb=" O GLN P 277 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 354 removed outlier: 3.941A pdb=" N ALA P 347 " --> pdb=" O PHE P 343 " (cutoff:3.500A) Processing helix chain 'P' and resid 375 through 386 removed outlier: 3.748A pdb=" N LYS P 379 " --> pdb=" O LEU P 375 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE P 381 " --> pdb=" O LEU P 377 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN P 382 " --> pdb=" O VAL P 378 " (cutoff:3.500A) Processing helix chain 'P' and resid 389 through 393 removed outlier: 3.845A pdb=" N ILE P 393 " --> pdb=" O PHE P 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 407 through 418 removed outlier: 3.953A pdb=" N LYS P 411 " --> pdb=" O THR P 407 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP P 418 " --> pdb=" O SER P 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 461 removed outlier: 3.975A pdb=" N LEU P 449 " --> pdb=" O HIS P 445 " (cutoff:3.500A) Processing helix chain 'P' and resid 462 through 465 Processing helix chain 'P' and resid 479 through 482 Processing helix chain 'P' and resid 497 through 503 Processing helix chain 'P' and resid 517 through 521 removed outlier: 3.937A pdb=" N GLU P 520 " --> pdb=" O ARG P 517 " (cutoff:3.500A) Processing helix chain 'P' and resid 522 through 529 removed outlier: 3.696A pdb=" N ALA P 527 " --> pdb=" O THR P 524 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS P 529 " --> pdb=" O LEU P 526 " (cutoff:3.500A) Processing helix chain 'P' and resid 539 through 549 removed outlier: 3.558A pdb=" N LEU P 543 " --> pdb=" O ASN P 539 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA P 549 " --> pdb=" O ALA P 545 " (cutoff:3.500A) Processing helix chain 'P' and resid 555 through 560 Processing helix chain 'P' and resid 561 through 564 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.619A pdb=" N ASN A 27 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N PHE A 303 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY A 29 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ASN A 305 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU A 31 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 28 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N PHE A 165 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A 30 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 164 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.522A pdb=" N SER A 189 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 3.530A 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 234 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.799A pdb=" N VAL B 28 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N PHE B 165 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL B 30 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 164 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN B 183 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU B 223 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE B 185 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.819A 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 removed outlier: 3.558A pdb=" N GLN B 195 " --> pdb=" O SER B 189 " (cutoff:3.500A) 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: 4.165A pdb=" N ASN C 8 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN C 5 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL C 30 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 6.486A 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 3 through 5 removed outlier: 8.417A pdb=" N THR D 367 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL D 329 " --> pdb=" O THR D 367 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL D 369 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE D 331 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL D 28 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N PHE D 165 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL D 30 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE D 164 " --> pdb=" O TYR D 224 " (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 205 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 8 through 9 removed outlier: 3.573A pdb=" N HIS E 328 " --> pdb=" O THR E 300 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL E 28 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N PHE E 165 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL E 30 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE E 164 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 188 through 189 removed outlier: 3.544A pdb=" N SER E 189 " --> pdb=" O GLN E 195 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 195 " --> pdb=" O SER E 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 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: 8.488A pdb=" N THR F 367 " --> pdb=" O PHE F 327 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL F 329 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL F 369 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE F 331 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR F 300 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL F 330 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU F 302 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N TYR F 332 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE F 304 " --> pdb=" O TYR F 332 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN F 27 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N PHE F 303 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY F 29 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ASN F 305 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU F 31 " --> pdb=" O ASN F 305 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA F 163 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE F 164 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F 221 " --> pdb=" O GLN F 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 188 through 189 removed outlier: 3.533A pdb=" N SER F 189 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 203 through 207 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 3 through 4 removed outlier: 3.613A pdb=" N TYR G 4 " --> pdb=" O VAL G 368 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR G 367 " --> pdb=" O VAL G 329 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL G 28 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE G 165 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL G 30 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA G 221 " --> pdb=" O GLN G 183 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 223 " --> pdb=" O PHE G 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 188 through 189 removed outlier: 3.655A pdb=" N SER G 189 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 3.633A 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 233 through 234 removed outlier: 3.780A pdb=" N TYR G 233 " --> pdb=" O ASN G 241 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 8 through 9 removed outlier: 8.235A pdb=" N THR H 367 " --> pdb=" O PHE H 327 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL H 329 " --> pdb=" O THR H 367 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL H 369 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE H 331 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR H 300 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N VAL H 330 " --> pdb=" O THR H 300 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU H 302 " --> pdb=" O VAL H 330 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N TYR H 332 " --> pdb=" O LEU H 302 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE H 304 " --> pdb=" O TYR H 332 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL H 28 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N PHE H 165 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL H 30 " --> pdb=" O PHE H 165 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE H 164 " --> pdb=" O TYR H 224 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA H 221 " --> pdb=" O GLN H 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 188 through 189 removed outlier: 3.598A pdb=" N SER H 189 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN H 195 " --> pdb=" O SER H 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 203 through 206 Processing sheet with id=AD2, first strand: chain 'H' and resid 232 through 234 Processing sheet with id=AD3, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.724A pdb=" N THR I 367 " --> pdb=" O VAL I 329 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN I 305 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL I 28 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE I 165 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL I 30 " --> pdb=" O PHE I 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU I 223 " --> pdb=" O PHE I 185 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 188 through 189 removed outlier: 3.502A pdb=" N SER I 189 " --> pdb=" O GLN I 195 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN I 195 " --> pdb=" O SER I 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'I' and resid 232 through 233 Processing sheet with id=AD6, first strand: chain 'J' and resid 8 through 10 removed outlier: 4.283A pdb=" N ILE J 3 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR J 367 " --> pdb=" O PHE J 327 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL J 329 " --> pdb=" O THR J 367 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL J 369 " --> pdb=" O VAL J 329 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE J 331 " --> pdb=" O VAL J 369 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL J 28 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N PHE J 165 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL J 30 " --> pdb=" O PHE J 165 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE J 164 " --> pdb=" O TYR J 224 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN J 183 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU J 223 " --> pdb=" O GLN J 183 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE J 185 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS J 225 " --> pdb=" O PHE J 185 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 188 through 189 removed outlier: 3.553A pdb=" N GLN J 195 " --> pdb=" O SER J 189 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AD9, first strand: chain 'J' and resid 232 through 234 Processing sheet with id=AE1, first strand: chain 'K' and resid 8 through 9 removed outlier: 6.649A pdb=" N ASN K 27 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N PHE K 303 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY K 29 " --> pdb=" O PHE K 303 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASN K 305 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU K 31 " --> pdb=" O ASN K 305 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE K 164 " --> pdb=" O TYR K 224 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 188 through 189 Processing sheet with id=AE3, first strand: chain 'K' and resid 232 through 233 Processing sheet with id=AE4, first strand: chain 'L' and resid 8 through 10 removed outlier: 3.659A pdb=" N ASN L 8 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN L 5 " --> pdb=" O ASN L 8 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE L 3 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR L 367 " --> pdb=" O VAL L 329 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN L 27 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N PHE L 303 " --> pdb=" O ASN L 27 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY L 29 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ASN L 305 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU L 31 " --> pdb=" O ASN L 305 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA L 163 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE L 164 " --> pdb=" O TYR L 224 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 188 through 189 removed outlier: 3.556A pdb=" N SER L 189 " --> pdb=" O GLN L 195 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN L 195 " --> pdb=" O SER L 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'L' and resid 232 through 234 Processing sheet with id=AE7, first strand: chain 'M' and resid 13 through 18 removed outlier: 5.936A pdb=" N VAL M 15 " --> pdb=" O ASN M 26 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN M 26 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY M 17 " --> pdb=" O ARG M 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 23 through 27 current: chain 'M' and resid 59 through 70 removed outlier: 6.380A pdb=" N LEU M 60 " --> pdb=" O PHE M 101 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE M 101 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL M 62 " --> pdb=" O ILE M 99 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE M 95 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET M 68 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN M 93 " --> pdb=" O MET M 68 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE M 101 " --> pdb=" O ILE M 112 " (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 60 through 70 removed outlier: 6.346A pdb=" N LEU N 60 " --> pdb=" O PHE N 101 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE N 101 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL N 62 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE N 95 " --> pdb=" O THR N 66 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET N 68 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN N 93 " --> pdb=" O MET N 68 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE N 101 " --> pdb=" O ILE N 112 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 109 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: 3.736A pdb=" N GLY O 100 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG O 64 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA O 98 " --> pdb=" O ARG O 64 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR O 66 " --> pdb=" O ALA O 96 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA O 96 " --> pdb=" O THR O 66 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET O 68 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE O 94 " --> pdb=" O MET O 68 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE O 70 " --> pdb=" O ARG O 92 " (cutoff:3.500A) removed outlier: 6.874A 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 110 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 67 removed outlier: 3.683A pdb=" N GLY P 100 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG P 64 " --> pdb=" O ALA P 98 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA P 98 " --> pdb=" O ARG P 64 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR P 66 " --> pdb=" O ALA P 96 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA P 96 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 36 through 37 Processing sheet with id=AE9, first strand: chain 'M' and resid 160 through 164 removed outlier: 4.020A pdb=" N GLY M 151 " --> pdb=" O ILE M 161 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA M 163 " --> pdb=" O GLU M 149 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU M 149 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE M 572 " --> pdb=" O TRP M 532 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 204 through 207 removed outlier: 6.019A pdb=" N ILE M 205 " --> pdb=" O VAL M 436 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS M 223 " --> pdb=" O ILE M 435 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASN M 437 " --> pdb=" O LYS M 223 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR M 225 " --> pdb=" O ASN M 437 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LYS M 254 " --> pdb=" O HIS M 224 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE M 226 " --> pdb=" O LYS M 254 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'M' and resid 298 through 300 removed outlier: 4.076A pdb=" N LEU M 300 " --> pdb=" O PHE M 308 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE M 308 " --> pdb=" O LEU M 300 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 35 through 37 removed outlier: 3.588A pdb=" N SER N 43 " --> pdb=" O ALA N 36 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 160 through 164 removed outlier: 7.157A pdb=" N ILE N 161 " --> pdb=" O LEU N 150 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE N 572 " --> pdb=" O TRP N 532 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 204 through 206 removed outlier: 3.594A pdb=" N PHE N 206 " --> pdb=" O LEU N 475 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR N 472 " --> pdb=" O SER N 510 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE N 512 " --> pdb=" O THR N 472 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU N 474 " --> pdb=" O ILE N 512 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 222 through 226 removed outlier: 6.533A pdb=" N LYS N 223 " --> pdb=" O ILE N 435 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN N 437 " --> pdb=" O LYS N 223 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR N 225 " --> pdb=" O ASN N 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'O' and resid 160 through 161 removed outlier: 4.267A pdb=" N GLY O 151 " --> pdb=" O ILE O 161 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE O 572 " --> pdb=" O TRP O 532 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 203 through 205 removed outlier: 6.831A pdb=" N ILE O 203 " --> pdb=" O HIS O 434 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N VAL O 436 " --> pdb=" O ILE O 203 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE O 205 " --> pdb=" O VAL O 436 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN O 437 " --> pdb=" O THR O 225 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 291 through 293 Processing sheet with id=AG1, first strand: chain 'P' and resid 36 through 38 Processing sheet with id=AG2, first strand: chain 'P' and resid 151 through 152 removed outlier: 3.514A pdb=" N SER P 583 " --> pdb=" O VAL P 152 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 173 through 175 removed outlier: 3.658A pdb=" N VAL P 513 " --> pdb=" O LEU P 173 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU P 474 " --> pdb=" O ILE P 512 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER P 514 " --> pdb=" O LEU P 474 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU P 476 " --> pdb=" O SER P 514 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU P 477 " --> pdb=" O PHE P 206 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 339 through 340 removed outlier: 4.071A pdb=" N GLY P 400 " --> pdb=" O TRP P 340 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 531 through 534 removed outlier: 3.670A pdb=" N PHE P 572 " --> pdb=" O TRP P 532 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER P 534 " --> pdb=" O VAL P 570 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL P 570 " --> pdb=" O SER P 534 " (cutoff:3.500A) 1954 hydrogen bonds defined for protein. 5544 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: 22.17 Time building geometry restraints manager: 12.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18357 1.34 - 1.46: 11721 1.46 - 1.58: 27520 1.58 - 1.69: 57 1.69 - 1.81: 185 Bond restraints: 57840 Sorted by residual: bond pdb=" C PRO A 385 " pdb=" N TYR A 386 " ideal model delta sigma weight residual 1.329 1.361 -0.032 1.86e-02 2.89e+03 2.96e+00 bond pdb=" C TYR I 197 " pdb=" O TYR I 197 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 2.09e+00 bond pdb=" CA GLY J 127 " pdb=" C GLY J 127 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.37e+00 bond pdb=" N GLY J 127 " pdb=" CA GLY J 127 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.10e+00 bond pdb=" C4 ADP O 701 " pdb=" C5 ADP O 701 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.97e-01 ... (remaining 57835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 77886 2.65 - 5.31: 338 5.31 - 7.96: 26 7.96 - 10.61: 2 10.61 - 13.26: 1 Bond angle restraints: 78253 Sorted by residual: angle pdb=" N VAL K 208 " pdb=" CA VAL K 208 " pdb=" C VAL K 208 " ideal model delta sigma weight residual 113.10 107.54 5.56 9.70e-01 1.06e+00 3.29e+01 angle pdb=" N ILE P 288 " pdb=" CA ILE P 288 " pdb=" C ILE P 288 " ideal model delta sigma weight residual 113.42 107.60 5.82 1.17e+00 7.31e-01 2.47e+01 angle pdb=" N ILE L 280 " pdb=" CA ILE L 280 " pdb=" C ILE L 280 " ideal model delta sigma weight residual 112.83 108.99 3.84 9.90e-01 1.02e+00 1.50e+01 angle pdb=" CA LEU D 238 " pdb=" CB LEU D 238 " pdb=" CG LEU D 238 " ideal model delta sigma weight residual 116.30 129.56 -13.26 3.50e+00 8.16e-02 1.44e+01 angle pdb=" N ILE M 208 " pdb=" CA ILE M 208 " pdb=" C ILE M 208 " ideal model delta sigma weight residual 113.53 110.08 3.45 9.80e-01 1.04e+00 1.24e+01 ... (remaining 78248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 33464 32.04 - 64.08: 978 64.08 - 96.13: 127 96.13 - 128.17: 2 128.17 - 160.21: 1 Dihedral angle restraints: 34572 sinusoidal: 14227 harmonic: 20345 Sorted by residual: dihedral pdb=" O1B ADP O 701 " pdb=" O3A ADP O 701 " pdb=" PB ADP O 701 " pdb=" PA ADP O 701 " ideal model delta sinusoidal sigma weight residual -60.00 -165.39 105.39 1 2.00e+01 2.50e-03 3.04e+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 -162.84 102.83 1 2.00e+01 2.50e-03 2.93e+01 dihedral pdb=" O1A AR6 L 501 " pdb=" O3A AR6 L 501 " pdb=" PA AR6 L 501 " pdb=" PB AR6 L 501 " ideal model delta sinusoidal sigma weight residual -82.51 77.70 -160.21 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 34569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 6947 0.049 - 0.098: 1231 0.098 - 0.147: 318 0.147 - 0.196: 2 0.196 - 0.245: 2 Chirality restraints: 8500 Sorted by residual: chirality pdb=" CG LEU N 521 " pdb=" CB LEU N 521 " pdb=" CD1 LEU N 521 " pdb=" CD2 LEU N 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB THR M 538 " pdb=" CA THR M 538 " pdb=" OG1 THR M 538 " pdb=" CG2 THR M 538 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB THR P 317 " pdb=" CA THR P 317 " pdb=" OG1 THR P 317 " pdb=" CG2 THR P 317 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 8497 not shown) Planarity restraints: 10034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR H 270 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO H 271 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO H 271 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 271 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 390 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO H 391 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 391 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 391 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 333 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.94e+00 pdb=" N PRO E 334 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 334 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 334 " -0.028 5.00e-02 4.00e+02 ... (remaining 10031 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 437 2.64 - 3.20: 47572 3.20 - 3.77: 75958 3.77 - 4.33: 104338 4.33 - 4.90: 179434 Nonbonded interactions: 407739 Sorted by model distance: nonbonded pdb=" OE1 GLU O 477 " pdb="MG MG O 702 " model vdw 2.072 2.170 nonbonded pdb=" OE2 GLU J 83 " pdb=" O2D AR6 J 501 " model vdw 2.196 3.040 nonbonded pdb=" OE1 GLN C 266 " pdb=" OH TYR C 276 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR O 258 " pdb=" O PRO O 341 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU K 106 " pdb=" NZ LYS K 110 " model vdw 2.222 3.120 ... (remaining 407734 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 4 through 328 or resid 336 through 356 or resid 375 throug \ h 585)) selection = (chain 'N' and (resid 4 through 328 or resid 336 through 356 or resid 375 throug \ h 484 or resid 498 through 585)) selection = (chain 'O' and (resid 4 through 71 or resid 89 through 328 or resid 336 through \ 356 or resid 375 through 484 or resid 498 through 585)) selection = (chain 'P' and (resid 4 through 484 or resid 498 through 585)) } 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: 1.480 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: 1.600 Check model and map are aligned: 0.310 Set scattering table: 0.440 Process input model: 97.670 Find NCS groups from input model: 3.030 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: 0.020 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.002 0.034 57840 Z= 0.137 Angle : 0.502 13.263 78253 Z= 0.275 Chirality : 0.040 0.245 8500 Planarity : 0.003 0.066 10034 Dihedral : 15.083 160.211 21568 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.75 (0.10), residues: 6943 helix: 0.50 (0.10), residues: 2788 sheet: 0.03 (0.19), residues: 721 loop : -1.47 (0.10), residues: 3434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 116 HIS 0.004 0.001 HIS N 292 PHE 0.032 0.001 PHE N 457 TYR 0.014 0.001 TYR D 284 ARG 0.004 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 589 time to evaluate : 4.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASN cc_start: 0.8382 (t0) cc_final: 0.8154 (t0) REVERT: E 4 TYR cc_start: 0.8434 (m-80) cc_final: 0.8084 (m-10) REVERT: G 48 VAL cc_start: 0.7084 (m) cc_final: 0.6849 (p) REVERT: G 313 HIS cc_start: 0.7154 (m90) cc_final: 0.6802 (m90) REVERT: J 287 MET cc_start: 0.8790 (mmt) cc_final: 0.8444 (mmt) REVERT: K 179 ASP cc_start: 0.7914 (t0) cc_final: 0.7666 (t0) REVERT: O 22 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7592 (mtt90) REVERT: P 150 LEU cc_start: 0.3735 (mm) cc_final: 0.3481 (tp) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.5644 time to fit residues: 549.8734 Evaluate side-chains 298 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 4.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 587 optimal weight: 5.9990 chunk 527 optimal weight: 8.9990 chunk 292 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 355 optimal weight: 6.9990 chunk 281 optimal weight: 0.9980 chunk 545 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 331 optimal weight: 8.9990 chunk 406 optimal weight: 0.9990 chunk 632 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS C 183 GLN D 405 ASN E 129 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN G 72 GLN G 135 GLN G 144 HIS G 383 HIS K 247 GLN L 154 ASN M 481 HIS ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 57840 Z= 0.232 Angle : 0.555 9.046 78253 Z= 0.287 Chirality : 0.042 0.201 8500 Planarity : 0.004 0.049 10034 Dihedral : 8.980 169.141 8267 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.60 % Allowed : 6.12 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.68 (0.10), residues: 6943 helix: 0.61 (0.10), residues: 2846 sheet: 0.15 (0.19), residues: 738 loop : -1.55 (0.10), residues: 3359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 532 HIS 0.006 0.001 HIS P 434 PHE 0.026 0.001 PHE N 420 TYR 0.024 0.001 TYR M 246 ARG 0.005 0.000 ARG O 536 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 329 time to evaluate : 4.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 TYR cc_start: 0.7889 (m-80) cc_final: 0.7552 (m-10) REVERT: G 48 VAL cc_start: 0.7271 (m) cc_final: 0.6963 (p) REVERT: J 287 MET cc_start: 0.8734 (mmt) cc_final: 0.8472 (mmt) REVERT: K 179 ASP cc_start: 0.7938 (t0) cc_final: 0.7730 (t0) REVERT: N 448 MET cc_start: 0.1527 (OUTLIER) cc_final: 0.1132 (mmt) REVERT: O 438 MET cc_start: -0.0074 (mmt) cc_final: -0.0556 (mmt) REVERT: P 32 GLN cc_start: 0.6069 (pp30) cc_final: 0.4521 (mm110) REVERT: P 456 MET cc_start: 0.1864 (mmt) cc_final: 0.1430 (mmm) outliers start: 36 outliers final: 23 residues processed: 354 average time/residue: 0.5631 time to fit residues: 338.6951 Evaluate side-chains 290 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 4.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 276 THR Chi-restraints excluded: chain N residue 396 LEU Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 256 ILE Chi-restraints excluded: chain O residue 593 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 351 optimal weight: 20.0000 chunk 196 optimal weight: 6.9990 chunk 526 optimal weight: 6.9990 chunk 430 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 633 optimal weight: 20.0000 chunk 684 optimal weight: 6.9990 chunk 563 optimal weight: 9.9990 chunk 627 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 507 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS B 378 ASN E 227 HIS G 144 HIS H 364 ASN I 218 HIS J 220 HIS L 8 ASN N 373 ASN N 445 HIS N 539 ASN N 560 GLN O 604 ASN P 200 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 57840 Z= 0.411 Angle : 0.662 11.510 78253 Z= 0.342 Chirality : 0.046 0.187 8500 Planarity : 0.004 0.051 10034 Dihedral : 8.893 161.718 8267 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.12 % Allowed : 9.65 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -1.07 (0.10), residues: 6943 helix: 0.27 (0.10), residues: 2851 sheet: -0.06 (0.19), residues: 720 loop : -1.75 (0.10), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 602 HIS 0.009 0.001 HIS F 313 PHE 0.028 0.002 PHE N 54 TYR 0.024 0.002 TYR I 386 ARG 0.008 0.001 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 279 time to evaluate : 4.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 TYR cc_start: 0.8005 (m-80) cc_final: 0.7568 (m-10) REVERT: G 312 TYR cc_start: 0.6934 (t80) cc_final: 0.6606 (t80) REVERT: J 205 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8615 (m-10) REVERT: K 105 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7538 (tm-30) REVERT: N 206 PHE cc_start: 0.0890 (OUTLIER) cc_final: 0.0115 (m-80) REVERT: N 448 MET cc_start: 0.1565 (OUTLIER) cc_final: 0.0916 (mmt) REVERT: N 460 ILE cc_start: 0.0913 (OUTLIER) cc_final: 0.0298 (mp) REVERT: O 169 LEU cc_start: 0.8512 (mt) cc_final: 0.8239 (mp) REVERT: O 438 MET cc_start: 0.0210 (mmt) cc_final: -0.0264 (mmt) REVERT: P 32 GLN cc_start: 0.6032 (pp30) cc_final: 0.4393 (mm110) outliers start: 67 outliers final: 44 residues processed: 334 average time/residue: 0.5372 time to fit residues: 306.3446 Evaluate side-chains 297 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 4.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 98 THR Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 562 SER Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 276 THR Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 593 SER Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 204 VAL Chi-restraints excluded: chain P residue 472 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 625 optimal weight: 6.9990 chunk 476 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 70 optimal weight: 0.4980 chunk 302 optimal weight: 1.9990 chunk 425 optimal weight: 2.9990 chunk 635 optimal weight: 8.9990 chunk 672 optimal weight: 9.9990 chunk 331 optimal weight: 10.0000 chunk 602 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN H 278 HIS J 383 HIS M 556 GLN P 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 57840 Z= 0.299 Angle : 0.587 10.960 78253 Z= 0.304 Chirality : 0.044 0.170 8500 Planarity : 0.004 0.052 10034 Dihedral : 8.682 164.507 8267 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.48 % Allowed : 11.31 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -1.04 (0.10), residues: 6943 helix: 0.32 (0.10), residues: 2846 sheet: -0.15 (0.19), residues: 749 loop : -1.75 (0.10), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP M 602 HIS 0.007 0.001 HIS L 227 PHE 0.020 0.002 PHE P 572 TYR 0.035 0.002 TYR I 386 ARG 0.008 0.000 ARG P 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 262 time to evaluate : 4.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: E 4 TYR cc_start: 0.7888 (m-80) cc_final: 0.7472 (m-10) REVERT: E 84 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8064 (tt) REVERT: K 105 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7612 (tm-30) REVERT: L 264 ARG cc_start: 0.7741 (mpp-170) cc_final: 0.7044 (mmt180) REVERT: N 448 MET cc_start: 0.1590 (OUTLIER) cc_final: 0.0928 (mmt) REVERT: N 460 ILE cc_start: 0.0651 (OUTLIER) cc_final: 0.0168 (mp) REVERT: O 169 LEU cc_start: 0.8535 (mt) cc_final: 0.8280 (mp) REVERT: O 396 LEU cc_start: 0.1999 (OUTLIER) cc_final: 0.1700 (pp) REVERT: O 438 MET cc_start: -0.0084 (mmt) cc_final: -0.0424 (mmt) REVERT: P 32 GLN cc_start: 0.5848 (pp30) cc_final: 0.4283 (mm110) REVERT: P 181 TYR cc_start: 0.4377 (OUTLIER) cc_final: 0.2889 (m-10) REVERT: P 420 PHE cc_start: 0.1037 (OUTLIER) cc_final: 0.0670 (m-10) outliers start: 89 outliers final: 54 residues processed: 336 average time/residue: 0.5152 time to fit residues: 298.2103 Evaluate side-chains 307 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 246 time to evaluate : 4.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 98 THR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 562 SER Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 276 THR Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 417 VAL Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 584 ILE Chi-restraints excluded: chain P residue 22 ARG Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 181 TYR Chi-restraints excluded: chain P residue 204 VAL Chi-restraints excluded: chain P residue 420 PHE Chi-restraints excluded: chain P residue 462 PHE Chi-restraints excluded: chain P residue 472 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 560 optimal weight: 5.9990 chunk 381 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 500 optimal weight: 0.4980 chunk 277 optimal weight: 0.0370 chunk 574 optimal weight: 20.0000 chunk 465 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 343 optimal weight: 0.6980 chunk 603 optimal weight: 0.2980 chunk 169 optimal weight: 0.7980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN M 432 ASN N 200 ASN O 187 ASN O 395 ASN ** P 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 57840 Z= 0.120 Angle : 0.479 10.790 78253 Z= 0.245 Chirality : 0.040 0.171 8500 Planarity : 0.003 0.042 10034 Dihedral : 8.017 174.121 8267 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.83 % Allowed : 12.66 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.55 (0.10), residues: 6943 helix: 0.77 (0.10), residues: 2834 sheet: 0.16 (0.19), residues: 761 loop : -1.52 (0.10), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP M 602 HIS 0.008 0.001 HIS P 434 PHE 0.014 0.001 PHE P 572 TYR 0.022 0.001 TYR I 386 ARG 0.004 0.000 ARG K 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 285 time to evaluate : 5.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7630 (tt) REVERT: I 386 TYR cc_start: 0.4977 (OUTLIER) cc_final: 0.4427 (m-80) REVERT: K 105 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7418 (tm-30) REVERT: N 206 PHE cc_start: 0.0566 (OUTLIER) cc_final: -0.0025 (m-80) REVERT: N 413 MET cc_start: 0.0447 (mmt) cc_final: 0.0096 (mmt) REVERT: N 448 MET cc_start: 0.1590 (OUTLIER) cc_final: 0.0996 (mmm) REVERT: O 92 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7111 (mtp180) REVERT: O 169 LEU cc_start: 0.8451 (mt) cc_final: 0.8196 (mp) REVERT: O 410 ASP cc_start: 0.3598 (m-30) cc_final: 0.3139 (t0) REVERT: O 438 MET cc_start: -0.0038 (mmt) cc_final: -0.0341 (mmt) REVERT: P 27 LEU cc_start: 0.3714 (OUTLIER) cc_final: 0.3379 (mm) REVERT: P 93 GLN cc_start: 0.1205 (OUTLIER) cc_final: 0.0330 (pp30) REVERT: P 420 PHE cc_start: 0.0833 (OUTLIER) cc_final: 0.0550 (m-10) REVERT: P 463 ARG cc_start: 0.2586 (mmm160) cc_final: -0.0425 (mpt180) REVERT: P 555 GLU cc_start: 0.3590 (tm-30) cc_final: 0.3107 (pp20) outliers start: 50 outliers final: 27 residues processed: 326 average time/residue: 0.5598 time to fit residues: 312.5539 Evaluate side-chains 274 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 4.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain O residue 92 ARG Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 561 ILE Chi-restraints excluded: chain O residue 593 SER Chi-restraints excluded: chain P residue 22 ARG Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 420 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 226 optimal weight: 7.9990 chunk 605 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 394 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 673 optimal weight: 8.9990 chunk 559 optimal weight: 7.9990 chunk 311 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 222 optimal weight: 9.9990 chunk 353 optimal weight: 0.0980 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS D 154 ASN P 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 57840 Z= 0.335 Angle : 0.597 11.017 78253 Z= 0.307 Chirality : 0.044 0.162 8500 Planarity : 0.004 0.051 10034 Dihedral : 8.465 162.604 8267 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.43 % Allowed : 13.09 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.84 (0.10), residues: 6943 helix: 0.51 (0.10), residues: 2848 sheet: 0.01 (0.19), residues: 735 loop : -1.66 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP M 602 HIS 0.008 0.001 HIS L 227 PHE 0.021 0.002 PHE G 291 TYR 0.019 0.002 TYR I 386 ARG 0.010 0.000 ARG H 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 253 time to evaluate : 4.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.7815 (tp30) cc_final: 0.7587 (tp30) REVERT: B 174 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: E 4 TYR cc_start: 0.7910 (m-80) cc_final: 0.7457 (m-10) REVERT: E 84 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8175 (tt) REVERT: I 386 TYR cc_start: 0.5051 (OUTLIER) cc_final: 0.4540 (m-80) REVERT: K 105 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7672 (tm-30) REVERT: L 264 ARG cc_start: 0.7671 (mpp-170) cc_final: 0.7032 (mmt180) REVERT: M 515 THR cc_start: 0.1834 (OUTLIER) cc_final: 0.1423 (m) REVERT: N 31 LEU cc_start: 0.7631 (tp) cc_final: 0.7428 (tp) REVERT: N 206 PHE cc_start: 0.0727 (OUTLIER) cc_final: 0.0182 (m-80) REVERT: N 413 MET cc_start: 0.1238 (mmt) cc_final: 0.0796 (mmt) REVERT: N 448 MET cc_start: 0.1721 (OUTLIER) cc_final: 0.0911 (mmt) REVERT: O 169 LEU cc_start: 0.8565 (mt) cc_final: 0.8297 (mp) REVERT: O 438 MET cc_start: 0.0145 (mmt) cc_final: -0.0116 (mmt) REVERT: P 27 LEU cc_start: 0.4198 (OUTLIER) cc_final: 0.3918 (mm) REVERT: P 181 TYR cc_start: 0.4271 (OUTLIER) cc_final: 0.3064 (m-10) REVERT: P 420 PHE cc_start: 0.0714 (OUTLIER) cc_final: 0.0403 (m-10) REVERT: P 463 ARG cc_start: 0.2757 (mmm160) cc_final: -0.0430 (mpt180) outliers start: 86 outliers final: 66 residues processed: 325 average time/residue: 0.5287 time to fit residues: 295.0032 Evaluate side-chains 314 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 239 time to evaluate : 4.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 515 THR Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 562 SER Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 276 THR Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 417 VAL Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 395 ASN Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 584 ILE Chi-restraints excluded: chain O residue 593 SER Chi-restraints excluded: chain O residue 597 VAL Chi-restraints excluded: chain P residue 22 ARG Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 32 GLN Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 181 TYR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 420 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 649 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 383 optimal weight: 1.9990 chunk 491 optimal weight: 10.0000 chunk 381 optimal weight: 5.9990 chunk 566 optimal weight: 40.0000 chunk 376 optimal weight: 0.7980 chunk 670 optimal weight: 0.0670 chunk 419 optimal weight: 4.9990 chunk 408 optimal weight: 6.9990 chunk 309 optimal weight: 0.9990 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN P 93 GLN P 432 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 57840 Z= 0.131 Angle : 0.491 12.339 78253 Z= 0.251 Chirality : 0.040 0.178 8500 Planarity : 0.003 0.046 10034 Dihedral : 8.079 168.833 8267 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.98 % Allowed : 14.01 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.54 (0.10), residues: 6943 helix: 0.80 (0.10), residues: 2825 sheet: 0.20 (0.19), residues: 742 loop : -1.54 (0.10), residues: 3376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP M 602 HIS 0.006 0.001 HIS P 434 PHE 0.018 0.001 PHE G 291 TYR 0.017 0.001 TYR I 386 ARG 0.005 0.000 ARG K 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 4.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: B 102 GLU cc_start: 0.7663 (tp30) cc_final: 0.7453 (tp30) REVERT: B 174 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: E 84 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7821 (tt) REVERT: F 45 MET cc_start: 0.7464 (mpp) cc_final: 0.7188 (mpp) REVERT: I 386 TYR cc_start: 0.4995 (OUTLIER) cc_final: 0.4285 (m-80) REVERT: K 105 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7596 (tm-30) REVERT: N 206 PHE cc_start: 0.0710 (OUTLIER) cc_final: 0.0083 (m-80) REVERT: N 413 MET cc_start: 0.0968 (mmt) cc_final: 0.0749 (mmt) REVERT: N 448 MET cc_start: 0.1629 (OUTLIER) cc_final: 0.0807 (mmm) REVERT: O 169 LEU cc_start: 0.8510 (mt) cc_final: 0.8214 (mp) REVERT: O 410 ASP cc_start: 0.3780 (m-30) cc_final: 0.3274 (t0) REVERT: P 32 GLN cc_start: 0.6231 (pp30) cc_final: 0.4705 (mm110) REVERT: P 181 TYR cc_start: 0.4260 (OUTLIER) cc_final: 0.2920 (m-10) REVERT: P 420 PHE cc_start: 0.1059 (OUTLIER) cc_final: 0.0789 (m-10) REVERT: P 463 ARG cc_start: 0.2702 (mmm160) cc_final: -0.0297 (mpt180) outliers start: 59 outliers final: 41 residues processed: 304 average time/residue: 0.5367 time to fit residues: 281.2517 Evaluate side-chains 289 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 5.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 593 SER Chi-restraints excluded: chain O residue 597 VAL Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 181 TYR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 420 PHE Chi-restraints excluded: chain P residue 462 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 415 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 400 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 426 optimal weight: 9.9990 chunk 457 optimal weight: 0.1980 chunk 331 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 527 optimal weight: 0.0470 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 57840 Z= 0.139 Angle : 0.486 14.224 78253 Z= 0.247 Chirality : 0.040 0.194 8500 Planarity : 0.003 0.044 10034 Dihedral : 7.920 168.634 8267 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.80 % Favored : 95.19 % Rotamer: Outliers : 1.10 % Allowed : 13.97 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.45 (0.10), residues: 6943 helix: 0.87 (0.10), residues: 2835 sheet: 0.25 (0.19), residues: 766 loop : -1.49 (0.10), residues: 3342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M 602 HIS 0.005 0.001 HIS P 434 PHE 0.017 0.001 PHE G 291 TYR 0.017 0.001 TYR H 263 ARG 0.007 0.000 ARG P 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 250 time to evaluate : 5.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: B 102 GLU cc_start: 0.7680 (tp30) cc_final: 0.7455 (tp30) REVERT: B 174 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: B 259 LYS cc_start: 0.7740 (ttpp) cc_final: 0.7528 (ttpp) REVERT: E 84 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7811 (tt) REVERT: F 45 MET cc_start: 0.7426 (mpp) cc_final: 0.7224 (mpp) REVERT: I 386 TYR cc_start: 0.4960 (OUTLIER) cc_final: 0.4214 (m-80) REVERT: K 105 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7547 (tm-30) REVERT: M 515 THR cc_start: 0.1290 (OUTLIER) cc_final: 0.0914 (m) REVERT: N 206 PHE cc_start: 0.0748 (OUTLIER) cc_final: 0.0126 (m-80) REVERT: N 413 MET cc_start: 0.0967 (mmt) cc_final: 0.0692 (mmt) REVERT: N 448 MET cc_start: 0.1678 (OUTLIER) cc_final: 0.0855 (mmm) REVERT: O 169 LEU cc_start: 0.8502 (mt) cc_final: 0.8209 (mp) REVERT: O 410 ASP cc_start: 0.3716 (m-30) cc_final: 0.3190 (t0) REVERT: P 181 TYR cc_start: 0.4255 (OUTLIER) cc_final: 0.2938 (m-10) REVERT: P 420 PHE cc_start: 0.1019 (OUTLIER) cc_final: 0.0749 (m-10) REVERT: P 463 ARG cc_start: 0.2921 (mmm160) cc_final: -0.0104 (mpt180) outliers start: 66 outliers final: 46 residues processed: 306 average time/residue: 0.5454 time to fit residues: 289.8657 Evaluate side-chains 295 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 4.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 515 THR Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 593 SER Chi-restraints excluded: chain O residue 597 VAL Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 181 TYR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 420 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 610 optimal weight: 0.8980 chunk 642 optimal weight: 0.9990 chunk 586 optimal weight: 9.9990 chunk 625 optimal weight: 2.9990 chunk 376 optimal weight: 0.9980 chunk 272 optimal weight: 0.0060 chunk 490 optimal weight: 20.0000 chunk 191 optimal weight: 0.0470 chunk 564 optimal weight: 5.9990 chunk 591 optimal weight: 6.9990 chunk 622 optimal weight: 6.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 57840 Z= 0.115 Angle : 0.462 9.880 78253 Z= 0.235 Chirality : 0.039 0.170 8500 Planarity : 0.003 0.041 10034 Dihedral : 7.619 170.881 8267 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.00 % Favored : 95.98 % Rotamer: Outliers : 0.85 % Allowed : 14.32 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.25 (0.10), residues: 6943 helix: 1.06 (0.10), residues: 2818 sheet: 0.37 (0.19), residues: 766 loop : -1.40 (0.10), residues: 3359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 602 HIS 0.007 0.000 HIS P 28 PHE 0.018 0.001 PHE G 291 TYR 0.013 0.001 TYR F 284 ARG 0.007 0.000 ARG K 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 5.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: B 174 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: B 259 LYS cc_start: 0.7847 (ttpp) cc_final: 0.7644 (ttpp) REVERT: C 361 MET cc_start: 0.8000 (ptp) cc_final: 0.7645 (ptp) REVERT: E 84 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7951 (mp) REVERT: E 317 ILE cc_start: 0.8801 (tp) cc_final: 0.8597 (tp) REVERT: G 312 TYR cc_start: 0.6844 (t80) cc_final: 0.6641 (t80) REVERT: I 386 TYR cc_start: 0.4960 (OUTLIER) cc_final: 0.4218 (m-80) REVERT: K 105 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7526 (tm-30) REVERT: M 515 THR cc_start: 0.1191 (OUTLIER) cc_final: 0.0824 (m) REVERT: N 206 PHE cc_start: 0.0475 (OUTLIER) cc_final: -0.0080 (m-80) REVERT: N 413 MET cc_start: 0.0758 (mmt) cc_final: 0.0510 (mmt) REVERT: N 448 MET cc_start: 0.1787 (OUTLIER) cc_final: 0.0932 (mmm) REVERT: N 456 MET cc_start: 0.4183 (mtp) cc_final: 0.3881 (mtm) REVERT: N 528 MET cc_start: 0.4594 (tmm) cc_final: 0.3854 (ptt) REVERT: O 169 LEU cc_start: 0.8401 (mt) cc_final: 0.8152 (mp) REVERT: O 410 ASP cc_start: 0.3691 (m-30) cc_final: 0.3165 (t0) REVERT: P 95 ILE cc_start: 0.5874 (mp) cc_final: 0.5484 (mp) REVERT: P 420 PHE cc_start: 0.0878 (OUTLIER) cc_final: 0.0618 (m-10) REVERT: P 463 ARG cc_start: 0.2898 (mmm160) cc_final: 0.0105 (mpt180) outliers start: 51 outliers final: 40 residues processed: 309 average time/residue: 0.5321 time to fit residues: 284.9150 Evaluate side-chains 292 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 5.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 515 THR Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 227 LEU Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain O residue 395 ASN Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 593 SER Chi-restraints excluded: chain O residue 597 VAL Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 420 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 410 optimal weight: 0.8980 chunk 661 optimal weight: 5.9990 chunk 403 optimal weight: 9.9990 chunk 313 optimal weight: 6.9990 chunk 459 optimal weight: 7.9990 chunk 693 optimal weight: 7.9990 chunk 638 optimal weight: 5.9990 chunk 552 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 426 optimal weight: 1.9990 chunk 338 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 57840 Z= 0.234 Angle : 0.533 10.538 78253 Z= 0.272 Chirality : 0.042 0.181 8500 Planarity : 0.003 0.045 10034 Dihedral : 7.892 163.007 8267 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.37 % Favored : 94.61 % Rotamer: Outliers : 1.00 % Allowed : 14.37 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.42 (0.10), residues: 6943 helix: 0.90 (0.10), residues: 2821 sheet: 0.33 (0.19), residues: 773 loop : -1.49 (0.10), residues: 3349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 602 HIS 0.006 0.001 HIS B 313 PHE 0.018 0.001 PHE G 291 TYR 0.018 0.001 TYR H 263 ARG 0.006 0.000 ARG B 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 241 time to evaluate : 4.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: B 174 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: B 259 LYS cc_start: 0.7768 (ttpp) cc_final: 0.7543 (ttpp) REVERT: E 84 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7987 (tt) REVERT: G 312 TYR cc_start: 0.6903 (t80) cc_final: 0.6676 (t80) REVERT: I 386 TYR cc_start: 0.4900 (OUTLIER) cc_final: 0.4200 (m-80) REVERT: K 105 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7616 (tm-30) REVERT: M 515 THR cc_start: 0.1346 (OUTLIER) cc_final: 0.0956 (m) REVERT: N 206 PHE cc_start: 0.0826 (OUTLIER) cc_final: 0.0178 (m-80) REVERT: N 413 MET cc_start: 0.1631 (mmt) cc_final: 0.1229 (mmt) REVERT: N 448 MET cc_start: 0.1879 (OUTLIER) cc_final: 0.0986 (mmm) REVERT: N 456 MET cc_start: 0.3957 (mtp) cc_final: 0.3600 (mtm) REVERT: N 528 MET cc_start: 0.5099 (tmm) cc_final: 0.4105 (ptt) REVERT: O 448 MET cc_start: 0.4779 (tpp) cc_final: 0.4515 (tpt) REVERT: P 95 ILE cc_start: 0.5654 (mp) cc_final: 0.5448 (mp) REVERT: P 420 PHE cc_start: 0.0952 (OUTLIER) cc_final: 0.0741 (m-10) REVERT: P 463 ARG cc_start: 0.2908 (mmm160) cc_final: 0.0237 (mpt180) outliers start: 60 outliers final: 48 residues processed: 293 average time/residue: 0.5188 time to fit residues: 264.0083 Evaluate side-chains 293 residues out of total 5997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 237 time to evaluate : 4.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 480 HIS Chi-restraints excluded: chain M residue 515 THR Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 227 LEU Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 395 ASN Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 593 SER Chi-restraints excluded: chain O residue 597 VAL Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 420 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 438 optimal weight: 0.8980 chunk 588 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 chunk 509 optimal weight: 50.0000 chunk 81 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 553 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 567 optimal weight: 20.0000 chunk 70 optimal weight: 0.0980 chunk 101 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.183738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.146000 restraints weight = 87123.102| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.75 r_work: 0.3388 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 57840 Z= 0.121 Angle : 0.472 9.942 78253 Z= 0.239 Chirality : 0.039 0.170 8500 Planarity : 0.003 0.040 10034 Dihedral : 7.621 165.984 8267 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.95 % Allowed : 14.49 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.23 (0.10), residues: 6943 helix: 1.06 (0.10), residues: 2823 sheet: 0.47 (0.19), residues: 760 loop : -1.40 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 602 HIS 0.005 0.000 HIS P 434 PHE 0.018 0.001 PHE F 294 TYR 0.013 0.001 TYR F 284 ARG 0.007 0.000 ARG K 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8136.75 seconds wall clock time: 146 minutes 2.08 seconds (8762.08 seconds total)