Starting phenix.real_space_refine on Mon Dec 30 21:49:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uae_42061/12_2024/8uae_42061_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uae_42061/12_2024/8uae_42061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uae_42061/12_2024/8uae_42061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uae_42061/12_2024/8uae_42061.map" model { file = "/net/cci-nas-00/data/ceres_data/8uae_42061/12_2024/8uae_42061_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uae_42061/12_2024/8uae_42061_neut.cif" } resolution = 3.25 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= 0.004 sd= 0.046 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 39 5.49 5 Mg 5 5.21 5 S 150 5.16 5 C 41284 2.51 5 N 10985 2.21 5 O 12161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 64624 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3054 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 11, 'TRANS': 369} Chain breaks: 1 Chain: "C" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "D" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3071 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 11, 'TRANS': 372} Chain breaks: 1 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: 3066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3066 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 11, 'TRANS': 371} Chain breaks: 1 Chain: "G" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3119 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 379} Chain breaks: 2 Chain: "H" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3071 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 11, 'TRANS': 372} Chain breaks: 1 Chain: "I" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3145 Classifications: {'peptide': 394} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Chain breaks: 2 Chain: "J" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3067 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 11, 'TRANS': 371} Chain breaks: 1 Chain: "K" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3182 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 2 Chain: "L" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3067 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 11, 'TRANS': 371} Chain breaks: 1 Chain: "M" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4536 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 550} Chain breaks: 2 Chain: "N" Number of atoms: 4548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4548 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 551} Chain breaks: 2 Chain: "O" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4637 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain breaks: 1 Chain: "P" Number of atoms: 4346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4346 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 526} Chain breaks: 4 Chain: "Q" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4389 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 530} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4170 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 19, 'TRANS': 504} Chain breaks: 3 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 28.43, per 1000 atoms: 0.44 Number of scatterers: 64624 At special positions: 0 Unit cell: (188.7, 195.36, 223.11, 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 150 16.00 P 39 15.00 Mg 5 11.99 O 12161 8.00 N 10985 7.00 C 41284 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.58 Conformation dependent library (CDL) restraints added in 5.9 seconds 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14852 Finding SS restraints... Secondary structure from input PDB file: 370 helices and 67 sheets defined 45.6% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.522A pdb=" N ARG A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.759A pdb=" N SER A 37 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 38 " --> pdb=" O GLY A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 38' Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.958A pdb=" N GLY A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 81 through 99 removed outlier: 3.558A pdb=" N ASP A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 122 removed outlier: 3.557A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 removed outlier: 4.449A pdb=" N ARG A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 132 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 removed outlier: 4.015A pdb=" N LYS A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ASP A 139 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 6.279A 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: 3.817A pdb=" N LYS A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.955A 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: 4.049A pdb=" N TYR A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.894A pdb=" N ASN A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.696A pdb=" N ALA A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.868A pdb=" N GLU A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 406 removed outlier: 4.029A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.858A pdb=" N SER B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.707A pdb=" N VAL B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.215A pdb=" N GLY B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 removed outlier: 3.811A pdb=" N ASP B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 101 through 121 removed outlier: 3.796A pdb=" N GLU B 105 " --> pdb=" O CYS B 101 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 127 through 132 removed outlier: 4.033A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.523A pdb=" N LYS B 137 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP B 139 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 140 " --> pdb=" O LYS B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 134 through 140' Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.555A pdb=" N LYS B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.517A pdb=" N LEU B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.552A pdb=" N LYS B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.574A pdb=" N ILE B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.612A pdb=" N ASN B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 317 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 4.007A pdb=" N LEU B 323 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 324' Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 349 through 360 removed outlier: 3.586A pdb=" N LYS B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.772A pdb=" N ALA B 375 " --> pdb=" O GLY B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.663A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 removed outlier: 3.644A pdb=" N CYS C 23 " --> pdb=" O VAL C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 37 removed outlier: 3.827A 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 Processing helix chain 'C' and resid 56 through 65 removed outlier: 4.110A pdb=" N LEU C 60 " --> pdb=" O TYR C 56 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 Processing helix chain 'C' and resid 81 through 100 removed outlier: 3.753A pdb=" N LEU C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 122 removed outlier: 3.719A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 removed outlier: 4.245A pdb=" N ARG C 131 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.967A pdb=" N LYS C 137 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS C 138 " --> pdb=" O GLN C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 138' Processing helix chain 'C' and resid 141 through 154 removed outlier: 3.991A pdb=" N LYS C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 181 removed outlier: 3.579A pdb=" N TRP C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.832A 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 253 through 259 removed outlier: 3.612A pdb=" N ILE C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.979A pdb=" N TYR C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.508A pdb=" N ASN C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 336 through 345 Processing helix chain 'C' and resid 349 through 360 Processing helix chain 'C' and resid 376 through 384 removed outlier: 3.573A pdb=" N VAL C 381 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 384 " --> pdb=" O PHE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 407 removed outlier: 3.708A pdb=" N ALA C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.713A 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 56 through 66 removed outlier: 3.895A pdb=" N LEU D 60 " --> pdb=" O TYR D 56 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY D 61 " --> pdb=" O PRO D 57 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 78 Processing helix chain 'D' and resid 81 through 99 removed outlier: 3.913A pdb=" N THR D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 4.040A pdb=" N LYS D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 132 removed outlier: 4.024A pdb=" N GLN D 129 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG D 131 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 138 removed outlier: 3.805A pdb=" N LYS D 137 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS D 138 " --> pdb=" O GLN D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 138' Processing helix chain 'D' and resid 141 through 154 removed outlier: 3.677A pdb=" N ASN D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.738A pdb=" N ASP D 179 " --> pdb=" O TRP D 175 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 removed outlier: 4.157A pdb=" N PHE D 201 " --> pdb=" O PRO D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.704A pdb=" N GLU D 286 " --> pdb=" O PHE D 282 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 321 removed outlier: 3.902A pdb=" N ILE D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 318 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 5.406A 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: 3.541A pdb=" N LYS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 361 removed outlier: 3.717A 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: 3.678A pdb=" N LEU D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 23 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.823A pdb=" N TRP E 49 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 65 removed outlier: 4.113A pdb=" N LEU E 60 " --> pdb=" O TYR E 56 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY E 61 " --> pdb=" O PRO E 57 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 78 Processing helix chain 'E' and resid 82 through 100 removed outlier: 3.532A pdb=" N ILE E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 122 removed outlier: 3.648A pdb=" N GLU E 105 " --> pdb=" O CYS E 101 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 140 removed outlier: 3.565A pdb=" N LYS E 137 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP E 139 " --> pdb=" O GLY E 136 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA E 140 " --> pdb=" O LYS E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 140' Processing helix chain 'E' and resid 141 through 153 removed outlier: 4.003A pdb=" N LYS E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 removed outlier: 3.701A pdb=" N ASP E 179 " --> pdb=" O TRP E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 201 removed outlier: 4.166A pdb=" N PHE E 201 " --> pdb=" O PRO E 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 201' Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 280 through 295 removed outlier: 4.159A pdb=" N TYR E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 322 removed outlier: 3.574A pdb=" N ASN E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 346 Processing helix chain 'E' and resid 349 through 360 Processing helix chain 'E' and resid 371 through 375 removed outlier: 3.516A pdb=" N LYS E 374 " --> pdb=" O GLY E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 384 removed outlier: 4.661A pdb=" N GLU E 382 " --> pdb=" O ASN E 378 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU E 384 " --> pdb=" O PHE E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 406 removed outlier: 4.040A pdb=" N LEU E 399 " --> pdb=" O ILE E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 23 removed outlier: 3.531A pdb=" N CYS F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 56 removed outlier: 3.631A pdb=" N VAL F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP F 49 " --> pdb=" O MET F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 66 removed outlier: 3.801A pdb=" N ALA F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 77 removed outlier: 3.513A pdb=" N ASN F 77 " --> pdb=" O ILE F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 99 removed outlier: 3.942A pdb=" N LEU F 85 " --> pdb=" O ASN F 81 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG F 99 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 122 removed outlier: 4.251A pdb=" N GLU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 removed outlier: 4.201A pdb=" N ARG F 131 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 removed outlier: 3.701A pdb=" N LYS F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 154 removed outlier: 3.588A pdb=" N GLU F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 removed outlier: 3.532A pdb=" N ASP F 179 " --> pdb=" O TRP F 175 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.969A 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 removed outlier: 3.588A pdb=" N ALA F 248 " --> pdb=" O SER F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 258 Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.668A pdb=" N GLU F 286 " --> pdb=" O PHE F 282 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.541A pdb=" N ASN F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY F 320 " --> pdb=" O ARG F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 336 through 345 removed outlier: 3.622A pdb=" N SER F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 360 removed outlier: 4.080A pdb=" N ALA F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 375 removed outlier: 3.726A pdb=" N LYS F 374 " --> pdb=" O GLY F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.962A pdb=" N LEU F 384 " --> pdb=" O PHE F 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 23 Processing helix chain 'G' and resid 35 through 41 removed outlier: 3.682A pdb=" N VAL G 38 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 56 removed outlier: 3.559A pdb=" N GLN G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 66 removed outlier: 3.791A pdb=" N LYS G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 78 Processing helix chain 'G' and resid 81 through 100 removed outlier: 3.871A pdb=" N LEU G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP G 87 " --> pdb=" O GLU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 122 removed outlier: 3.635A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER G 114 " --> pdb=" O LYS G 110 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 132 removed outlier: 3.760A pdb=" N GLN G 129 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE G 130 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU G 132 " --> pdb=" O GLN G 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 126 through 132' Processing helix chain 'G' and resid 134 through 138 removed outlier: 3.810A pdb=" N LYS G 137 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS G 138 " --> pdb=" O GLN G 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 134 through 138' Processing helix chain 'G' and resid 142 through 155 removed outlier: 3.754A pdb=" N GLU G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN G 154 " --> pdb=" O LYS G 150 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 181 removed outlier: 4.142A pdb=" N TRP G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 201 removed outlier: 4.020A 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 Processing helix chain 'G' and resid 277 through 296 removed outlier: 4.530A pdb=" N VAL G 283 " --> pdb=" O THR G 279 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR G 284 " --> pdb=" O ILE G 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU G 286 " --> pdb=" O PHE G 282 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET G 287 " --> pdb=" O VAL G 283 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 321 removed outlier: 3.574A pdb=" N ASN G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE G 317 " --> pdb=" O HIS G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 324 No H-bonds generated for 'chain 'G' and resid 322 through 324' Processing helix chain 'G' and resid 336 through 345 Processing helix chain 'G' and resid 349 through 358 removed outlier: 3.693A pdb=" N LEU G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 384 removed outlier: 3.715A pdb=" N LEU G 384 " --> pdb=" O PHE G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 406 Processing helix chain 'H' and resid 11 through 23 Processing helix chain 'H' and resid 44 through 54 removed outlier: 3.758A pdb=" N TRP H 49 " --> pdb=" O MET H 45 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 66 removed outlier: 3.529A pdb=" N LEU H 60 " --> pdb=" O TYR H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 78 Processing helix chain 'H' and resid 81 through 99 removed outlier: 3.503A pdb=" N LEU H 85 " --> pdb=" O ASN H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 123 removed outlier: 4.144A pdb=" N GLU H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU H 115 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR H 120 " --> pdb=" O TYR H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 154 removed outlier: 3.599A pdb=" N ASN H 154 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 181 removed outlier: 3.676A pdb=" N ASP H 179 " --> pdb=" O TRP H 175 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY H 181 " --> pdb=" O ALA H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.949A pdb=" N PHE H 201 " --> pdb=" O PRO H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 244 through 252 Processing helix chain 'H' and resid 254 through 259 Processing helix chain 'H' and resid 281 through 295 removed outlier: 4.030A pdb=" N GLY H 285 " --> pdb=" O GLY H 281 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE H 288 " --> pdb=" O TYR H 284 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG H 289 " --> pdb=" O GLY H 285 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE H 295 " --> pdb=" O PHE H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 321 Processing helix chain 'H' and resid 335 through 345 removed outlier: 3.801A pdb=" N ALA H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS H 345 " --> pdb=" O THR H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 360 removed outlier: 3.738A pdb=" N ALA H 354 " --> pdb=" O GLU H 350 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE H 355 " --> pdb=" O ALA H 351 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 375 removed outlier: 3.880A pdb=" N LYS H 374 " --> pdb=" O GLY H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 384 removed outlier: 4.088A pdb=" N GLU H 382 " --> pdb=" O ASN H 378 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS H 383 " --> pdb=" O SER H 379 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU H 384 " --> pdb=" O PHE H 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 23 removed outlier: 3.610A pdb=" N SER I 17 " --> pdb=" O ASP I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 41 removed outlier: 3.525A pdb=" N GLY I 41 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 51 Processing helix chain 'I' and resid 51 through 56 removed outlier: 3.820A pdb=" N ASN I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 66 removed outlier: 3.763A pdb=" N LEU I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 78 Processing helix chain 'I' and resid 81 through 99 removed outlier: 3.794A pdb=" N LEU I 85 " --> pdb=" O ASN I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 123 removed outlier: 4.213A pdb=" N LYS I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA I 123 " --> pdb=" O VAL I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 132 removed outlier: 3.879A pdb=" N GLN I 129 " --> pdb=" O THR I 126 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG I 131 " --> pdb=" O GLU I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 138 removed outlier: 3.636A pdb=" N LYS I 137 " --> pdb=" O ASN I 134 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS I 138 " --> pdb=" O GLN I 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 134 through 138' Processing helix chain 'I' and resid 141 through 154 removed outlier: 3.836A pdb=" N LYS I 145 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU I 147 " --> pdb=" O TYR I 143 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE I 148 " --> pdb=" O HIS I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 179 removed outlier: 3.652A pdb=" N GLU I 178 " --> pdb=" O GLU I 174 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP I 179 " --> pdb=" O TRP I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 201 removed outlier: 3.783A pdb=" N PHE I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 198 through 201' Processing helix chain 'I' and resid 244 through 252 Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 280 through 295 removed outlier: 4.099A pdb=" N TYR I 284 " --> pdb=" O ILE I 280 " (cutoff:3.500A) removed outlier: 3.852A 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 335 through 345 removed outlier: 3.570A pdb=" N LYS I 345 " --> pdb=" O THR I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 358 Processing helix chain 'I' and resid 376 through 383 removed outlier: 3.706A pdb=" N GLU I 382 " --> pdb=" O ASN I 378 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS I 383 " --> pdb=" O SER I 379 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 406 removed outlier: 3.832A pdb=" N VAL I 400 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU I 401 " --> pdb=" O ASP I 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 23 Processing helix chain 'J' and resid 44 through 56 removed outlier: 3.508A pdb=" N TRP J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 66 removed outlier: 3.579A pdb=" N LEU J 60 " --> pdb=" O TYR J 56 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY J 61 " --> pdb=" O PRO J 57 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 78 Processing helix chain 'J' and resid 81 through 100 removed outlier: 3.933A pdb=" N LEU J 85 " --> pdb=" O ASN J 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE J 86 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 124 removed outlier: 3.519A pdb=" N ILE J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR J 120 " --> pdb=" O TYR J 116 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA J 123 " --> pdb=" O VAL J 119 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU J 124 " --> pdb=" O THR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 removed outlier: 4.392A pdb=" N ARG J 131 " --> pdb=" O GLU J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 140 No H-bonds generated for 'chain 'J' and resid 138 through 140' Processing helix chain 'J' and resid 141 through 154 removed outlier: 3.958A pdb=" N LYS J 145 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 181 removed outlier: 3.585A pdb=" N ASP J 179 " --> pdb=" O TRP J 175 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 201 removed outlier: 3.990A 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: 3.726A pdb=" N TYR J 249 " --> pdb=" O ALA J 245 " (cutoff:3.500A) removed outlier: 4.681A 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: 4.224A pdb=" N GLY J 285 " --> pdb=" O GLY J 281 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU J 286 " --> pdb=" O PHE J 282 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET J 287 " --> pdb=" O VAL J 283 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE J 288 " --> pdb=" O TYR J 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE J 295 " --> pdb=" O PHE J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 321 Processing helix chain 'J' and resid 336 through 345 removed outlier: 3.579A pdb=" N THR J 341 " --> pdb=" O LYS J 337 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS J 342 " --> pdb=" O GLU J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 360 removed outlier: 3.690A pdb=" N ALA J 354 " --> pdb=" O GLU J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 371 through 375 removed outlier: 3.674A pdb=" N LYS J 374 " --> pdb=" O GLY J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 376 through 384 removed outlier: 3.727A pdb=" N LEU J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 22 Processing helix chain 'K' and resid 37 through 41 removed outlier: 3.529A pdb=" N GLY K 41 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 56 Processing helix chain 'K' and resid 59 through 66 removed outlier: 3.563A pdb=" N LEU K 63 " --> pdb=" O LEU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 78 removed outlier: 3.540A pdb=" N ASP K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 100 removed outlier: 3.687A pdb=" N LEU K 85 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER K 94 " --> pdb=" O THR K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 121 removed outlier: 3.527A pdb=" N GLU K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU K 107 " --> pdb=" O ASP K 103 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 124 No H-bonds generated for 'chain 'K' and resid 122 through 124' Processing helix chain 'K' and resid 127 through 132 removed outlier: 4.053A pdb=" N ARG K 131 " --> pdb=" O GLU K 128 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU K 132 " --> pdb=" O GLN K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 140 No H-bonds generated for 'chain 'K' and resid 138 through 140' Processing helix chain 'K' and resid 141 through 153 removed outlier: 4.138A pdb=" N LYS K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU K 146 " --> pdb=" O LYS K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 181 removed outlier: 3.579A pdb=" N TRP K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP K 179 " --> pdb=" O TRP K 175 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 201 removed outlier: 3.989A pdb=" N PHE K 201 " --> pdb=" O PRO K 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 198 through 201' Processing helix chain 'K' and resid 244 through 252 Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 279 through 295 removed outlier: 4.110A pdb=" N VAL K 283 " --> pdb=" O THR K 279 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR K 284 " --> pdb=" O ILE K 280 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG K 290 " --> pdb=" O GLU K 286 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE K 291 " --> pdb=" O MET K 287 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY K 292 " --> pdb=" O PHE K 288 " (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 344 Processing helix chain 'K' and resid 349 through 361 Processing helix chain 'K' and resid 376 through 384 removed outlier: 3.906A pdb=" N GLU K 382 " --> pdb=" O ASN K 378 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS K 383 " --> pdb=" O SER K 379 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU K 384 " --> pdb=" O PHE K 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 406 removed outlier: 3.800A pdb=" N LEU K 399 " --> pdb=" O ILE K 395 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU K 406 " --> pdb=" O ALA K 402 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 23 removed outlier: 3.559A pdb=" N SER L 17 " --> pdb=" O ASP L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 38 removed outlier: 3.948A pdb=" N SER L 37 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL L 38 " --> pdb=" O GLY L 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 34 through 38' Processing helix chain 'L' and resid 44 through 56 removed outlier: 3.609A pdb=" N VAL L 48 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 66 Processing helix chain 'L' and resid 71 through 77 removed outlier: 3.536A pdb=" N SER L 75 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN L 77 " --> pdb=" O ILE L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 99 removed outlier: 3.618A pdb=" N LEU L 85 " --> pdb=" O ASN L 81 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE L 86 " --> pdb=" O VAL L 82 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP L 87 " --> pdb=" O GLU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 122 removed outlier: 3.588A pdb=" N GLU L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 removed outlier: 4.233A pdb=" N ARG L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 140 removed outlier: 3.836A pdb=" N LYS L 137 " --> pdb=" O ASN L 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS L 138 " --> pdb=" O GLN L 135 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP L 139 " --> pdb=" O GLY L 136 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA L 140 " --> pdb=" O LYS L 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 134 through 140' Processing helix chain 'L' and resid 141 through 153 removed outlier: 3.969A pdb=" N LYS L 145 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU L 146 " --> pdb=" O LYS L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 181 Processing helix chain 'L' and resid 198 through 201 removed outlier: 3.667A pdb=" N PHE L 201 " --> pdb=" O PRO L 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 198 through 201' Processing helix chain 'L' and resid 244 through 252 Processing helix chain 'L' and resid 252 through 258 Processing helix chain 'L' and resid 282 through 296 removed outlier: 3.627A pdb=" N GLU L 286 " --> pdb=" O PHE L 282 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET L 287 " --> pdb=" O VAL L 283 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE L 288 " --> pdb=" O TYR L 284 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG L 289 " --> pdb=" O GLY L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 321 Processing helix chain 'L' and resid 322 through 324 No H-bonds generated for 'chain 'L' and resid 322 through 324' Processing helix chain 'L' and resid 336 through 345 removed outlier: 3.813A 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: 3.588A pdb=" N LYS L 374 " --> pdb=" O GLY L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 384 removed outlier: 3.948A pdb=" N LEU L 384 " --> pdb=" O PHE L 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 137 removed outlier: 3.698A pdb=" N ASN M 134 " --> pdb=" O SER M 130 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE M 135 " --> pdb=" O ASP M 131 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE M 136 " --> pdb=" O PHE M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 145 Proline residue: M 145 - end of helix Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 182 through 198 removed outlier: 3.746A pdb=" N PHE M 186 " --> pdb=" O GLY M 182 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU M 196 " --> pdb=" O ARG M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 217 removed outlier: 3.675A pdb=" N PHE M 216 " --> pdb=" O ALA M 213 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR M 217 " --> pdb=" O GLN M 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 213 through 217' Processing helix chain 'M' and resid 261 through 271 removed outlier: 3.668A pdb=" N ILE M 267 " --> pdb=" O PHE M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 286 Processing helix chain 'M' and resid 287 through 291 Processing helix chain 'M' and resid 321 through 331 removed outlier: 3.617A pdb=" N TRP M 325 " --> pdb=" O LYS M 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 356 removed outlier: 4.087A pdb=" N THR M 348 " --> pdb=" O LYS M 344 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL M 356 " --> pdb=" O GLU M 352 " (cutoff:3.500A) Processing helix chain 'M' and resid 371 through 373 No H-bonds generated for 'chain 'M' and resid 371 through 373' Processing helix chain 'M' and resid 374 through 386 removed outlier: 3.551A pdb=" N ALA M 385 " --> pdb=" O ILE M 381 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU M 386 " --> pdb=" O GLN M 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 392 removed outlier: 3.657A pdb=" N SER M 392 " --> pdb=" O ARG M 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 389 through 392' Processing helix chain 'M' and resid 407 through 422 removed outlier: 3.582A pdb=" N LYS M 411 " --> pdb=" O THR M 407 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA M 412 " --> pdb=" O HIS M 408 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N MET M 413 " --> pdb=" O TRP M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 442 through 444 No H-bonds generated for 'chain 'M' and resid 442 through 444' Processing helix chain 'M' and resid 445 through 450 Processing helix chain 'M' and resid 452 through 465 Processing helix chain 'M' and resid 479 through 482 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 539 through 550 removed outlier: 3.524A pdb=" N LEU M 543 " --> pdb=" O ASN M 539 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN M 544 " --> pdb=" O GLU M 540 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA M 545 " --> pdb=" O ARG M 541 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU M 546 " --> pdb=" O ASP M 542 " (cutoff:3.500A) Processing helix chain 'M' and resid 557 through 564 removed outlier: 3.994A pdb=" N SER M 562 " --> pdb=" O LYS M 559 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY M 563 " --> pdb=" O GLN M 560 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU M 564 " --> pdb=" O ILE M 561 " (cutoff:3.500A) Processing helix chain 'M' and resid 597 through 603 removed outlier: 3.973A pdb=" N GLU M 601 " --> pdb=" O VAL M 597 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP M 602 " --> pdb=" O PHE M 598 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 33 removed outlier: 3.983A pdb=" N GLY N 33 " --> pdb=" O GLY N 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 30 through 33' Processing helix chain 'N' and resid 129 through 137 removed outlier: 3.589A pdb=" N LEU N 133 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN N 134 " --> pdb=" O SER N 130 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE N 135 " --> pdb=" O ASP N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 145 No H-bonds generated for 'chain 'N' and resid 143 through 145' Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 182 through 198 removed outlier: 4.000A pdb=" N LYS N 197 " --> pdb=" O LYS N 193 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR N 198 " --> pdb=" O VAL N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 217 removed outlier: 3.559A pdb=" N PHE N 216 " --> pdb=" O ALA N 213 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR N 217 " --> pdb=" O GLN N 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 213 through 217' Processing helix chain 'N' and resid 259 through 261 No H-bonds generated for 'chain 'N' and resid 259 through 261' Processing helix chain 'N' and resid 262 through 270 removed outlier: 3.716A pdb=" N ILE N 267 " --> pdb=" O PHE N 263 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS N 268 " --> pdb=" O ALA N 264 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU N 269 " --> pdb=" O GLY N 265 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU N 270 " --> pdb=" O LEU N 266 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 288 removed outlier: 3.637A pdb=" N ALA N 280 " --> pdb=" O THR N 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 291 No H-bonds generated for 'chain 'N' and resid 289 through 291' Processing helix chain 'N' and resid 322 through 331 removed outlier: 3.717A pdb=" N ARG N 331 " --> pdb=" O ASP N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 344 through 355 removed outlier: 4.350A pdb=" N THR N 348 " --> pdb=" O LYS N 344 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU N 349 " --> pdb=" O SER N 345 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 372 removed outlier: 4.051A pdb=" N SER N 372 " --> pdb=" O ALA N 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 385 removed outlier: 3.846A pdb=" N VAL N 378 " --> pdb=" O VAL N 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 387 through 392 removed outlier: 3.678A pdb=" N SER N 392 " --> pdb=" O ILE N 388 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 422 removed outlier: 4.223A pdb=" N LYS N 411 " --> pdb=" O THR N 407 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA N 412 " --> pdb=" O HIS N 408 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU N 416 " --> pdb=" O ALA N 412 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL N 417 " --> pdb=" O MET N 413 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 465 removed outlier: 3.509A pdb=" N LEU N 449 " --> pdb=" O HIS N 445 " (cutoff:3.500A) Processing helix chain 'N' and resid 498 through 503 Processing helix chain 'N' and resid 504 through 507 Processing helix chain 'N' and resid 517 through 521 removed outlier: 3.552A pdb=" N GLU N 520 " --> pdb=" O ARG N 517 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU N 521 " --> pdb=" O PRO N 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 517 through 521' Processing helix chain 'N' and resid 522 through 527 Processing helix chain 'N' and resid 539 through 550 removed outlier: 3.666A pdb=" N ALA N 545 " --> pdb=" O ARG N 541 " (cutoff:3.500A) Processing helix chain 'N' and resid 557 through 564 removed outlier: 3.668A pdb=" N GLN N 560 " --> pdb=" O ILE N 557 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE N 561 " --> pdb=" O LEU N 558 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER N 562 " --> pdb=" O LYS N 559 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY N 563 " --> pdb=" O GLN N 560 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 137 removed outlier: 3.565A pdb=" N LEU O 133 " --> pdb=" O THR O 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 145 No H-bonds generated for 'chain 'O' and resid 143 through 145' Processing helix chain 'O' and resid 165 through 171 removed outlier: 4.480A pdb=" N ARG O 171 " --> pdb=" O LYS O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 198 Processing helix chain 'O' and resid 213 through 217 Processing helix chain 'O' and resid 262 through 271 Processing helix chain 'O' and resid 276 through 287 removed outlier: 3.944A pdb=" N ALA O 280 " --> pdb=" O THR O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 318 through 320 No H-bonds generated for 'chain 'O' and resid 318 through 320' Processing helix chain 'O' and resid 321 through 331 removed outlier: 3.662A pdb=" N TRP O 325 " --> pdb=" O LYS O 321 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 344 No H-bonds generated for 'chain 'O' and resid 342 through 344' Processing helix chain 'O' and resid 345 through 354 removed outlier: 3.918A pdb=" N LEU O 349 " --> pdb=" O SER O 345 " (cutoff:3.500A) Processing helix chain 'O' and resid 367 through 386 removed outlier: 4.394A pdb=" N PHE O 371 " --> pdb=" O ASP O 367 " (cutoff:3.500A) Proline residue: O 376 - end of helix Processing helix chain 'O' and resid 387 through 392 removed outlier: 3.728A pdb=" N LYS O 391 " --> pdb=" O ASP O 387 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER O 392 " --> pdb=" O ILE O 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 387 through 392' Processing helix chain 'O' and resid 407 through 422 removed outlier: 3.567A pdb=" N LYS O 411 " --> pdb=" O THR O 407 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA O 412 " --> pdb=" O HIS O 408 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP O 418 " --> pdb=" O SER O 414 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR O 419 " --> pdb=" O ASP O 415 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE O 420 " --> pdb=" O GLU O 416 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 465 removed outlier: 3.559A pdb=" N LEU O 449 " --> pdb=" O HIS O 445 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY O 465 " --> pdb=" O LEU O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 479 through 482 Processing helix chain 'O' and resid 495 through 507 removed outlier: 3.840A pdb=" N ARG O 499 " --> pdb=" O LYS O 495 " (cutoff:3.500A) Processing helix chain 'O' and resid 517 through 521 Processing helix chain 'O' and resid 522 through 527 removed outlier: 3.874A pdb=" N LEU O 526 " --> pdb=" O SER O 522 " (cutoff:3.500A) Processing helix chain 'O' and resid 539 through 550 removed outlier: 3.939A pdb=" N LEU O 543 " --> pdb=" O ASN O 539 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN O 544 " --> pdb=" O GLU O 540 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA O 545 " --> pdb=" O ARG O 541 " (cutoff:3.500A) Processing helix chain 'O' and resid 557 through 564 removed outlier: 3.673A pdb=" N GLN O 560 " --> pdb=" O ILE O 557 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE O 561 " --> pdb=" O LEU O 558 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N SER O 562 " --> pdb=" O LYS O 559 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU O 564 " --> pdb=" O ILE O 561 " (cutoff:3.500A) Processing helix chain 'O' and resid 597 through 604 removed outlier: 3.754A pdb=" N GLU O 601 " --> pdb=" O VAL O 597 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 33 removed outlier: 3.522A pdb=" N GLY P 33 " --> pdb=" O GLY P 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 30 through 33' Processing helix chain 'P' and resid 129 through 137 removed outlier: 3.554A pdb=" N LEU P 133 " --> pdb=" O THR P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 145 removed outlier: 3.522A pdb=" N GLU P 143 " --> pdb=" O ASP P 140 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU P 144 " --> pdb=" O LYS P 141 " (cutoff:3.500A) Proline residue: P 145 - end of helix No H-bonds generated for 'chain 'P' and resid 140 through 145' Processing helix chain 'P' and resid 165 through 170 Processing helix chain 'P' and resid 182 through 198 Processing helix chain 'P' and resid 213 through 217 removed outlier: 3.732A pdb=" N PHE P 216 " --> pdb=" O ALA P 213 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR P 217 " --> pdb=" O GLN P 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 213 through 217' Processing helix chain 'P' and resid 262 through 270 removed outlier: 3.618A pdb=" N ILE P 267 " --> pdb=" O PHE P 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 276 through 287 removed outlier: 4.195A pdb=" N ALA P 280 " --> pdb=" O THR P 276 " (cutoff:3.500A) Processing helix chain 'P' and resid 318 through 322 removed outlier: 3.719A pdb=" N LYS P 321 " --> pdb=" O ASN P 318 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU P 322 " --> pdb=" O GLN P 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 318 through 322' Processing helix chain 'P' and resid 344 through 353 removed outlier: 3.833A pdb=" N THR P 348 " --> pdb=" O LYS P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 376 through 386 removed outlier: 3.794A pdb=" N ILE P 380 " --> pdb=" O PRO P 376 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE P 381 " --> pdb=" O LEU P 377 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLN P 382 " --> pdb=" O VAL P 378 " (cutoff:3.500A) Processing helix chain 'P' and resid 389 through 392 Processing helix chain 'P' and resid 407 through 418 removed outlier: 3.589A pdb=" N ASP P 418 " --> pdb=" O SER P 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 465 removed outlier: 3.730A pdb=" N LEU P 449 " --> pdb=" O HIS P 445 " (cutoff:3.500A) Processing helix chain 'P' and resid 479 through 482 Processing helix chain 'P' and resid 498 through 503 Processing helix chain 'P' and resid 504 through 507 Processing helix chain 'P' and resid 517 through 521 removed outlier: 3.679A pdb=" N LEU P 521 " --> pdb=" O PRO P 518 " (cutoff:3.500A) Processing helix chain 'P' and resid 522 through 528 removed outlier: 3.700A pdb=" N LEU P 526 " --> pdb=" O SER P 522 " (cutoff:3.500A) Processing helix chain 'P' and resid 539 through 548 Processing helix chain 'P' and resid 557 through 564 removed outlier: 3.715A pdb=" N GLN P 560 " --> pdb=" O ILE P 557 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER P 562 " --> pdb=" O LYS P 559 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU P 564 " --> pdb=" O ILE P 561 " (cutoff:3.500A) Processing helix chain 'P' and resid 597 through 601 removed outlier: 3.686A pdb=" N GLU P 600 " --> pdb=" O VAL P 597 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 138 removed outlier: 3.629A pdb=" N LEU Q 133 " --> pdb=" O THR Q 129 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN Q 134 " --> pdb=" O SER Q 130 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE Q 135 " --> pdb=" O ASP Q 131 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 145 removed outlier: 3.889A pdb=" N LEU Q 144 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Proline residue: Q 145 - end of helix Processing helix chain 'Q' and resid 165 through 170 Processing helix chain 'Q' and resid 182 through 198 removed outlier: 3.717A pdb=" N PHE Q 186 " --> pdb=" O GLY Q 182 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 217 removed outlier: 3.628A pdb=" N PHE Q 216 " --> pdb=" O ALA Q 213 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR Q 217 " --> pdb=" O GLN Q 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 213 through 217' Processing helix chain 'Q' and resid 261 through 270 removed outlier: 3.736A pdb=" N GLY Q 265 " --> pdb=" O LEU Q 261 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 287 Processing helix chain 'Q' and resid 321 through 332 Processing helix chain 'Q' and resid 344 through 354 removed outlier: 4.210A pdb=" N THR Q 348 " --> pdb=" O LYS Q 344 " (cutoff:3.500A) Processing helix chain 'Q' and resid 370 through 373 Processing helix chain 'Q' and resid 374 through 384 Processing helix chain 'Q' and resid 389 through 392 Processing helix chain 'Q' and resid 407 through 421 removed outlier: 3.547A pdb=" N LYS Q 411 " --> pdb=" O THR Q 407 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU Q 416 " --> pdb=" O ALA Q 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 445 through 465 removed outlier: 3.577A pdb=" N LEU Q 449 " --> pdb=" O HIS Q 445 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG Q 463 " --> pdb=" O GLU Q 459 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY Q 465 " --> pdb=" O LEU Q 461 " (cutoff:3.500A) Processing helix chain 'Q' and resid 498 through 504 removed outlier: 3.905A pdb=" N LYS Q 502 " --> pdb=" O GLU Q 498 " (cutoff:3.500A) Processing helix chain 'Q' and resid 517 through 521 Processing helix chain 'Q' and resid 539 through 550 removed outlier: 3.845A pdb=" N ALA Q 549 " --> pdb=" O ALA Q 545 " (cutoff:3.500A) Processing helix chain 'Q' and resid 557 through 564 removed outlier: 3.573A pdb=" N ILE Q 561 " --> pdb=" O LEU Q 558 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER Q 562 " --> pdb=" O LYS Q 559 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 138 Processing helix chain 'R' and resid 140 through 144 Processing helix chain 'R' and resid 165 through 170 Processing helix chain 'R' and resid 182 through 198 removed outlier: 3.811A pdb=" N LYS R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 271 Processing helix chain 'R' and resid 276 through 286 removed outlier: 3.551A pdb=" N ALA R 280 " --> pdb=" O THR R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 332 Processing helix chain 'R' and resid 343 through 353 removed outlier: 4.280A pdb=" N ALA R 347 " --> pdb=" O PHE R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 386 removed outlier: 3.687A pdb=" N PHE R 371 " --> pdb=" O ASP R 367 " (cutoff:3.500A) Proline residue: R 376 - end of helix Processing helix chain 'R' and resid 403 through 407 removed outlier: 4.394A pdb=" N GLY R 406 " --> pdb=" O ALA R 403 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR R 407 " --> pdb=" O ASP R 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 403 through 407' Processing helix chain 'R' and resid 408 through 422 removed outlier: 3.617A pdb=" N ALA R 412 " --> pdb=" O HIS R 408 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET R 413 " --> pdb=" O TRP R 409 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU R 416 " --> pdb=" O ALA R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 451 removed outlier: 3.603A pdb=" N SER R 451 " --> pdb=" O PRO R 447 " (cutoff:3.500A) Processing helix chain 'R' and resid 451 through 465 removed outlier: 4.049A pdb=" N GLU R 455 " --> pdb=" O SER R 451 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET R 456 " --> pdb=" O ALA R 452 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE R 457 " --> pdb=" O LEU R 453 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY R 465 " --> pdb=" O LEU R 461 " (cutoff:3.500A) Processing helix chain 'R' and resid 478 through 483 removed outlier: 4.181A pdb=" N TYR R 482 " --> pdb=" O GLU R 478 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 507 removed outlier: 3.565A pdb=" N ARG R 505 " --> pdb=" O ALA R 501 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS R 506 " --> pdb=" O LYS R 502 " (cutoff:3.500A) Processing helix chain 'R' and resid 524 through 528 removed outlier: 3.741A pdb=" N MET R 528 " --> pdb=" O VAL R 525 " (cutoff:3.500A) Processing helix chain 'R' and resid 540 through 549 removed outlier: 3.726A pdb=" N ALA R 549 " --> pdb=" O ALA R 545 " (cutoff:3.500A) Processing helix chain 'R' and resid 554 through 561 Processing helix chain 'R' and resid 562 through 564 No H-bonds generated for 'chain 'R' and resid 562 through 564' Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.606A pdb=" N GLN A 5 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 300 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A 330 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 302 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N TYR A 332 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE A 304 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 28 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N PHE A 165 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 30 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 164 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 185 Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.601A pdb=" N SER A 189 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 195 " --> pdb=" O SER A 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 207 Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 10 removed outlier: 4.400A pdb=" N ILE B 3 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 367 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 300 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL B 330 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 302 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N TYR B 332 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE B 304 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL B 28 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N PHE B 165 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 30 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 164 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN B 183 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 223 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE B 185 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LYS B 225 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 188 through 189 removed outlier: 3.544A pdb=" N SER B 189 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 195 " --> pdb=" O SER B 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 203 through 207 Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AB1, first strand: chain 'C' and resid 8 through 10 removed outlier: 3.619A pdb=" N ASN C 8 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE C 3 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR C 367 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 329 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL C 369 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE C 331 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 28 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE C 165 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL C 30 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE C 164 " --> pdb=" O TYR C 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB3, first strand: chain 'C' and resid 232 through 234 Processing sheet with id=AB4, first strand: chain 'D' and resid 8 through 10 removed outlier: 4.174A pdb=" N ILE D 3 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N THR D 367 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL D 329 " --> pdb=" O THR D 367 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL D 369 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE D 331 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR D 300 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL D 330 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU D 302 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N TYR D 332 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE D 304 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL D 28 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N PHE D 165 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL D 30 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE D 164 " --> pdb=" O TYR D 224 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN D 183 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU D 223 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE D 185 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LYS D 225 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 188 through 189 Processing sheet with id=AB6, first strand: chain 'D' and resid 203 through 207 Processing sheet with id=AB7, first strand: chain 'D' and resid 232 through 234 Processing sheet with id=AB8, first strand: chain 'E' and resid 8 through 9 removed outlier: 3.612A pdb=" N ASN E 8 " --> pdb=" O GLN E 5 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N THR E 367 " --> pdb=" O PHE E 327 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL E 329 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL E 369 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE E 331 " --> pdb=" O VAL E 369 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS E 328 " --> pdb=" O THR E 300 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL E 28 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N PHE E 165 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL E 30 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 223 " --> pdb=" O PHE E 185 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 188 through 189 Processing sheet with id=AC1, first strand: chain 'E' and resid 232 through 234 Processing sheet with id=AC2, first strand: chain 'F' and resid 8 through 9 removed outlier: 8.550A pdb=" N THR F 367 " --> pdb=" O PHE F 327 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL F 329 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL F 369 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE F 331 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR F 300 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N VAL F 330 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU F 302 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N TYR F 332 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE F 304 " --> pdb=" O TYR F 332 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN F 27 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N PHE F 303 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY F 29 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA F 163 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE F 164 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN F 183 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU F 223 " --> pdb=" O GLN F 183 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE F 185 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LYS F 225 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 188 through 189 removed outlier: 3.566A pdb=" N GLN F 195 " --> pdb=" O SER F 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 203 through 207 Processing sheet with id=AC5, first strand: chain 'F' and resid 232 through 234 Processing sheet with id=AC6, first strand: chain 'G' and resid 183 through 185 removed outlier: 6.814A pdb=" N VAL G 28 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N PHE G 165 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL G 30 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS G 328 " --> pdb=" O THR G 300 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 188 through 189 Processing sheet with id=AC8, first strand: chain 'G' and resid 232 through 233 Processing sheet with id=AC9, first strand: chain 'H' and resid 8 through 9 removed outlier: 8.339A pdb=" N THR H 367 " --> pdb=" O PHE H 327 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL H 329 " --> pdb=" O THR H 367 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL H 369 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE H 331 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL H 28 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N PHE H 165 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL H 30 " --> pdb=" O PHE H 165 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE H 164 " --> pdb=" O TYR H 224 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN H 183 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU H 223 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE H 185 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LYS H 225 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 188 through 189 removed outlier: 4.555A pdb=" N ARG H 194 " --> pdb=" O GLU H 242 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU H 242 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE H 196 " --> pdb=" O VAL H 240 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL H 240 " --> pdb=" O PHE H 196 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 203 through 207 Processing sheet with id=AD3, first strand: chain 'I' and resid 8 through 9 removed outlier: 3.903A pdb=" N ASN I 8 " --> pdb=" O GLN I 5 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR I 300 " --> pdb=" O HIS I 328 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL I 330 " --> pdb=" O THR I 300 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU I 302 " --> pdb=" O VAL I 330 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N TYR I 332 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE I 304 " --> pdb=" O TYR I 332 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN I 27 " --> pdb=" O ALA I 301 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N PHE I 303 " --> pdb=" O ASN I 27 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY I 29 " --> pdb=" O PHE I 303 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASN I 305 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU I 31 " --> pdb=" O ASN I 305 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL I 28 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N PHE I 165 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL I 30 " --> pdb=" O PHE I 165 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE I 164 " --> pdb=" O TYR I 224 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN I 183 " --> pdb=" O ALA I 221 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU I 223 " --> pdb=" O GLN I 183 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE I 185 " --> pdb=" O LEU I 223 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LYS I 225 " --> pdb=" O PHE I 185 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 188 through 189 removed outlier: 3.634A pdb=" N SER I 189 " --> pdb=" O GLN I 195 " (cutoff:3.500A) 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: 4.359A pdb=" N ILE J 3 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR J 300 " --> pdb=" O HIS J 328 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL J 330 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU J 302 " --> pdb=" O VAL J 330 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N TYR J 332 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE J 304 " --> pdb=" O TYR J 332 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL J 28 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE J 165 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL J 30 " --> pdb=" O PHE J 165 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE J 164 " --> pdb=" O TYR J 224 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA J 221 " --> pdb=" O GLN J 183 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 188 through 189 removed outlier: 3.708A 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 207 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: 3.732A pdb=" N ASN K 8 " --> pdb=" O GLN K 5 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N THR K 367 " --> pdb=" O PHE K 327 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL K 329 " --> pdb=" O THR K 367 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL K 369 " --> pdb=" O VAL K 329 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE K 331 " --> pdb=" O VAL K 369 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR K 332 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN K 27 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N PHE K 303 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY K 29 " --> pdb=" O PHE K 303 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ASN K 305 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU K 31 " --> pdb=" O ASN K 305 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA K 163 " --> pdb=" O VAL K 28 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 188 through 189 removed outlier: 3.555A pdb=" N SER K 189 " --> pdb=" O GLN K 195 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN K 195 " --> pdb=" O SER K 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 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: 4.397A pdb=" N ILE L 3 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR L 300 " --> pdb=" O HIS L 328 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL L 330 " --> pdb=" O THR L 300 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU L 302 " --> pdb=" O VAL L 330 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N TYR L 332 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE L 304 " --> pdb=" O TYR L 332 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN L 27 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE L 303 " --> pdb=" O ASN L 27 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY L 29 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ASN L 305 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU L 31 " --> pdb=" O ASN L 305 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA L 163 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE L 164 " --> pdb=" O TYR L 224 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA L 221 " --> pdb=" O GLN L 183 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 188 through 189 removed outlier: 3.523A pdb=" N SER L 189 " --> pdb=" O GLN L 195 " (cutoff:3.500A) removed outlier: 3.815A 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: 7.009A pdb=" N ARG M 24 " --> pdb=" O VAL M 16 " (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: 3.952A pdb=" N GLY M 100 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG M 64 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA M 98 " --> pdb=" O ARG M 64 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR M 66 " --> pdb=" O ALA M 96 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ALA M 96 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N MET M 68 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE M 94 " --> pdb=" O MET M 68 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE M 70 " --> pdb=" O ARG M 92 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ARG M 92 " --> pdb=" O PHE M 70 " (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: 6.363A pdb=" N LEU N 60 " --> pdb=" O PHE N 101 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE N 101 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL N 62 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE N 95 " --> pdb=" O THR N 66 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET N 68 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN N 93 " --> pdb=" O MET N 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 110 through 112 current: chain 'O' and resid 22 through 27 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 22 through 27 current: chain 'O' and resid 60 through 70 removed outlier: 6.282A pdb=" N LEU O 60 " --> pdb=" O PHE O 101 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE O 101 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL O 62 " --> pdb=" O ILE O 99 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE O 95 " --> pdb=" O THR O 66 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET O 68 " --> pdb=" O GLN O 93 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN O 93 " --> pdb=" O MET O 68 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE O 101 " --> pdb=" O ILE O 112 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 109 through 113 current: chain 'P' and resid 23 through 27 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 23 through 27 current: chain 'P' and resid 60 through 70 removed outlier: 6.308A pdb=" N LEU P 60 " --> pdb=" O PHE P 101 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE P 101 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL P 62 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE P 95 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET P 68 " --> pdb=" O GLN P 93 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLN P 93 " --> pdb=" O MET P 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 109 through 112 current: chain 'Q' and resid 23 through 27 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 23 through 27 current: chain 'Q' and resid 60 through 70 removed outlier: 6.640A pdb=" N LEU Q 60 " --> pdb=" O PHE Q 101 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE Q 101 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL Q 62 " --> pdb=" O ILE Q 99 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE Q 95 " --> pdb=" O THR Q 66 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N MET Q 68 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLN Q 93 " --> pdb=" O MET Q 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 109 through 112 current: chain 'R' and resid 22 through 27 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 22 through 27 current: chain 'R' and resid 59 through 65 removed outlier: 3.768A pdb=" N GLY R 100 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG R 64 " --> pdb=" O ALA R 98 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA R 98 " --> pdb=" O ARG R 64 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE R 101 " --> pdb=" O ILE R 112 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS R 103 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL R 110 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'M' and resid 160 through 164 removed outlier: 7.288A pdb=" N ILE M 161 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS M 172 " --> pdb=" O CYS M 529 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN M 531 " --> pdb=" O HIS M 172 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA M 174 " --> pdb=" O ASN M 531 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR M 515 " --> pdb=" O VAL M 175 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL M 204 " --> pdb=" O LEU M 475 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLU M 477 " --> pdb=" O VAL M 204 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE M 206 " --> pdb=" O GLU M 477 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE M 203 " --> pdb=" O HIS M 434 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL M 436 " --> pdb=" O ILE M 203 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE M 205 " --> pdb=" O VAL M 436 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS M 223 " --> pdb=" O ILE M 435 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN M 437 " --> pdb=" O LYS M 223 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR M 225 " --> pdb=" O ASN M 437 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 256 through 257 removed outlier: 6.542A pdb=" N ILE M 256 " --> pdb=" O ASN M 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'M' and resid 292 through 294 Processing sheet with id=AF3, first strand: chain 'N' and resid 35 through 37 removed outlier: 3.602A 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: 4.177A pdb=" N GLY N 151 " --> pdb=" O ILE N 161 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA N 163 " --> pdb=" O GLU N 149 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU N 149 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL N 152 " --> pdb=" O SER N 583 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL N 580 " --> pdb=" O ALA N 571 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA N 174 " --> pdb=" O ASN N 531 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER N 510 " --> pdb=" O THR N 472 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU N 477 " --> pdb=" O PHE N 206 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS N 223 " --> pdb=" O ILE N 435 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ASN N 437 " --> pdb=" O LYS N 223 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR N 225 " --> pdb=" O ASN N 437 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N CYS N 252 " --> pdb=" O VAL N 222 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N HIS N 224 " --> pdb=" O CYS N 252 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS N 254 " --> pdb=" O HIS N 224 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE N 226 " --> pdb=" O LYS N 254 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 256 through 257 removed outlier: 6.676A pdb=" N ILE N 256 " --> pdb=" O ASN N 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'N' and resid 292 through 293 removed outlier: 3.808A pdb=" N TYR N 299 " --> pdb=" O HIS N 292 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE N 298 " --> pdb=" O LEU N 310 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE N 308 " --> pdb=" O LEU N 300 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 356 through 358 Processing sheet with id=AF8, first strand: chain 'O' and resid 35 through 37 Processing sheet with id=AF9, first strand: chain 'O' and resid 160 through 164 removed outlier: 7.200A pdb=" N ILE O 161 " --> pdb=" O LEU O 150 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU O 477 " --> pdb=" O PHE O 206 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE O 203 " --> pdb=" O HIS O 434 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL O 436 " --> pdb=" O ILE O 203 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE O 205 " --> pdb=" O VAL O 436 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LYS O 254 " --> pdb=" O HIS O 224 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE O 226 " --> pdb=" O LYS O 254 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 256 through 257 removed outlier: 6.837A pdb=" N ILE O 256 " --> pdb=" O ASN O 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'O' and resid 292 through 293 removed outlier: 4.890A pdb=" N ILE O 298 " --> pdb=" O LEU O 310 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE O 308 " --> pdb=" O LEU O 300 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 35 through 37 Processing sheet with id=AG4, first strand: chain 'P' and resid 160 through 164 removed outlier: 7.317A pdb=" N ILE P 161 " --> pdb=" O LEU P 150 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL P 152 " --> pdb=" O SER P 583 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE P 572 " --> pdb=" O TRP P 532 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N HIS P 172 " --> pdb=" O CYS P 529 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN P 531 " --> pdb=" O HIS P 172 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA P 174 " --> pdb=" O ASN P 531 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU P 477 " --> pdb=" O PHE P 206 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE P 203 " --> pdb=" O HIS P 434 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL P 436 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE P 205 " --> pdb=" O VAL P 436 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N CYS P 252 " --> pdb=" O VAL P 222 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N HIS P 224 " --> pdb=" O CYS P 252 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LYS P 254 " --> pdb=" O HIS P 224 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE P 226 " --> pdb=" O LYS P 254 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 256 through 257 removed outlier: 7.077A pdb=" N ILE P 256 " --> pdb=" O ASN P 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'P' and resid 292 through 293 removed outlier: 3.910A pdb=" N HIS P 292 " --> pdb=" O TYR P 299 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR P 299 " --> pdb=" O HIS P 292 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU P 300 " --> pdb=" O PHE P 308 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 160 through 164 removed outlier: 7.473A pdb=" N ILE Q 161 " --> pdb=" O LEU Q 150 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Q 150 " --> pdb=" O ILE Q 161 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE Q 572 " --> pdb=" O TRP Q 532 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL Q 204 " --> pdb=" O LEU Q 475 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS Q 223 " --> pdb=" O ILE Q 435 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASN Q 437 " --> pdb=" O LYS Q 223 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR Q 225 " --> pdb=" O ASN Q 437 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LYS Q 254 " --> pdb=" O HIS Q 224 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE Q 226 " --> pdb=" O LYS Q 254 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 256 through 257 removed outlier: 6.848A pdb=" N ILE Q 256 " --> pdb=" O ASN Q 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'Q' and resid 292 through 293 Processing sheet with id=AH1, first strand: chain 'R' and resid 160 through 164 removed outlier: 4.145A pdb=" N GLY R 151 " --> pdb=" O ILE R 161 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA R 163 " --> pdb=" O GLU R 149 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLU R 149 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL R 152 " --> pdb=" O SER R 583 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA R 174 " --> pdb=" O ASN R 531 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE R 533 " --> pdb=" O ALA R 174 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR R 515 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'R' and resid 252 through 253 removed outlier: 3.510A pdb=" N ILE R 226 " --> pdb=" O CYS R 252 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N THR R 225 " --> pdb=" O ASN R 437 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE R 203 " --> pdb=" O HIS R 434 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL R 436 " --> pdb=" O ILE R 203 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE R 205 " --> pdb=" O VAL R 436 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N MET R 438 " --> pdb=" O ILE R 205 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 256 through 257 removed outlier: 7.389A pdb=" N ILE R 256 " --> pdb=" O ASN R 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'R' and resid 300 through 301 removed outlier: 3.645A pdb=" N LEU R 300 " --> pdb=" O PHE R 308 " (cutoff:3.500A) 2190 hydrogen bonds defined for protein. 6279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.03 Time building geometry restraints manager: 13.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 21484 1.37 - 1.52: 22310 1.52 - 1.66: 22020 1.66 - 1.81: 242 1.81 - 1.96: 8 Bond restraints: 66064 Sorted by residual: bond pdb=" C2' AGS O 701 " pdb=" C3' AGS O 701 " ideal model delta sigma weight residual 1.530 1.282 0.248 1.30e-02 5.92e+03 3.64e+02 bond pdb=" C2' AGS N 701 " pdb=" C3' AGS N 701 " ideal model delta sigma weight residual 1.530 1.283 0.247 1.30e-02 5.92e+03 3.61e+02 bond pdb=" C2' AGS Q 701 " pdb=" C3' AGS Q 701 " ideal model delta sigma weight residual 1.530 1.288 0.242 1.30e-02 5.92e+03 3.47e+02 bond pdb=" C2' AGS P 701 " pdb=" C3' AGS P 701 " ideal model delta sigma weight residual 1.530 1.291 0.239 1.30e-02 5.92e+03 3.39e+02 bond pdb=" C2' AGS M 701 " pdb=" C3' AGS M 701 " ideal model delta sigma weight residual 1.530 1.291 0.239 1.30e-02 5.92e+03 3.39e+02 ... (remaining 66059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 89175 3.73 - 7.46: 177 7.46 - 11.19: 18 11.19 - 14.92: 0 14.92 - 18.65: 1 Bond angle restraints: 89371 Sorted by residual: angle pdb=" C5 AGS M 701 " pdb=" N7 AGS M 701 " pdb=" C8 AGS M 701 " ideal model delta sigma weight residual 103.67 108.44 -4.77 4.26e-01 5.51e+00 1.26e+02 angle pdb=" C5 AGS Q 701 " pdb=" N7 AGS Q 701 " pdb=" C8 AGS Q 701 " ideal model delta sigma weight residual 103.67 108.41 -4.74 4.26e-01 5.51e+00 1.24e+02 angle pdb=" C5 AGS O 701 " pdb=" N7 AGS O 701 " pdb=" C8 AGS O 701 " ideal model delta sigma weight residual 103.67 108.40 -4.73 4.26e-01 5.51e+00 1.23e+02 angle pdb=" C5 AGS P 701 " pdb=" N7 AGS P 701 " pdb=" C8 AGS P 701 " ideal model delta sigma weight residual 103.67 108.33 -4.66 4.26e-01 5.51e+00 1.20e+02 angle pdb=" C5 AGS N 701 " pdb=" C4 AGS N 701 " pdb=" N3 AGS N 701 " ideal model delta sigma weight residual 126.80 119.10 7.70 7.41e-01 1.82e+00 1.08e+02 ... (remaining 89366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 38487 35.54 - 71.08: 937 71.08 - 106.63: 109 106.63 - 142.17: 4 142.17 - 177.71: 3 Dihedral angle restraints: 39540 sinusoidal: 16314 harmonic: 23226 Sorted by residual: dihedral pdb=" CA SER N 273 " pdb=" C SER N 273 " pdb=" N ASP N 274 " pdb=" CA ASP N 274 " ideal model delta harmonic sigma weight residual -180.00 -151.99 -28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" O1B AGS N 701 " pdb=" O3B AGS N 701 " pdb=" PB AGS N 701 " pdb=" PG AGS N 701 " ideal model delta sinusoidal sigma weight residual 68.91 -108.80 177.71 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS Q 701 " pdb=" O3A AGS Q 701 " pdb=" PA AGS Q 701 " pdb=" PB AGS Q 701 " ideal model delta sinusoidal sigma weight residual -67.73 86.34 -154.07 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 39537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.030: 9704 1.030 - 2.060: 0 2.060 - 3.090: 0 3.090 - 4.120: 0 4.120 - 5.151: 6 Chirality restraints: 9710 Sorted by residual: chirality pdb=" C2' AGS O 701 " pdb=" C1' AGS O 701 " pdb=" C3' AGS O 701 " pdb=" O2' AGS O 701 " both_signs ideal model delta sigma weight residual False -2.67 2.48 -5.15 2.00e-01 2.50e+01 6.63e+02 chirality pdb=" C4' AGS O 701 " pdb=" C3' AGS O 701 " pdb=" C5' AGS O 701 " pdb=" O4' AGS O 701 " both_signs ideal model delta sigma weight residual False -2.49 2.61 -5.09 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C4' AGS P 701 " pdb=" C3' AGS P 701 " pdb=" C5' AGS P 701 " pdb=" O4' AGS P 701 " both_signs ideal model delta sigma weight residual False -2.49 2.60 -5.09 2.00e-01 2.50e+01 6.48e+02 ... (remaining 9707 not shown) Planarity restraints: 11449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 324 " 0.038 5.00e-02 4.00e+02 5.89e-02 5.54e+00 pdb=" N PRO K 325 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO K 325 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 325 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 297 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO E 298 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 470 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO R 471 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO R 471 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 471 " 0.030 5.00e-02 4.00e+02 ... (remaining 11446 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 8 2.09 - 2.79: 14919 2.79 - 3.49: 77967 3.49 - 4.20: 127777 4.20 - 4.90: 239651 Nonbonded interactions: 460322 Sorted by model distance: nonbonded pdb=" S1G AGS N 701 " pdb="MG MG N 702 " model vdw 1.383 2.530 nonbonded pdb=" S1G AGS M 701 " pdb="MG MG M 702 " model vdw 1.650 2.530 nonbonded pdb=" O2G AGS P 701 " pdb="MG MG P 702 " model vdw 1.806 2.170 nonbonded pdb=" S1G AGS O 701 " pdb="MG MG O 702 " model vdw 1.816 2.530 nonbonded pdb=" OE1 GLU M 211 " pdb="MG MG M 702 " model vdw 1.836 2.170 ... (remaining 460317 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 501)) selection = (chain 'B' and (resid 2 through 387 or resid 501)) selection = (chain 'C' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'D' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'E' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'F' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'G' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'H' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'I' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'J' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'K' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'L' and (resid 2 through 208 or resid 218 through 387 or resid 501)) } ncs_group { reference = (chain 'M' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 584)) selection = (chain 'N' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'O' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'P' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 355 or resid 375 through 484 or resid 498 through 584)) selection = (chain 'Q' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'R' and (resid 10 through 227 or resid 238 through 328 or resid 336 throu \ gh 355 or resid 375 through 484 or resid 498 through 584)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.860 Check model and map are aligned: 0.370 Set scattering table: 0.440 Process input model: 110.930 Find NCS groups from input model: 3.690 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.004 0.248 66064 Z= 0.288 Angle : 0.537 18.648 89371 Z= 0.332 Chirality : 0.132 5.151 9710 Planarity : 0.004 0.059 11449 Dihedral : 15.780 177.710 24688 Min Nonbonded Distance : 1.383 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.01 % Allowed : 0.10 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.09), residues: 7933 helix: 0.53 (0.10), residues: 3036 sheet: 0.83 (0.17), residues: 1034 loop : -1.60 (0.09), residues: 3863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 116 HIS 0.005 0.001 HIS F 313 PHE 0.015 0.001 PHE F 288 TYR 0.020 0.001 TYR D 284 ARG 0.003 0.000 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2001 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2000 time to evaluate : 5.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7908 (m-30) cc_final: 0.7643 (m-30) REVERT: A 47 ASP cc_start: 0.8129 (m-30) cc_final: 0.7894 (m-30) REVERT: A 58 GLU cc_start: 0.7600 (mp0) cc_final: 0.7281 (mp0) REVERT: A 80 VAL cc_start: 0.8866 (t) cc_final: 0.8611 (p) REVERT: A 128 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 139 ASP cc_start: 0.7866 (t0) cc_final: 0.7466 (t0) REVERT: A 159 GLN cc_start: 0.8405 (mt0) cc_final: 0.8088 (mt0) REVERT: A 179 ASP cc_start: 0.8070 (t0) cc_final: 0.7862 (t70) REVERT: A 234 GLN cc_start: 0.8417 (pt0) cc_final: 0.8126 (pt0) REVERT: A 374 LYS cc_start: 0.8362 (mttt) cc_final: 0.8063 (mttm) REVERT: B 59 LEU cc_start: 0.8383 (mt) cc_final: 0.8181 (mt) REVERT: B 70 VAL cc_start: 0.8671 (t) cc_final: 0.8386 (m) REVERT: B 97 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8212 (ttmt) REVERT: B 102 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7466 (mm-30) REVERT: B 132 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 202 ASP cc_start: 0.8349 (m-30) cc_final: 0.8084 (m-30) REVERT: B 205 PHE cc_start: 0.8976 (m-80) cc_final: 0.8773 (m-10) REVERT: B 233 TYR cc_start: 0.8028 (p90) cc_final: 0.7741 (p90) REVERT: B 240 VAL cc_start: 0.8690 (t) cc_final: 0.8468 (t) REVERT: B 257 ILE cc_start: 0.8417 (mm) cc_final: 0.8119 (mt) REVERT: B 258 ASN cc_start: 0.7944 (m-40) cc_final: 0.7528 (m-40) REVERT: B 289 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7913 (ttp80) REVERT: B 374 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8284 (mttp) REVERT: B 382 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7564 (tm-30) REVERT: C 88 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7508 (mm-30) REVERT: C 104 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7145 (mm-30) REVERT: C 180 LEU cc_start: 0.8150 (mt) cc_final: 0.7888 (mt) REVERT: C 202 ASP cc_start: 0.8035 (m-30) cc_final: 0.7828 (m-30) REVERT: C 286 GLU cc_start: 0.8074 (tp30) cc_final: 0.7841 (tp30) REVERT: C 296 SER cc_start: 0.8919 (m) cc_final: 0.8655 (t) REVERT: C 342 LYS cc_start: 0.8819 (mttp) cc_final: 0.8618 (mttp) REVERT: D 24 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8375 (mp10) REVERT: D 72 GLN cc_start: 0.6675 (tp40) cc_final: 0.6466 (mm-40) REVERT: D 76 ASP cc_start: 0.7305 (m-30) cc_final: 0.6840 (m-30) REVERT: D 109 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7519 (mtt-85) REVERT: D 113 SER cc_start: 0.8850 (m) cc_final: 0.8624 (t) REVERT: D 121 LYS cc_start: 0.8831 (ptmt) cc_final: 0.8622 (ttpt) REVERT: D 128 GLU cc_start: 0.7887 (mp0) cc_final: 0.7547 (mp0) REVERT: D 129 GLN cc_start: 0.8254 (mm110) cc_final: 0.7855 (mm-40) REVERT: D 131 ARG cc_start: 0.8379 (ptm-80) cc_final: 0.8097 (ptm160) REVERT: D 137 LYS cc_start: 0.8359 (mttt) cc_final: 0.8063 (mmtp) REVERT: D 179 ASP cc_start: 0.7936 (t70) cc_final: 0.7690 (t70) REVERT: D 290 ARG cc_start: 0.8135 (mmt180) cc_final: 0.7905 (mmt-90) REVERT: E 73 ILE cc_start: 0.7798 (mp) cc_final: 0.7590 (tt) REVERT: E 99 ARG cc_start: 0.8609 (ttm-80) cc_final: 0.8345 (ttp-170) REVERT: E 118 GLU cc_start: 0.7872 (tp30) cc_final: 0.7577 (tp30) REVERT: E 286 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7626 (tp30) REVERT: E 335 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7341 (mm-30) REVERT: F 11 ASN cc_start: 0.7906 (t0) cc_final: 0.7703 (p0) REVERT: F 14 ASP cc_start: 0.7343 (m-30) cc_final: 0.6479 (m-30) REVERT: F 17 SER cc_start: 0.8373 (m) cc_final: 0.8126 (t) REVERT: F 20 TYR cc_start: 0.8465 (t80) cc_final: 0.8230 (t80) REVERT: F 45 MET cc_start: 0.8253 (tpp) cc_final: 0.7810 (mmt) REVERT: F 109 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7672 (tpp80) REVERT: F 114 SER cc_start: 0.8741 (m) cc_final: 0.8217 (p) REVERT: F 137 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8305 (ttmm) REVERT: F 154 ASN cc_start: 0.7761 (m-40) cc_final: 0.7501 (m110) REVERT: F 233 TYR cc_start: 0.7682 (p90) cc_final: 0.7111 (p90) REVERT: F 286 GLU cc_start: 0.7157 (tp30) cc_final: 0.6767 (tp30) REVERT: F 296 SER cc_start: 0.8918 (m) cc_final: 0.8496 (t) REVERT: F 363 PHE cc_start: 0.8672 (m-80) cc_final: 0.8407 (m-80) REVERT: G 51 SER cc_start: 0.8732 (m) cc_final: 0.8378 (t) REVERT: G 53 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7692 (mtmt) REVERT: G 77 ASN cc_start: 0.8384 (t0) cc_final: 0.8167 (t0) REVERT: G 107 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7675 (tm-30) REVERT: G 200 ASN cc_start: 0.8395 (m110) cc_final: 0.8075 (m-40) REVERT: G 202 ASP cc_start: 0.7629 (m-30) cc_final: 0.7332 (m-30) REVERT: G 225 LYS cc_start: 0.8641 (mttt) cc_final: 0.8402 (mtpt) REVERT: G 275 LYS cc_start: 0.8148 (mttt) cc_final: 0.7944 (mtpp) REVERT: G 291 PHE cc_start: 0.7945 (t80) cc_final: 0.7688 (t80) REVERT: G 353 LYS cc_start: 0.8422 (mttt) cc_final: 0.8158 (mttt) REVERT: G 403 ILE cc_start: 0.8258 (mt) cc_final: 0.7968 (tp) REVERT: H 43 LYS cc_start: 0.8069 (mtpp) cc_final: 0.7801 (mtmm) REVERT: H 46 LYS cc_start: 0.8117 (mttt) cc_final: 0.7883 (mtpp) REVERT: H 65 ASP cc_start: 0.6985 (m-30) cc_final: 0.6718 (m-30) REVERT: H 68 LEU cc_start: 0.8638 (mt) cc_final: 0.8379 (mt) REVERT: H 107 GLU cc_start: 0.8190 (tp30) cc_final: 0.7783 (tp30) REVERT: H 110 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8276 (ttmm) REVERT: H 286 GLU cc_start: 0.8000 (tp30) cc_final: 0.7719 (tp30) REVERT: I 65 ASP cc_start: 0.8113 (m-30) cc_final: 0.7868 (m-30) REVERT: I 74 ASP cc_start: 0.7798 (m-30) cc_final: 0.7586 (m-30) REVERT: I 76 ASP cc_start: 0.7587 (m-30) cc_final: 0.6996 (m-30) REVERT: I 80 VAL cc_start: 0.8753 (t) cc_final: 0.8542 (p) REVERT: I 142 LYS cc_start: 0.8848 (tttt) cc_final: 0.8630 (ttmt) REVERT: I 250 ASP cc_start: 0.8196 (m-30) cc_final: 0.7831 (m-30) REVERT: I 342 LYS cc_start: 0.8378 (mttt) cc_final: 0.8154 (mtpp) REVERT: J 17 SER cc_start: 0.8014 (m) cc_final: 0.7726 (t) REVERT: J 99 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7284 (ttm-80) REVERT: J 300 THR cc_start: 0.8663 (m) cc_final: 0.8388 (p) REVERT: K 14 ASP cc_start: 0.6882 (m-30) cc_final: 0.6491 (m-30) REVERT: K 58 GLU cc_start: 0.7676 (pm20) cc_final: 0.7325 (pm20) REVERT: K 68 LEU cc_start: 0.8936 (mp) cc_final: 0.8721 (mt) REVERT: K 119 VAL cc_start: 0.7897 (p) cc_final: 0.7686 (t) REVERT: K 131 ARG cc_start: 0.8400 (ptm-80) cc_final: 0.8159 (ptm-80) REVERT: K 178 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7857 (mt-10) REVERT: K 255 ASP cc_start: 0.8515 (m-30) cc_final: 0.8299 (m-30) REVERT: K 262 PHE cc_start: 0.8565 (t80) cc_final: 0.8323 (t80) REVERT: K 266 GLN cc_start: 0.7883 (mt0) cc_final: 0.7552 (mt0) REVERT: K 291 PHE cc_start: 0.7868 (t80) cc_final: 0.7464 (t80) REVERT: L 63 LEU cc_start: 0.8049 (tp) cc_final: 0.7657 (tp) REVERT: L 142 LYS cc_start: 0.8528 (tttm) cc_final: 0.8321 (tttm) REVERT: L 233 TYR cc_start: 0.8185 (p90) cc_final: 0.7814 (p90) REVERT: L 293 GLU cc_start: 0.7739 (tt0) cc_final: 0.7464 (tt0) REVERT: L 374 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8300 (mtmt) REVERT: M 23 ILE cc_start: 0.8541 (mt) cc_final: 0.8316 (mt) REVERT: M 50 ASP cc_start: 0.8146 (m-30) cc_final: 0.7831 (m-30) REVERT: M 196 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7669 (mt-10) REVERT: M 204 VAL cc_start: 0.8427 (t) cc_final: 0.8075 (m) REVERT: M 254 LYS cc_start: 0.8844 (tttp) cc_final: 0.8580 (tttm) REVERT: M 271 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7512 (ttm-80) REVERT: M 300 LEU cc_start: 0.7976 (mt) cc_final: 0.7714 (mp) REVERT: M 318 ASN cc_start: 0.8460 (t0) cc_final: 0.8233 (t0) REVERT: M 319 GLN cc_start: 0.8679 (pp30) cc_final: 0.8461 (pp30) REVERT: M 327 ASP cc_start: 0.8458 (t0) cc_final: 0.8234 (t0) REVERT: M 386 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7422 (mt-10) REVERT: M 424 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6476 (mt-10) REVERT: M 428 GLU cc_start: 0.6741 (tm-30) cc_final: 0.6316 (tm-30) REVERT: M 444 ASP cc_start: 0.7725 (m-30) cc_final: 0.7399 (m-30) REVERT: M 511 LEU cc_start: 0.7906 (mt) cc_final: 0.7642 (mt) REVERT: M 559 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8197 (mmpt) REVERT: M 560 GLN cc_start: 0.8378 (mt0) cc_final: 0.8158 (mt0) REVERT: M 574 SER cc_start: 0.8416 (p) cc_final: 0.8101 (t) REVERT: N 19 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7341 (mp0) REVERT: N 29 GLU cc_start: 0.6916 (mp0) cc_final: 0.6462 (mp0) REVERT: N 143 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7288 (mp0) REVERT: N 249 GLU cc_start: 0.7055 (pt0) cc_final: 0.6807 (pm20) REVERT: N 291 THR cc_start: 0.8836 (m) cc_final: 0.8418 (t) REVERT: N 302 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7864 (mttm) REVERT: N 315 ARG cc_start: 0.7458 (mtp85) cc_final: 0.7032 (mtt180) REVERT: N 336 ARG cc_start: 0.8347 (ptp90) cc_final: 0.8037 (mtm-85) REVERT: N 355 CYS cc_start: 0.7875 (p) cc_final: 0.7530 (p) REVERT: N 383 GLN cc_start: 0.8135 (mt0) cc_final: 0.7882 (mm-40) REVERT: N 388 ILE cc_start: 0.8326 (tp) cc_final: 0.8083 (tt) REVERT: N 394 VAL cc_start: 0.8876 (t) cc_final: 0.8508 (p) REVERT: N 401 GLU cc_start: 0.7117 (mp0) cc_final: 0.6852 (mp0) REVERT: N 427 GLN cc_start: 0.7938 (mp10) cc_final: 0.7641 (mp10) REVERT: N 478 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7662 (mm-30) REVERT: N 506 LYS cc_start: 0.8568 (mttm) cc_final: 0.8366 (mtpp) REVERT: N 559 LYS cc_start: 0.8590 (mtmt) cc_final: 0.8284 (mtmm) REVERT: O 19 GLU cc_start: 0.7470 (mp0) cc_final: 0.7198 (mp0) REVERT: O 43 SER cc_start: 0.8632 (p) cc_final: 0.8286 (t) REVERT: O 47 GLN cc_start: 0.8097 (pt0) cc_final: 0.7860 (pt0) REVERT: O 91 LEU cc_start: 0.8427 (tp) cc_final: 0.8128 (tp) REVERT: O 134 ASN cc_start: 0.8647 (t0) cc_final: 0.8416 (m-40) REVERT: O 166 ASP cc_start: 0.7713 (m-30) cc_final: 0.7291 (m-30) REVERT: O 171 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7272 (mmm-85) REVERT: O 352 GLU cc_start: 0.7911 (pp20) cc_final: 0.7565 (mm-30) REVERT: O 373 ASN cc_start: 0.7645 (m-40) cc_final: 0.7345 (m-40) REVERT: O 383 GLN cc_start: 0.7874 (mm110) cc_final: 0.7668 (mm110) REVERT: O 391 LYS cc_start: 0.8050 (tttp) cc_final: 0.7704 (ttpp) REVERT: O 517 ARG cc_start: 0.8385 (mtp85) cc_final: 0.8026 (ttm-80) REVERT: O 539 ASN cc_start: 0.8305 (t0) cc_final: 0.8034 (t0) REVERT: O 559 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8541 (mtpp) REVERT: P 19 GLU cc_start: 0.7206 (mp0) cc_final: 0.6977 (mp0) REVERT: P 50 ASP cc_start: 0.7986 (m-30) cc_final: 0.7733 (m-30) REVERT: P 55 ASP cc_start: 0.8012 (p0) cc_final: 0.7745 (p0) REVERT: P 115 ASP cc_start: 0.7689 (p0) cc_final: 0.7416 (p0) REVERT: P 165 VAL cc_start: 0.8707 (p) cc_final: 0.8470 (t) REVERT: P 241 GLN cc_start: 0.7976 (mp10) cc_final: 0.7561 (mp10) REVERT: P 263 PHE cc_start: 0.8125 (t80) cc_final: 0.7915 (t80) REVERT: P 283 ASN cc_start: 0.8344 (m-40) cc_final: 0.8060 (m110) REVERT: P 349 LEU cc_start: 0.9006 (mm) cc_final: 0.8799 (mt) REVERT: P 401 GLU cc_start: 0.7986 (mp0) cc_final: 0.7697 (mp0) REVERT: P 411 LYS cc_start: 0.7515 (mtmt) cc_final: 0.7251 (mtmt) REVERT: P 423 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7986 (mtmm) REVERT: P 444 ASP cc_start: 0.7233 (t0) cc_final: 0.6913 (t0) REVERT: P 459 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7620 (mm-30) REVERT: P 461 LEU cc_start: 0.8618 (tp) cc_final: 0.8404 (tp) REVERT: Q 67 ASP cc_start: 0.7713 (m-30) cc_final: 0.7458 (m-30) REVERT: Q 104 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7558 (ttm170) REVERT: Q 152 VAL cc_start: 0.8184 (t) cc_final: 0.7957 (p) REVERT: Q 170 SER cc_start: 0.8295 (t) cc_final: 0.7984 (p) REVERT: Q 209 ASN cc_start: 0.8576 (m110) cc_final: 0.8044 (m-40) REVERT: Q 211 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7421 (mt-10) REVERT: Q 242 LYS cc_start: 0.8107 (tppt) cc_final: 0.7906 (tppt) REVERT: Q 268 LYS cc_start: 0.8758 (tttm) cc_final: 0.8525 (ttmm) REVERT: Q 283 ASN cc_start: 0.8875 (m-40) cc_final: 0.8485 (m110) REVERT: Q 306 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6867 (tm-30) REVERT: Q 308 PHE cc_start: 0.7897 (t80) cc_final: 0.7390 (t80) REVERT: Q 311 TYR cc_start: 0.6614 (m-80) cc_final: 0.6303 (m-80) REVERT: Q 319 GLN cc_start: 0.7823 (pm20) cc_final: 0.7511 (pt0) REVERT: Q 327 ASP cc_start: 0.7705 (t0) cc_final: 0.7334 (t0) REVERT: Q 401 GLU cc_start: 0.7470 (tp30) cc_final: 0.7235 (tm-30) REVERT: Q 402 LEU cc_start: 0.7857 (mp) cc_final: 0.6436 (mp) REVERT: Q 440 ASN cc_start: 0.8552 (m-40) cc_final: 0.8345 (m110) REVERT: Q 468 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7541 (mtm-85) REVERT: Q 601 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7920 (mt-10) REVERT: R 140 ASP cc_start: 0.6726 (m-30) cc_final: 0.6486 (m-30) REVERT: R 189 LEU cc_start: 0.8703 (mp) cc_final: 0.8409 (mm) REVERT: R 245 LEU cc_start: 0.7036 (pp) cc_final: 0.6301 (mp) REVERT: R 294 LYS cc_start: 0.8199 (tppt) cc_final: 0.7324 (mptt) REVERT: R 371 PHE cc_start: 0.7843 (t80) cc_final: 0.7612 (t80) REVERT: R 418 ASP cc_start: 0.7535 (t70) cc_final: 0.7139 (t70) REVERT: R 423 LYS cc_start: 0.8445 (mptt) cc_final: 0.7840 (mmtm) REVERT: R 427 GLN cc_start: 0.7224 (tt0) cc_final: 0.6917 (tt0) REVERT: R 508 LYS cc_start: 0.7981 (mttp) cc_final: 0.7760 (mttp) REVERT: R 514 SER cc_start: 0.7676 (m) cc_final: 0.7475 (t) REVERT: R 516 GLN cc_start: 0.7732 (tt0) cc_final: 0.7499 (tt0) REVERT: R 559 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8106 (mtmt) outliers start: 1 outliers final: 0 residues processed: 2000 average time/residue: 0.6639 time to fit residues: 2159.0062 Evaluate side-chains 1665 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1665 time to evaluate : 5.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 672 optimal weight: 2.9990 chunk 603 optimal weight: 0.7980 chunk 334 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 406 optimal weight: 0.0570 chunk 322 optimal weight: 0.7980 chunk 623 optimal weight: 0.0270 chunk 241 optimal weight: 0.7980 chunk 379 optimal weight: 4.9990 chunk 464 optimal weight: 8.9990 chunk 722 optimal weight: 0.8980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 200 ASN A 247 GLN C 129 GLN C 315 ASN D 5 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN E 129 GLN E 200 ASN F 324 ASN G 135 GLN ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN G 218 HIS H 129 GLN H 258 ASN I 258 ASN I 365 GLN J 24 GLN J 183 GLN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN L 234 GLN M 209 ASN N 480 HIS N 544 GLN N 586 GLN O 221 ASN O 224 HIS P 187 ASN P 586 GLN Q 47 GLN Q 427 GLN Q 480 HIS ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 66064 Z= 0.150 Angle : 0.527 13.276 89371 Z= 0.273 Chirality : 0.041 0.202 9710 Planarity : 0.004 0.054 11449 Dihedral : 9.830 167.077 9438 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.18 % Allowed : 8.94 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.09), residues: 7933 helix: 0.77 (0.10), residues: 3112 sheet: 0.93 (0.17), residues: 1015 loop : -1.49 (0.09), residues: 3806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 409 HIS 0.003 0.001 HIS C 328 PHE 0.019 0.001 PHE M 462 TYR 0.021 0.001 TYR R 258 ARG 0.008 0.000 ARG R 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1763 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1682 time to evaluate : 6.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8185 (m-30) cc_final: 0.7936 (m-30) REVERT: A 58 GLU cc_start: 0.7589 (mp0) cc_final: 0.7292 (mp0) REVERT: A 74 ASP cc_start: 0.7972 (m-30) cc_final: 0.7735 (m-30) REVERT: A 80 VAL cc_start: 0.8930 (t) cc_final: 0.8661 (p) REVERT: A 128 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 139 ASP cc_start: 0.7830 (t0) cc_final: 0.7462 (t0) REVERT: B 14 ASP cc_start: 0.7796 (m-30) cc_final: 0.7588 (m-30) REVERT: B 70 VAL cc_start: 0.8705 (t) cc_final: 0.8415 (m) REVERT: B 97 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8228 (ttmt) REVERT: B 102 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 132 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7482 (mp0) REVERT: B 179 ASP cc_start: 0.8281 (t0) cc_final: 0.8055 (t0) REVERT: B 199 GLN cc_start: 0.8488 (mp10) cc_final: 0.8230 (mp10) REVERT: B 202 ASP cc_start: 0.8451 (m-30) cc_final: 0.8128 (m-30) REVERT: B 233 TYR cc_start: 0.8009 (p90) cc_final: 0.7708 (p90) REVERT: B 240 VAL cc_start: 0.8767 (t) cc_final: 0.8521 (t) REVERT: B 257 ILE cc_start: 0.8404 (mm) cc_final: 0.8078 (mt) REVERT: B 258 ASN cc_start: 0.8048 (m-40) cc_final: 0.7589 (m-40) REVERT: B 374 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8336 (mttp) REVERT: B 382 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7606 (tp30) REVERT: C 16 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7735 (mtt90) REVERT: C 58 GLU cc_start: 0.7897 (pm20) cc_final: 0.7669 (pm20) REVERT: C 88 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7477 (mm-30) REVERT: C 286 GLU cc_start: 0.8092 (tp30) cc_final: 0.7863 (tp30) REVERT: C 296 SER cc_start: 0.8844 (m) cc_final: 0.8605 (t) REVERT: C 316 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.7570 (ttp-170) REVERT: C 361 MET cc_start: 0.8004 (mmm) cc_final: 0.7800 (tpp) REVERT: D 24 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8388 (mp10) REVERT: D 72 GLN cc_start: 0.6746 (tp40) cc_final: 0.6516 (mm-40) REVERT: D 109 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7447 (mtt-85) REVERT: D 128 GLU cc_start: 0.7881 (mp0) cc_final: 0.7618 (mp0) REVERT: D 129 GLN cc_start: 0.8174 (mm110) cc_final: 0.7834 (mm110) REVERT: D 131 ARG cc_start: 0.8354 (ptm-80) cc_final: 0.8096 (ptm160) REVERT: D 203 LEU cc_start: 0.8469 (mp) cc_final: 0.8263 (mt) REVERT: D 290 ARG cc_start: 0.8127 (mmt180) cc_final: 0.7909 (mmt-90) REVERT: E 77 ASN cc_start: 0.7593 (m-40) cc_final: 0.7307 (m-40) REVERT: E 79 LEU cc_start: 0.8728 (mm) cc_final: 0.8513 (mm) REVERT: E 99 ARG cc_start: 0.8589 (ttm-80) cc_final: 0.8342 (ttp-170) REVERT: E 118 GLU cc_start: 0.7970 (tp30) cc_final: 0.7683 (tp30) REVERT: E 286 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7590 (tp30) REVERT: E 300 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7909 (p) REVERT: E 335 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7407 (mm-30) REVERT: E 341 THR cc_start: 0.8557 (m) cc_final: 0.8336 (p) REVERT: E 361 MET cc_start: 0.7808 (mpp) cc_final: 0.7374 (mpp) REVERT: F 11 ASN cc_start: 0.7664 (t0) cc_final: 0.7203 (p0) REVERT: F 14 ASP cc_start: 0.7457 (m-30) cc_final: 0.6392 (m-30) REVERT: F 17 SER cc_start: 0.8381 (m) cc_final: 0.8115 (t) REVERT: F 20 TYR cc_start: 0.8496 (t80) cc_final: 0.8167 (t80) REVERT: F 43 LYS cc_start: 0.8360 (mttt) cc_final: 0.8152 (mttp) REVERT: F 45 MET cc_start: 0.8086 (tpp) cc_final: 0.7654 (mmt) REVERT: F 65 ASP cc_start: 0.7597 (m-30) cc_final: 0.7207 (m-30) REVERT: F 114 SER cc_start: 0.8627 (m) cc_final: 0.8175 (p) REVERT: F 132 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7053 (mp0) REVERT: F 137 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8211 (ttmm) REVERT: F 233 TYR cc_start: 0.7376 (p90) cc_final: 0.6742 (p90) REVERT: F 296 SER cc_start: 0.8868 (m) cc_final: 0.8448 (t) REVERT: F 317 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8112 (mt) REVERT: F 363 PHE cc_start: 0.8696 (m-80) cc_final: 0.8402 (m-80) REVERT: G 51 SER cc_start: 0.8480 (m) cc_final: 0.8184 (p) REVERT: G 77 ASN cc_start: 0.8426 (t0) cc_final: 0.8222 (t0) REVERT: G 105 GLU cc_start: 0.7508 (tt0) cc_final: 0.7281 (tt0) REVERT: G 107 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7720 (tm-30) REVERT: G 200 ASN cc_start: 0.8399 (m110) cc_final: 0.8026 (m-40) REVERT: G 202 ASP cc_start: 0.7640 (m-30) cc_final: 0.7399 (m-30) REVERT: G 225 LYS cc_start: 0.8652 (mttt) cc_final: 0.8411 (mtpt) REVERT: G 255 ASP cc_start: 0.7707 (t0) cc_final: 0.7420 (t0) REVERT: G 275 LYS cc_start: 0.8183 (mttt) cc_final: 0.7973 (mtpp) REVERT: G 353 LYS cc_start: 0.8516 (mttt) cc_final: 0.8138 (mttt) REVERT: G 403 ILE cc_start: 0.8162 (mt) cc_final: 0.7844 (tp) REVERT: H 43 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7995 (mtmm) REVERT: H 46 LYS cc_start: 0.8007 (mttt) cc_final: 0.7803 (mtpp) REVERT: H 107 GLU cc_start: 0.8169 (tp30) cc_final: 0.7756 (tp30) REVERT: H 110 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8255 (ttmm) REVERT: H 118 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7479 (mm-30) REVERT: H 286 GLU cc_start: 0.7975 (tp30) cc_final: 0.7722 (tp30) REVERT: H 388 VAL cc_start: 0.8563 (p) cc_final: 0.8282 (m) REVERT: I 65 ASP cc_start: 0.8036 (m-30) cc_final: 0.7834 (m-30) REVERT: I 74 ASP cc_start: 0.7761 (m-30) cc_final: 0.7528 (m-30) REVERT: I 76 ASP cc_start: 0.7585 (m-30) cc_final: 0.7021 (m-30) REVERT: I 80 VAL cc_start: 0.8767 (t) cc_final: 0.8565 (p) REVERT: I 142 LYS cc_start: 0.8857 (tttt) cc_final: 0.8638 (ttmt) REVERT: I 288 PHE cc_start: 0.8401 (t80) cc_final: 0.8087 (m-80) REVERT: I 342 LYS cc_start: 0.8326 (mttt) cc_final: 0.8110 (mtpp) REVERT: J 17 SER cc_start: 0.8084 (m) cc_final: 0.7842 (t) REVERT: J 99 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7245 (ttm-80) REVERT: J 185 PHE cc_start: 0.8725 (m-80) cc_final: 0.8376 (m-80) REVERT: J 202 ASP cc_start: 0.7995 (m-30) cc_final: 0.7771 (m-30) REVERT: J 233 TYR cc_start: 0.7911 (p90) cc_final: 0.7603 (p90) REVERT: J 300 THR cc_start: 0.8840 (m) cc_final: 0.8517 (p) REVERT: K 14 ASP cc_start: 0.6982 (m-30) cc_final: 0.6591 (m-30) REVERT: K 68 LEU cc_start: 0.8944 (mp) cc_final: 0.8729 (mt) REVERT: K 131 ARG cc_start: 0.8449 (ptm-80) cc_final: 0.7924 (ptm-80) REVERT: K 250 ASP cc_start: 0.7823 (m-30) cc_final: 0.7589 (m-30) REVERT: K 262 PHE cc_start: 0.8526 (t80) cc_final: 0.8290 (t80) REVERT: K 379 SER cc_start: 0.8804 (m) cc_final: 0.8259 (t) REVERT: L 63 LEU cc_start: 0.8043 (tp) cc_final: 0.7673 (tp) REVERT: L 142 LYS cc_start: 0.8525 (tttm) cc_final: 0.8241 (tttp) REVERT: L 233 TYR cc_start: 0.8068 (p90) cc_final: 0.7770 (p90) REVERT: L 293 GLU cc_start: 0.7711 (tt0) cc_final: 0.7469 (tt0) REVERT: L 374 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8326 (mtmt) REVERT: M 50 ASP cc_start: 0.8129 (m-30) cc_final: 0.7772 (m-30) REVERT: M 93 GLN cc_start: 0.8433 (mt0) cc_final: 0.8191 (mm-40) REVERT: M 191 THR cc_start: 0.8090 (m) cc_final: 0.7822 (p) REVERT: M 196 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7662 (mt-10) REVERT: M 254 LYS cc_start: 0.8879 (tttp) cc_final: 0.8551 (tttm) REVERT: M 271 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7579 (ttm-80) REVERT: M 318 ASN cc_start: 0.8454 (t0) cc_final: 0.8144 (t0) REVERT: M 327 ASP cc_start: 0.8211 (t0) cc_final: 0.7927 (t0) REVERT: M 444 ASP cc_start: 0.7845 (m-30) cc_final: 0.7516 (m-30) REVERT: M 478 GLU cc_start: 0.8113 (mp0) cc_final: 0.7780 (mp0) REVERT: M 528 MET cc_start: 0.8022 (mtp) cc_final: 0.7749 (mtp) REVERT: M 574 SER cc_start: 0.8338 (p) cc_final: 0.8015 (t) REVERT: M 599 SER cc_start: 0.7734 (p) cc_final: 0.7164 (m) REVERT: N 19 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7371 (mt-10) REVERT: N 29 GLU cc_start: 0.6871 (mp0) cc_final: 0.6410 (mp0) REVERT: N 187 ASN cc_start: 0.8676 (m110) cc_final: 0.8318 (m110) REVERT: N 249 GLU cc_start: 0.7066 (pt0) cc_final: 0.6818 (pm20) REVERT: N 271 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7257 (mtt180) REVERT: N 291 THR cc_start: 0.9019 (m) cc_final: 0.8720 (p) REVERT: N 301 GLU cc_start: 0.7655 (tt0) cc_final: 0.7265 (tt0) REVERT: N 336 ARG cc_start: 0.8324 (ptp90) cc_final: 0.8053 (mtm-85) REVERT: N 355 CYS cc_start: 0.7606 (p) cc_final: 0.7332 (p) REVERT: N 383 GLN cc_start: 0.8011 (mt0) cc_final: 0.7770 (mm-40) REVERT: N 394 VAL cc_start: 0.8932 (t) cc_final: 0.8508 (p) REVERT: N 401 GLU cc_start: 0.7168 (mp0) cc_final: 0.6913 (mp0) REVERT: N 427 GLN cc_start: 0.7916 (mp10) cc_final: 0.7593 (mp10) REVERT: N 478 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7783 (mm-30) REVERT: N 506 LYS cc_start: 0.8590 (mttm) cc_final: 0.8383 (mtpp) REVERT: N 559 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8273 (mtmm) REVERT: O 171 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7266 (mmm-85) REVERT: O 308 PHE cc_start: 0.7632 (t80) cc_final: 0.7393 (t80) REVERT: O 326 LEU cc_start: 0.7660 (mt) cc_final: 0.7402 (mt) REVERT: O 373 ASN cc_start: 0.7460 (m-40) cc_final: 0.7254 (m-40) REVERT: O 383 GLN cc_start: 0.7895 (mm110) cc_final: 0.7671 (mm110) REVERT: O 391 LYS cc_start: 0.7940 (tttp) cc_final: 0.7630 (ttpp) REVERT: O 517 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7999 (ttm-80) REVERT: O 559 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8557 (mtpp) REVERT: P 19 GLU cc_start: 0.7298 (mp0) cc_final: 0.7002 (mp0) REVERT: P 50 ASP cc_start: 0.7951 (m-30) cc_final: 0.7713 (m-30) REVERT: P 55 ASP cc_start: 0.8006 (p0) cc_final: 0.7736 (p0) REVERT: P 153 ASP cc_start: 0.7621 (p0) cc_final: 0.7350 (p0) REVERT: P 166 ASP cc_start: 0.8025 (t70) cc_final: 0.7684 (t70) REVERT: P 241 GLN cc_start: 0.8040 (mp10) cc_final: 0.7620 (mp10) REVERT: P 266 LEU cc_start: 0.7165 (mt) cc_final: 0.6962 (mt) REVERT: P 283 ASN cc_start: 0.8402 (m-40) cc_final: 0.8191 (m110) REVERT: P 349 LEU cc_start: 0.8936 (mm) cc_final: 0.8685 (mt) REVERT: P 401 GLU cc_start: 0.7973 (mp0) cc_final: 0.7703 (mp0) REVERT: P 411 LYS cc_start: 0.7524 (mtmt) cc_final: 0.7274 (mtmt) REVERT: P 423 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7963 (mtmm) REVERT: P 444 ASP cc_start: 0.7222 (t0) cc_final: 0.6857 (t0) REVERT: P 459 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7604 (mm-30) REVERT: P 528 MET cc_start: 0.8473 (mmt) cc_final: 0.8223 (mmm) REVERT: Q 67 ASP cc_start: 0.7704 (m-30) cc_final: 0.7444 (m-30) REVERT: Q 104 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7415 (ttm170) REVERT: Q 140 ASP cc_start: 0.6160 (p0) cc_final: 0.5514 (p0) REVERT: Q 209 ASN cc_start: 0.8599 (m110) cc_final: 0.8031 (m-40) REVERT: Q 211 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7461 (mt-10) REVERT: Q 268 LYS cc_start: 0.8777 (tttm) cc_final: 0.8540 (ttmm) REVERT: Q 283 ASN cc_start: 0.8963 (m-40) cc_final: 0.8546 (m-40) REVERT: Q 293 PHE cc_start: 0.8426 (t80) cc_final: 0.8121 (t80) REVERT: Q 297 ASN cc_start: 0.6817 (t0) cc_final: 0.6504 (t0) REVERT: Q 306 GLU cc_start: 0.7488 (tm-30) cc_final: 0.6920 (tm-30) REVERT: Q 308 PHE cc_start: 0.7793 (t80) cc_final: 0.7322 (t80) REVERT: Q 311 TYR cc_start: 0.6730 (m-80) cc_final: 0.6525 (m-80) REVERT: Q 327 ASP cc_start: 0.7483 (t0) cc_final: 0.7182 (t0) REVERT: Q 402 LEU cc_start: 0.7860 (mp) cc_final: 0.6452 (mp) REVERT: Q 416 GLU cc_start: 0.8054 (tp30) cc_final: 0.7820 (tp30) REVERT: Q 544 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7792 (tp-100) REVERT: Q 601 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7934 (mt-10) REVERT: R 140 ASP cc_start: 0.6420 (m-30) cc_final: 0.6154 (m-30) REVERT: R 160 LYS cc_start: 0.8156 (mppt) cc_final: 0.7818 (mppt) REVERT: R 189 LEU cc_start: 0.8629 (mp) cc_final: 0.8363 (mm) REVERT: R 192 ARG cc_start: 0.7446 (tpp80) cc_final: 0.6263 (tpp80) REVERT: R 245 LEU cc_start: 0.7056 (pp) cc_final: 0.6636 (mp) REVERT: R 294 LYS cc_start: 0.8180 (tppt) cc_final: 0.7443 (mptt) REVERT: R 418 ASP cc_start: 0.7690 (t70) cc_final: 0.7317 (t70) REVERT: R 423 LYS cc_start: 0.8512 (mptt) cc_final: 0.7905 (mmtm) REVERT: R 427 GLN cc_start: 0.7233 (tt0) cc_final: 0.6910 (tt0) REVERT: R 508 LYS cc_start: 0.7945 (mttp) cc_final: 0.7718 (mttp) REVERT: R 559 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8011 (mtmt) outliers start: 81 outliers final: 53 residues processed: 1710 average time/residue: 0.6379 time to fit residues: 1782.8101 Evaluate side-chains 1681 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 1626 time to evaluate : 5.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 234 GLN Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 353 PHE Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 401 optimal weight: 0.0470 chunk 224 optimal weight: 0.7980 chunk 601 optimal weight: 0.7980 chunk 492 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 724 optimal weight: 4.9990 chunk 782 optimal weight: 0.9980 chunk 644 optimal weight: 1.9990 chunk 718 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 580 optimal weight: 7.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN E 200 ASN F 324 ASN ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 365 GLN J 183 GLN J 328 HIS ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 GLN O 221 ASN P 434 HIS Q 443 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 66064 Z= 0.177 Angle : 0.513 14.511 89371 Z= 0.263 Chirality : 0.041 0.246 9710 Planarity : 0.003 0.051 11449 Dihedral : 9.101 165.676 9438 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.75 % Allowed : 10.88 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.09), residues: 7933 helix: 0.94 (0.10), residues: 3098 sheet: 0.91 (0.17), residues: 1003 loop : -1.48 (0.09), residues: 3832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 409 HIS 0.005 0.001 HIS Q 434 PHE 0.020 0.001 PHE G 380 TYR 0.024 0.001 TYR R 258 ARG 0.009 0.000 ARG Q 499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1741 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1621 time to evaluate : 5.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8034 (m-30) cc_final: 0.7830 (m-30) REVERT: A 58 GLU cc_start: 0.7604 (mp0) cc_final: 0.7272 (mp0) REVERT: A 74 ASP cc_start: 0.7990 (m-30) cc_final: 0.7660 (m-30) REVERT: A 80 VAL cc_start: 0.8921 (t) cc_final: 0.8619 (p) REVERT: A 128 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 139 ASP cc_start: 0.7884 (t0) cc_final: 0.7506 (t0) REVERT: A 159 GLN cc_start: 0.8455 (mt0) cc_final: 0.8203 (mt0) REVERT: A 179 ASP cc_start: 0.8229 (t70) cc_final: 0.7996 (t70) REVERT: A 352 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7038 (mt-10) REVERT: B 70 VAL cc_start: 0.8723 (t) cc_final: 0.8444 (m) REVERT: B 97 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8245 (ttmt) REVERT: B 102 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7422 (mm-30) REVERT: B 121 LYS cc_start: 0.8590 (mtmt) cc_final: 0.8386 (ttmt) REVERT: B 132 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7454 (mp0) REVERT: B 179 ASP cc_start: 0.8321 (t0) cc_final: 0.8062 (t0) REVERT: B 233 TYR cc_start: 0.8040 (p90) cc_final: 0.7702 (p90) REVERT: B 240 VAL cc_start: 0.8777 (t) cc_final: 0.8527 (t) REVERT: B 257 ILE cc_start: 0.8417 (mm) cc_final: 0.8093 (mt) REVERT: B 258 ASN cc_start: 0.8125 (m-40) cc_final: 0.7662 (m-40) REVERT: B 374 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8328 (mttp) REVERT: B 382 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7613 (tp30) REVERT: C 16 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7413 (mtt90) REVERT: C 58 GLU cc_start: 0.7861 (pm20) cc_final: 0.7611 (pm20) REVERT: C 88 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7497 (mm-30) REVERT: C 132 GLU cc_start: 0.7733 (mp0) cc_final: 0.7331 (mp0) REVERT: C 286 GLU cc_start: 0.8117 (tp30) cc_final: 0.7897 (tp30) REVERT: C 316 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7541 (ttp-170) REVERT: C 361 MET cc_start: 0.8076 (mmm) cc_final: 0.7788 (tpp) REVERT: D 24 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8369 (mp10) REVERT: D 109 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7386 (mtt-85) REVERT: D 129 GLN cc_start: 0.8240 (mm110) cc_final: 0.7893 (mm110) REVERT: D 131 ARG cc_start: 0.8356 (ptm-80) cc_final: 0.8090 (ptm160) REVERT: D 182 ILE cc_start: 0.8519 (mm) cc_final: 0.8114 (mt) REVERT: D 203 LEU cc_start: 0.8531 (mp) cc_final: 0.8315 (mt) REVERT: D 238 LEU cc_start: 0.4852 (OUTLIER) cc_final: 0.4576 (tt) REVERT: D 290 ARG cc_start: 0.8155 (mmt180) cc_final: 0.7891 (mmt-90) REVERT: D 374 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8456 (mtmm) REVERT: E 77 ASN cc_start: 0.7572 (m-40) cc_final: 0.7319 (m-40) REVERT: E 79 LEU cc_start: 0.8711 (mm) cc_final: 0.8472 (mm) REVERT: E 99 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8323 (ttp-170) REVERT: E 118 GLU cc_start: 0.8054 (tp30) cc_final: 0.7805 (tp30) REVERT: E 133 LYS cc_start: 0.8633 (mttm) cc_final: 0.8410 (mttt) REVERT: E 300 THR cc_start: 0.8280 (m) cc_final: 0.8059 (p) REVERT: E 361 MET cc_start: 0.7718 (mpp) cc_final: 0.7244 (mpp) REVERT: E 405 ASN cc_start: 0.7988 (t0) cc_final: 0.7695 (t0) REVERT: F 11 ASN cc_start: 0.7643 (t0) cc_final: 0.7052 (p0) REVERT: F 14 ASP cc_start: 0.7437 (m-30) cc_final: 0.6249 (m-30) REVERT: F 17 SER cc_start: 0.8379 (m) cc_final: 0.8075 (t) REVERT: F 20 TYR cc_start: 0.8578 (t80) cc_final: 0.8225 (t80) REVERT: F 45 MET cc_start: 0.8170 (tpp) cc_final: 0.7711 (mmt) REVERT: F 65 ASP cc_start: 0.7542 (m-30) cc_final: 0.7228 (m-30) REVERT: F 76 ASP cc_start: 0.7103 (m-30) cc_final: 0.6517 (m-30) REVERT: F 114 SER cc_start: 0.8656 (m) cc_final: 0.8172 (p) REVERT: F 137 LYS cc_start: 0.8433 (ttmt) cc_final: 0.8164 (ttmm) REVERT: F 233 TYR cc_start: 0.7419 (p90) cc_final: 0.6775 (p90) REVERT: F 296 SER cc_start: 0.8869 (m) cc_final: 0.8467 (t) REVERT: F 317 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8138 (mt) REVERT: F 363 PHE cc_start: 0.8793 (m-80) cc_final: 0.8443 (m-80) REVERT: G 51 SER cc_start: 0.8569 (m) cc_final: 0.8161 (p) REVERT: G 53 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7654 (mttt) REVERT: G 77 ASN cc_start: 0.8335 (t0) cc_final: 0.8129 (t0) REVERT: G 107 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7547 (tm-30) REVERT: G 117 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8278 (tttm) REVERT: G 191 LEU cc_start: 0.8350 (tp) cc_final: 0.8107 (tp) REVERT: G 199 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8205 (mt0) REVERT: G 200 ASN cc_start: 0.8395 (m110) cc_final: 0.8044 (m-40) REVERT: G 202 ASP cc_start: 0.7666 (m-30) cc_final: 0.7452 (m-30) REVERT: G 255 ASP cc_start: 0.7801 (t0) cc_final: 0.7416 (t0) REVERT: G 275 LYS cc_start: 0.8261 (mttt) cc_final: 0.8033 (mtpp) REVERT: G 337 LYS cc_start: 0.7832 (ptpt) cc_final: 0.7614 (ptpt) REVERT: G 338 GLU cc_start: 0.7710 (mp0) cc_final: 0.7505 (mp0) REVERT: G 353 LYS cc_start: 0.8552 (mttt) cc_final: 0.8239 (mttt) REVERT: G 403 ILE cc_start: 0.8186 (mt) cc_final: 0.7854 (tp) REVERT: H 43 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7900 (mttm) REVERT: H 46 LYS cc_start: 0.8080 (mttt) cc_final: 0.7843 (mtpp) REVERT: H 107 GLU cc_start: 0.8163 (tp30) cc_final: 0.7903 (tt0) REVERT: H 110 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8233 (ttmm) REVERT: H 202 ASP cc_start: 0.8633 (m-30) cc_final: 0.7799 (m-30) REVERT: H 286 GLU cc_start: 0.7946 (tp30) cc_final: 0.7692 (tp30) REVERT: H 388 VAL cc_start: 0.8578 (p) cc_final: 0.8306 (m) REVERT: I 65 ASP cc_start: 0.8025 (m-30) cc_final: 0.7807 (m-30) REVERT: I 74 ASP cc_start: 0.7737 (m-30) cc_final: 0.7430 (m-30) REVERT: I 76 ASP cc_start: 0.7620 (m-30) cc_final: 0.7030 (m-30) REVERT: I 80 VAL cc_start: 0.8784 (t) cc_final: 0.8566 (p) REVERT: I 142 LYS cc_start: 0.8879 (tttt) cc_final: 0.8607 (ttmt) REVERT: J 17 SER cc_start: 0.8051 (m) cc_final: 0.7794 (t) REVERT: J 74 ASP cc_start: 0.7723 (m-30) cc_final: 0.7392 (t0) REVERT: J 99 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7119 (ttm-80) REVERT: J 185 PHE cc_start: 0.8721 (m-80) cc_final: 0.8490 (m-80) REVERT: J 233 TYR cc_start: 0.7868 (p90) cc_final: 0.7602 (p90) REVERT: J 300 THR cc_start: 0.8896 (m) cc_final: 0.8566 (p) REVERT: K 14 ASP cc_start: 0.7035 (m-30) cc_final: 0.6668 (m-30) REVERT: K 45 MET cc_start: 0.7172 (mmm) cc_final: 0.6883 (mmp) REVERT: K 68 LEU cc_start: 0.8963 (mp) cc_final: 0.8749 (mt) REVERT: K 379 SER cc_start: 0.8805 (m) cc_final: 0.8291 (t) REVERT: L 63 LEU cc_start: 0.8008 (tp) cc_final: 0.7606 (tp) REVERT: L 142 LYS cc_start: 0.8523 (tttm) cc_final: 0.8310 (tttm) REVERT: L 233 TYR cc_start: 0.8085 (p90) cc_final: 0.7820 (p90) REVERT: L 293 GLU cc_start: 0.7702 (tt0) cc_final: 0.7451 (tt0) REVERT: L 374 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8351 (mtmm) REVERT: M 50 ASP cc_start: 0.8155 (m-30) cc_final: 0.7735 (m-30) REVERT: M 271 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7590 (ttm-80) REVERT: M 318 ASN cc_start: 0.8474 (t0) cc_final: 0.8150 (t0) REVERT: M 327 ASP cc_start: 0.8011 (t0) cc_final: 0.7715 (t0) REVERT: M 444 ASP cc_start: 0.7916 (m-30) cc_final: 0.7648 (m-30) REVERT: M 478 GLU cc_start: 0.8084 (mp0) cc_final: 0.7775 (mp0) REVERT: M 503 GLU cc_start: 0.7802 (mp0) cc_final: 0.7332 (mp0) REVERT: M 574 SER cc_start: 0.8316 (p) cc_final: 0.8005 (t) REVERT: M 599 SER cc_start: 0.7750 (p) cc_final: 0.7173 (m) REVERT: N 19 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7313 (mt-10) REVERT: N 249 GLU cc_start: 0.7117 (pt0) cc_final: 0.6709 (pm20) REVERT: N 271 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7285 (mtt180) REVERT: N 291 THR cc_start: 0.9066 (m) cc_final: 0.8766 (p) REVERT: N 301 GLU cc_start: 0.7661 (tt0) cc_final: 0.7248 (tt0) REVERT: N 315 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.7217 (mtt180) REVERT: N 336 ARG cc_start: 0.8359 (ptp90) cc_final: 0.8065 (mtm-85) REVERT: N 355 CYS cc_start: 0.7702 (p) cc_final: 0.7347 (p) REVERT: N 383 GLN cc_start: 0.7978 (mt0) cc_final: 0.7749 (mm-40) REVERT: N 394 VAL cc_start: 0.8903 (t) cc_final: 0.8469 (p) REVERT: N 401 GLU cc_start: 0.7196 (mp0) cc_final: 0.6935 (mp0) REVERT: N 427 GLN cc_start: 0.7921 (mp10) cc_final: 0.7687 (mp10) REVERT: N 478 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7752 (mm-30) REVERT: N 506 LYS cc_start: 0.8614 (mttm) cc_final: 0.8295 (mtpp) REVERT: N 559 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8248 (mtmm) REVERT: O 68 MET cc_start: 0.8809 (mtp) cc_final: 0.8601 (mtp) REVERT: O 107 ASN cc_start: 0.7557 (t0) cc_final: 0.7344 (t0) REVERT: O 115 ASP cc_start: 0.8089 (p0) cc_final: 0.7463 (p0) REVERT: O 171 ARG cc_start: 0.7566 (mmm-85) cc_final: 0.7252 (mmm-85) REVERT: O 249 GLU cc_start: 0.7922 (pm20) cc_final: 0.7623 (pm20) REVERT: O 299 TYR cc_start: 0.8397 (p90) cc_final: 0.7962 (p90) REVERT: O 308 PHE cc_start: 0.7523 (t80) cc_final: 0.7282 (t80) REVERT: O 391 LYS cc_start: 0.7950 (tttp) cc_final: 0.7627 (ttpp) REVERT: O 517 ARG cc_start: 0.8313 (mtp85) cc_final: 0.8013 (ttm-80) REVERT: O 559 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8537 (mtpp) REVERT: P 19 GLU cc_start: 0.7345 (mp0) cc_final: 0.7049 (mp0) REVERT: P 50 ASP cc_start: 0.7921 (m-30) cc_final: 0.7702 (m-30) REVERT: P 55 ASP cc_start: 0.7967 (p0) cc_final: 0.7702 (p0) REVERT: P 153 ASP cc_start: 0.7626 (p0) cc_final: 0.7348 (p0) REVERT: P 241 GLN cc_start: 0.7964 (mp10) cc_final: 0.7612 (mp-120) REVERT: P 283 ASN cc_start: 0.8447 (m-40) cc_final: 0.8182 (m110) REVERT: P 349 LEU cc_start: 0.8967 (mm) cc_final: 0.8710 (mt) REVERT: P 401 GLU cc_start: 0.7985 (mp0) cc_final: 0.7725 (mp0) REVERT: P 411 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7316 (mtmt) REVERT: P 413 MET cc_start: 0.7705 (ttm) cc_final: 0.7427 (ttm) REVERT: P 423 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7934 (mtmm) REVERT: P 444 ASP cc_start: 0.7258 (t0) cc_final: 0.6888 (t0) REVERT: P 459 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7601 (mm-30) REVERT: P 528 MET cc_start: 0.8512 (mmt) cc_final: 0.8266 (mmm) REVERT: P 559 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8194 (mtmm) REVERT: Q 67 ASP cc_start: 0.7686 (m-30) cc_final: 0.7433 (m-30) REVERT: Q 104 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7524 (ttm170) REVERT: Q 140 ASP cc_start: 0.6115 (p0) cc_final: 0.5533 (p0) REVERT: Q 209 ASN cc_start: 0.8597 (m110) cc_final: 0.8043 (m-40) REVERT: Q 211 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7486 (mt-10) REVERT: Q 244 GLU cc_start: 0.7236 (pt0) cc_final: 0.6826 (pt0) REVERT: Q 268 LYS cc_start: 0.8817 (tttm) cc_final: 0.8573 (ttmm) REVERT: Q 283 ASN cc_start: 0.8960 (m-40) cc_final: 0.8557 (m-40) REVERT: Q 297 ASN cc_start: 0.6891 (t0) cc_final: 0.6525 (t0) REVERT: Q 306 GLU cc_start: 0.7528 (tm-30) cc_final: 0.6948 (tm-30) REVERT: Q 308 PHE cc_start: 0.7759 (t80) cc_final: 0.7187 (t80) REVERT: Q 327 ASP cc_start: 0.7405 (t0) cc_final: 0.7167 (t0) REVERT: Q 416 GLU cc_start: 0.8056 (tp30) cc_final: 0.7780 (tp30) REVERT: Q 417 VAL cc_start: 0.8553 (t) cc_final: 0.8328 (p) REVERT: Q 459 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8157 (mm-30) REVERT: Q 544 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7859 (tm-30) REVERT: R 140 ASP cc_start: 0.6353 (m-30) cc_final: 0.6113 (m-30) REVERT: R 158 THR cc_start: 0.6770 (p) cc_final: 0.6374 (p) REVERT: R 160 LYS cc_start: 0.8096 (mppt) cc_final: 0.7784 (mppt) REVERT: R 192 ARG cc_start: 0.7439 (tpp80) cc_final: 0.6219 (tpp80) REVERT: R 198 TYR cc_start: 0.8864 (m-80) cc_final: 0.8508 (m-80) REVERT: R 240 GLN cc_start: 0.8039 (mp10) cc_final: 0.7752 (mt0) REVERT: R 244 GLU cc_start: 0.8312 (pp20) cc_final: 0.8108 (pp20) REVERT: R 245 LEU cc_start: 0.7354 (pp) cc_final: 0.6814 (mp) REVERT: R 418 ASP cc_start: 0.7743 (t70) cc_final: 0.7403 (t70) REVERT: R 423 LYS cc_start: 0.8433 (mptt) cc_final: 0.7875 (mmtm) REVERT: R 427 GLN cc_start: 0.7183 (tt0) cc_final: 0.6899 (tt0) REVERT: R 439 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7460 (pttp) REVERT: R 508 LYS cc_start: 0.7946 (mttp) cc_final: 0.7715 (mttp) REVERT: R 559 LYS cc_start: 0.8523 (mtmt) cc_final: 0.7984 (mtmt) REVERT: R 578 LEU cc_start: 0.7749 (tt) cc_final: 0.7510 (mp) outliers start: 120 outliers final: 87 residues processed: 1663 average time/residue: 0.6471 time to fit residues: 1755.5948 Evaluate side-chains 1668 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1577 time to evaluate : 5.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 374 LYS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 515 THR Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 477 GLU Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 313 ASP Chi-restraints excluded: chain O residue 353 PHE Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 297 ASN Chi-restraints excluded: chain P residue 348 THR Chi-restraints excluded: chain P residue 380 ILE Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 515 THR Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain R residue 439 LYS Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 715 optimal weight: 2.9990 chunk 544 optimal weight: 2.9990 chunk 375 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 345 optimal weight: 3.9990 chunk 486 optimal weight: 5.9990 chunk 726 optimal weight: 0.8980 chunk 769 optimal weight: 20.0000 chunk 379 optimal weight: 2.9990 chunk 688 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN D 313 HIS E 129 GLN E 195 GLN F 324 ASN ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN H 364 ASN I 77 ASN K 78 ASN P 434 HIS Q 47 GLN R 277 GLN R 318 ASN ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 66064 Z= 0.434 Angle : 0.643 19.348 89371 Z= 0.332 Chirality : 0.047 0.181 9710 Planarity : 0.004 0.057 11449 Dihedral : 9.285 163.327 9438 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.41 % Allowed : 12.22 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.09), residues: 7933 helix: 0.66 (0.10), residues: 3115 sheet: 0.75 (0.16), residues: 1010 loop : -1.72 (0.09), residues: 3808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 325 HIS 0.013 0.002 HIS J 227 PHE 0.022 0.002 PHE M 70 TYR 0.026 0.002 TYR R 258 ARG 0.016 0.001 ARG N 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1824 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 1659 time to evaluate : 5.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8072 (m-30) cc_final: 0.7684 (m-30) REVERT: A 58 GLU cc_start: 0.7699 (mp0) cc_final: 0.7363 (mp0) REVERT: A 74 ASP cc_start: 0.7985 (m-30) cc_final: 0.7654 (m-30) REVERT: B 67 TYR cc_start: 0.8548 (m-80) cc_final: 0.8227 (m-80) REVERT: B 70 VAL cc_start: 0.8804 (t) cc_final: 0.8537 (m) REVERT: B 97 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8289 (ttmt) REVERT: B 102 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7636 (mm-30) REVERT: B 132 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7589 (mp0) REVERT: B 179 ASP cc_start: 0.8290 (t0) cc_final: 0.8069 (t0) REVERT: B 240 VAL cc_start: 0.8762 (t) cc_final: 0.8549 (t) REVERT: B 257 ILE cc_start: 0.8521 (mm) cc_final: 0.8231 (mt) REVERT: B 258 ASN cc_start: 0.8347 (m-40) cc_final: 0.7910 (m-40) REVERT: B 374 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8318 (mttp) REVERT: B 382 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7599 (tp30) REVERT: C 58 GLU cc_start: 0.7923 (pm20) cc_final: 0.7585 (pm20) REVERT: C 88 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7611 (mm-30) REVERT: C 97 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8082 (ttmm) REVERT: C 102 GLU cc_start: 0.8020 (tp30) cc_final: 0.7776 (tp30) REVERT: C 104 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7509 (mm-30) REVERT: C 146 GLU cc_start: 0.7639 (tt0) cc_final: 0.7167 (tt0) REVERT: C 286 GLU cc_start: 0.8192 (tp30) cc_final: 0.7933 (tp30) REVERT: C 290 ARG cc_start: 0.8871 (mmt180) cc_final: 0.8596 (mmt180) REVERT: C 316 ARG cc_start: 0.7767 (ttp-170) cc_final: 0.7552 (ttp-170) REVERT: C 386 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.6775 (m-80) REVERT: D 109 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7393 (mtt-85) REVERT: D 128 GLU cc_start: 0.8043 (mp0) cc_final: 0.7787 (mp0) REVERT: D 129 GLN cc_start: 0.8393 (mm110) cc_final: 0.8094 (mm-40) REVERT: D 131 ARG cc_start: 0.8397 (ptm-80) cc_final: 0.8135 (ptm160) REVERT: D 132 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7492 (mm-30) REVERT: D 182 ILE cc_start: 0.8639 (mm) cc_final: 0.8376 (mt) REVERT: D 203 LEU cc_start: 0.8523 (mp) cc_final: 0.8301 (mt) REVERT: D 238 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4697 (tt) REVERT: D 352 GLU cc_start: 0.7273 (mp0) cc_final: 0.7019 (mp0) REVERT: E 77 ASN cc_start: 0.7767 (m-40) cc_final: 0.7509 (m-40) REVERT: E 79 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8353 (mm) REVERT: E 84 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8588 (mp) REVERT: E 99 ARG cc_start: 0.8902 (ttm-80) cc_final: 0.8660 (ttp-170) REVERT: E 118 GLU cc_start: 0.8113 (tp30) cc_final: 0.7900 (tp30) REVERT: E 195 GLN cc_start: 0.7993 (mm110) cc_final: 0.7763 (mm-40) REVERT: E 257 ILE cc_start: 0.8614 (mm) cc_final: 0.8392 (mt) REVERT: E 405 ASN cc_start: 0.8070 (t0) cc_final: 0.7818 (t0) REVERT: F 11 ASN cc_start: 0.7684 (t0) cc_final: 0.7082 (p0) REVERT: F 14 ASP cc_start: 0.7429 (m-30) cc_final: 0.6261 (m-30) REVERT: F 17 SER cc_start: 0.8369 (m) cc_final: 0.8075 (t) REVERT: F 45 MET cc_start: 0.8475 (tpp) cc_final: 0.7996 (mmt) REVERT: F 65 ASP cc_start: 0.7609 (m-30) cc_final: 0.7272 (m-30) REVERT: F 76 ASP cc_start: 0.7241 (m-30) cc_final: 0.6678 (m-30) REVERT: F 114 SER cc_start: 0.8728 (m) cc_final: 0.8182 (p) REVERT: F 137 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8274 (ttmm) REVERT: F 154 ASN cc_start: 0.7633 (m-40) cc_final: 0.7259 (m110) REVERT: F 233 TYR cc_start: 0.7689 (p90) cc_final: 0.6992 (p90) REVERT: F 296 SER cc_start: 0.9008 (m) cc_final: 0.8600 (t) REVERT: G 74 ASP cc_start: 0.7572 (m-30) cc_final: 0.7234 (t0) REVERT: G 102 GLU cc_start: 0.7222 (mp0) cc_final: 0.7013 (mp0) REVERT: G 117 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8353 (tttm) REVERT: G 133 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8449 (mtmt) REVERT: G 199 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8282 (mt0) REVERT: G 202 ASP cc_start: 0.7772 (m-30) cc_final: 0.7562 (m-30) REVERT: G 255 ASP cc_start: 0.7732 (t0) cc_final: 0.7276 (t0) REVERT: G 275 LYS cc_start: 0.8476 (mttt) cc_final: 0.8211 (mtpp) REVERT: G 353 LYS cc_start: 0.8515 (mttt) cc_final: 0.8238 (mttt) REVERT: G 403 ILE cc_start: 0.8242 (mt) cc_final: 0.7887 (tp) REVERT: G 405 ASN cc_start: 0.7786 (t0) cc_final: 0.7186 (m110) REVERT: H 43 LYS cc_start: 0.8391 (mtpp) cc_final: 0.8054 (mttp) REVERT: H 46 LYS cc_start: 0.8257 (mttt) cc_final: 0.7956 (mtpp) REVERT: H 59 LEU cc_start: 0.8749 (mt) cc_final: 0.8493 (mm) REVERT: H 110 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8278 (ttmm) REVERT: H 118 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7732 (mm-30) REVERT: H 264 ARG cc_start: 0.6666 (mtt90) cc_final: 0.6315 (mtt90) REVERT: H 286 GLU cc_start: 0.7997 (tp30) cc_final: 0.7695 (tp30) REVERT: H 388 VAL cc_start: 0.8565 (p) cc_final: 0.8290 (m) REVERT: I 65 ASP cc_start: 0.8068 (m-30) cc_final: 0.7796 (m-30) REVERT: I 74 ASP cc_start: 0.7763 (m-30) cc_final: 0.7305 (m-30) REVERT: I 76 ASP cc_start: 0.7628 (m-30) cc_final: 0.7009 (m-30) REVERT: I 77 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7212 (t0) REVERT: I 80 VAL cc_start: 0.8803 (t) cc_final: 0.8570 (p) REVERT: I 142 LYS cc_start: 0.8883 (tttt) cc_final: 0.8611 (ttmt) REVERT: I 251 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7229 (mt-10) REVERT: I 266 GLN cc_start: 0.7856 (pp30) cc_final: 0.7417 (pp30) REVERT: J 17 SER cc_start: 0.8089 (m) cc_final: 0.7836 (t) REVERT: J 74 ASP cc_start: 0.7788 (m-30) cc_final: 0.7450 (t0) REVERT: J 202 ASP cc_start: 0.8155 (m-30) cc_final: 0.7912 (m-30) REVERT: J 233 TYR cc_start: 0.7863 (p90) cc_final: 0.7609 (p90) REVERT: J 300 THR cc_start: 0.8979 (m) cc_final: 0.8698 (p) REVERT: K 14 ASP cc_start: 0.7198 (m-30) cc_final: 0.6765 (m-30) REVERT: K 68 LEU cc_start: 0.8937 (mp) cc_final: 0.8699 (mt) REVERT: K 102 GLU cc_start: 0.7253 (pm20) cc_final: 0.6876 (pm20) REVERT: K 202 ASP cc_start: 0.8491 (m-30) cc_final: 0.8282 (m-30) REVERT: K 255 ASP cc_start: 0.8402 (m-30) cc_final: 0.8200 (m-30) REVERT: K 379 SER cc_start: 0.8795 (m) cc_final: 0.8349 (t) REVERT: K 398 GLU cc_start: 0.7655 (tp30) cc_final: 0.7160 (tp30) REVERT: L 14 ASP cc_start: 0.7512 (m-30) cc_final: 0.7160 (m-30) REVERT: L 54 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: L 63 LEU cc_start: 0.8077 (tp) cc_final: 0.7725 (tp) REVERT: L 116 TYR cc_start: 0.8639 (m-80) cc_final: 0.8270 (m-80) REVERT: L 233 TYR cc_start: 0.8195 (p90) cc_final: 0.7863 (p90) REVERT: L 293 GLU cc_start: 0.7597 (tt0) cc_final: 0.7390 (tt0) REVERT: L 374 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8346 (mtmm) REVERT: M 50 ASP cc_start: 0.8262 (m-30) cc_final: 0.7931 (m-30) REVERT: M 271 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7573 (ttm-80) REVERT: M 318 ASN cc_start: 0.8509 (t0) cc_final: 0.8220 (t0) REVERT: M 327 ASP cc_start: 0.8105 (t0) cc_final: 0.7699 (t0) REVERT: M 444 ASP cc_start: 0.7944 (m-30) cc_final: 0.7739 (m-30) REVERT: M 478 GLU cc_start: 0.8162 (mp0) cc_final: 0.7605 (mp0) REVERT: M 503 GLU cc_start: 0.7742 (mp0) cc_final: 0.7405 (mp0) REVERT: M 574 SER cc_start: 0.8314 (p) cc_final: 0.8026 (t) REVERT: N 29 GLU cc_start: 0.6869 (mp0) cc_final: 0.6661 (mp0) REVERT: N 249 GLU cc_start: 0.7251 (pt0) cc_final: 0.6674 (pm20) REVERT: N 291 THR cc_start: 0.9097 (m) cc_final: 0.8810 (p) REVERT: N 301 GLU cc_start: 0.7754 (tt0) cc_final: 0.7443 (tt0) REVERT: N 336 ARG cc_start: 0.8404 (ptp90) cc_final: 0.8118 (mtm-85) REVERT: N 355 CYS cc_start: 0.8053 (p) cc_final: 0.7805 (p) REVERT: N 383 GLN cc_start: 0.8028 (mt0) cc_final: 0.7770 (mm-40) REVERT: N 394 VAL cc_start: 0.8904 (t) cc_final: 0.8450 (p) REVERT: N 401 GLU cc_start: 0.7239 (mp0) cc_final: 0.7019 (mp0) REVERT: N 427 GLN cc_start: 0.7974 (mp10) cc_final: 0.7656 (mp10) REVERT: N 506 LYS cc_start: 0.8677 (mttm) cc_final: 0.8336 (mtpp) REVERT: N 530 SER cc_start: 0.8882 (m) cc_final: 0.8666 (t) REVERT: O 19 GLU cc_start: 0.7666 (mp0) cc_final: 0.7384 (mp0) REVERT: O 107 ASN cc_start: 0.7871 (t0) cc_final: 0.7550 (t0) REVERT: O 171 ARG cc_start: 0.7716 (mmm-85) cc_final: 0.7410 (mmm-85) REVERT: O 327 ASP cc_start: 0.7962 (t70) cc_final: 0.7736 (t0) REVERT: O 366 ARG cc_start: 0.7847 (ptp-170) cc_final: 0.7598 (ptp-170) REVERT: O 391 LYS cc_start: 0.8046 (tttp) cc_final: 0.7730 (ttpp) REVERT: P 19 GLU cc_start: 0.7438 (mp0) cc_final: 0.7103 (mp0) REVERT: P 50 ASP cc_start: 0.7872 (m-30) cc_final: 0.7655 (m-30) REVERT: P 55 ASP cc_start: 0.7897 (p0) cc_final: 0.7651 (p0) REVERT: P 158 THR cc_start: 0.8787 (p) cc_final: 0.8468 (t) REVERT: P 239 LYS cc_start: 0.8074 (mtmm) cc_final: 0.7429 (tmtt) REVERT: P 283 ASN cc_start: 0.8654 (m-40) cc_final: 0.8294 (m110) REVERT: P 349 LEU cc_start: 0.9007 (mm) cc_final: 0.8749 (mt) REVERT: P 401 GLU cc_start: 0.8037 (mp0) cc_final: 0.7752 (mp0) REVERT: P 411 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7426 (mtmt) REVERT: P 423 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7958 (mtmm) REVERT: P 444 ASP cc_start: 0.7584 (t0) cc_final: 0.7188 (t0) REVERT: P 459 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7712 (mm-30) REVERT: P 517 ARG cc_start: 0.8521 (mmt180) cc_final: 0.8264 (mmt180) REVERT: P 559 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8262 (mtmm) REVERT: Q 67 ASP cc_start: 0.7721 (m-30) cc_final: 0.7452 (m-30) REVERT: Q 104 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7628 (ttm170) REVERT: Q 209 ASN cc_start: 0.8640 (m110) cc_final: 0.8107 (m-40) REVERT: Q 211 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7462 (mt-10) REVERT: Q 268 LYS cc_start: 0.8833 (tttm) cc_final: 0.8571 (ttmm) REVERT: Q 283 ASN cc_start: 0.9053 (m-40) cc_final: 0.8595 (m-40) REVERT: Q 288 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8654 (tt) REVERT: Q 297 ASN cc_start: 0.6938 (t0) cc_final: 0.6580 (t0) REVERT: Q 306 GLU cc_start: 0.7544 (tm-30) cc_final: 0.6948 (tm-30) REVERT: Q 308 PHE cc_start: 0.7805 (t80) cc_final: 0.7270 (t80) REVERT: Q 327 ASP cc_start: 0.7460 (t0) cc_final: 0.7249 (t0) REVERT: Q 477 GLU cc_start: 0.8097 (tp30) cc_final: 0.7857 (tp30) REVERT: Q 544 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7853 (tp-100) REVERT: Q 601 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8039 (tp30) REVERT: R 24 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7403 (mtp85) REVERT: R 140 ASP cc_start: 0.6463 (m-30) cc_final: 0.6229 (m-30) REVERT: R 158 THR cc_start: 0.6939 (p) cc_final: 0.6390 (p) REVERT: R 159 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8240 (t) REVERT: R 160 LYS cc_start: 0.8023 (mppt) cc_final: 0.7759 (mppt) REVERT: R 192 ARG cc_start: 0.7408 (tpp80) cc_final: 0.6119 (tpp80) REVERT: R 198 TYR cc_start: 0.8948 (m-80) cc_final: 0.8726 (m-80) REVERT: R 240 GLN cc_start: 0.8152 (mp10) cc_final: 0.7917 (mt0) REVERT: R 244 GLU cc_start: 0.8368 (pp20) cc_final: 0.8084 (pp20) REVERT: R 245 LEU cc_start: 0.7443 (pp) cc_final: 0.6838 (mt) REVERT: R 418 ASP cc_start: 0.7792 (t70) cc_final: 0.7525 (t70) REVERT: R 423 LYS cc_start: 0.8479 (mptt) cc_final: 0.8170 (mmtm) REVERT: R 508 LYS cc_start: 0.7998 (mttp) cc_final: 0.7759 (mttp) REVERT: R 559 LYS cc_start: 0.8524 (mtmt) cc_final: 0.7957 (mtmt) outliers start: 165 outliers final: 118 residues processed: 1718 average time/residue: 0.6609 time to fit residues: 1842.5323 Evaluate side-chains 1770 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1644 time to evaluate : 5.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 341 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 515 THR Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 248 GLU Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 273 SER Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 326 LEU Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 225 THR Chi-restraints excluded: chain P residue 267 ILE Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 297 ASN Chi-restraints excluded: chain P residue 348 THR Chi-restraints excluded: chain P residue 380 ILE Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain P residue 578 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 416 GLU Chi-restraints excluded: chain R residue 456 MET Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 517 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 640 optimal weight: 0.6980 chunk 436 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 572 optimal weight: 4.9990 chunk 317 optimal weight: 0.9990 chunk 656 optimal weight: 9.9990 chunk 531 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 392 optimal weight: 0.9990 chunk 690 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN C 315 ASN D 234 GLN G 200 ASN H 129 GLN P 382 GLN Q 47 GLN Q 443 GLN R 277 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 66064 Z= 0.163 Angle : 0.520 18.549 89371 Z= 0.266 Chirality : 0.041 0.170 9710 Planarity : 0.004 0.053 11449 Dihedral : 8.929 164.245 9438 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.97 % Allowed : 14.30 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.09), residues: 7933 helix: 0.93 (0.10), residues: 3088 sheet: 0.79 (0.16), residues: 1011 loop : -1.61 (0.09), residues: 3834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 409 HIS 0.004 0.001 HIS D 227 PHE 0.021 0.001 PHE K 262 TYR 0.026 0.001 TYR R 258 ARG 0.008 0.000 ARG P 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1768 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 1633 time to evaluate : 5.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8018 (m-30) cc_final: 0.7632 (m-30) REVERT: A 58 GLU cc_start: 0.7592 (mp0) cc_final: 0.7233 (mp0) REVERT: A 74 ASP cc_start: 0.7994 (m-30) cc_final: 0.7688 (m-30) REVERT: B 67 TYR cc_start: 0.8489 (m-80) cc_final: 0.8214 (m-80) REVERT: B 70 VAL cc_start: 0.8817 (t) cc_final: 0.8535 (m) REVERT: B 97 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8189 (ttmt) REVERT: B 102 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7541 (mm-30) REVERT: B 132 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7406 (mp0) REVERT: B 179 ASP cc_start: 0.8319 (t0) cc_final: 0.8046 (t0) REVERT: B 240 VAL cc_start: 0.8761 (t) cc_final: 0.8532 (t) REVERT: B 257 ILE cc_start: 0.8509 (mm) cc_final: 0.8198 (mt) REVERT: B 258 ASN cc_start: 0.8312 (m-40) cc_final: 0.7853 (m-40) REVERT: B 374 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8300 (mttp) REVERT: B 382 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7612 (tp30) REVERT: C 16 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7763 (mtt90) REVERT: C 58 GLU cc_start: 0.7956 (pm20) cc_final: 0.7626 (pm20) REVERT: C 102 GLU cc_start: 0.7978 (tp30) cc_final: 0.7738 (tp30) REVERT: C 104 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7560 (mm-30) REVERT: C 286 GLU cc_start: 0.8156 (tp30) cc_final: 0.7922 (tp30) REVERT: C 316 ARG cc_start: 0.7759 (ttp-170) cc_final: 0.7550 (ttp-170) REVERT: D 109 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7299 (mtt-85) REVERT: D 128 GLU cc_start: 0.8101 (mp0) cc_final: 0.7857 (mp0) REVERT: D 129 GLN cc_start: 0.8396 (mm110) cc_final: 0.8024 (mm-40) REVERT: D 131 ARG cc_start: 0.8371 (ptm-80) cc_final: 0.8099 (ptm160) REVERT: D 132 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7384 (mm-30) REVERT: D 182 ILE cc_start: 0.8629 (mm) cc_final: 0.8354 (mt) REVERT: D 208 VAL cc_start: 0.8077 (t) cc_final: 0.7875 (m) REVERT: D 238 LEU cc_start: 0.4883 (OUTLIER) cc_final: 0.4599 (tt) REVERT: D 290 ARG cc_start: 0.8185 (mmt-90) cc_final: 0.7845 (mmt-90) REVERT: D 343 VAL cc_start: 0.8251 (t) cc_final: 0.8036 (t) REVERT: E 63 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8264 (tp) REVERT: E 77 ASN cc_start: 0.7642 (m-40) cc_final: 0.7408 (m-40) REVERT: E 79 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8475 (mm) REVERT: E 99 ARG cc_start: 0.8657 (ttm-80) cc_final: 0.8343 (ttp-170) REVERT: E 195 GLN cc_start: 0.7921 (mm110) cc_final: 0.7667 (mm-40) REVERT: E 283 VAL cc_start: 0.7547 (OUTLIER) cc_final: 0.7092 (m) REVERT: E 286 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7674 (tp30) REVERT: E 300 THR cc_start: 0.8427 (m) cc_final: 0.8155 (p) REVERT: E 335 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7305 (mm-30) REVERT: E 405 ASN cc_start: 0.8078 (t0) cc_final: 0.7834 (t0) REVERT: F 17 SER cc_start: 0.8366 (m) cc_final: 0.8057 (t) REVERT: F 45 MET cc_start: 0.8410 (tpp) cc_final: 0.7944 (mmt) REVERT: F 65 ASP cc_start: 0.7595 (m-30) cc_final: 0.7255 (m-30) REVERT: F 76 ASP cc_start: 0.7216 (m-30) cc_final: 0.6617 (m-30) REVERT: F 97 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8536 (ttmm) REVERT: F 114 SER cc_start: 0.8734 (m) cc_final: 0.8205 (p) REVERT: F 137 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8206 (ttmm) REVERT: F 233 TYR cc_start: 0.7592 (p90) cc_final: 0.6924 (p90) REVERT: F 296 SER cc_start: 0.8958 (m) cc_final: 0.8544 (t) REVERT: F 363 PHE cc_start: 0.8917 (m-80) cc_final: 0.8478 (m-80) REVERT: G 51 SER cc_start: 0.8508 (m) cc_final: 0.7975 (p) REVERT: G 107 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7626 (tm-30) REVERT: G 117 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8342 (tttp) REVERT: G 133 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8410 (mtmt) REVERT: G 199 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8268 (mt0) REVERT: G 202 ASP cc_start: 0.7660 (m-30) cc_final: 0.7327 (m-30) REVERT: G 255 ASP cc_start: 0.7868 (t0) cc_final: 0.7377 (t0) REVERT: G 275 LYS cc_start: 0.8383 (mttt) cc_final: 0.8134 (mtpp) REVERT: G 353 LYS cc_start: 0.8434 (mttt) cc_final: 0.8193 (mttt) REVERT: G 401 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7214 (tm-30) REVERT: G 403 ILE cc_start: 0.8242 (mt) cc_final: 0.7878 (tp) REVERT: G 405 ASN cc_start: 0.7717 (t0) cc_final: 0.7121 (m110) REVERT: H 43 LYS cc_start: 0.8308 (mtpp) cc_final: 0.8003 (mttm) REVERT: H 46 LYS cc_start: 0.8261 (mttt) cc_final: 0.7931 (mtpp) REVERT: H 59 LEU cc_start: 0.8737 (mt) cc_final: 0.8518 (mm) REVERT: H 110 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8226 (ttmm) REVERT: H 118 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7588 (mm-30) REVERT: H 286 GLU cc_start: 0.7915 (tp30) cc_final: 0.7621 (tp30) REVERT: H 388 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8277 (m) REVERT: I 50 LYS cc_start: 0.8381 (ptmt) cc_final: 0.8009 (ttpp) REVERT: I 65 ASP cc_start: 0.8018 (m-30) cc_final: 0.7775 (m-30) REVERT: I 74 ASP cc_start: 0.7773 (m-30) cc_final: 0.7204 (m-30) REVERT: I 76 ASP cc_start: 0.7612 (m-30) cc_final: 0.6980 (m-30) REVERT: I 77 ASN cc_start: 0.7510 (t0) cc_final: 0.7067 (t0) REVERT: I 107 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: I 142 LYS cc_start: 0.8892 (tttt) cc_final: 0.8621 (ttmt) REVERT: I 266 GLN cc_start: 0.7809 (pp30) cc_final: 0.7460 (pp30) REVERT: I 358 LEU cc_start: 0.8391 (tp) cc_final: 0.8174 (mp) REVERT: J 17 SER cc_start: 0.8035 (m) cc_final: 0.7750 (t) REVERT: J 74 ASP cc_start: 0.7759 (m-30) cc_final: 0.7431 (t0) REVERT: J 185 PHE cc_start: 0.8713 (m-80) cc_final: 0.8484 (m-80) REVERT: J 202 ASP cc_start: 0.8118 (m-30) cc_final: 0.7875 (m-30) REVERT: J 233 TYR cc_start: 0.7811 (p90) cc_final: 0.7571 (p90) REVERT: J 300 THR cc_start: 0.8915 (m) cc_final: 0.8619 (p) REVERT: K 14 ASP cc_start: 0.7064 (m-30) cc_final: 0.6662 (m-30) REVERT: K 68 LEU cc_start: 0.8910 (mp) cc_final: 0.8680 (mt) REVERT: K 99 ARG cc_start: 0.8051 (ttp-170) cc_final: 0.7836 (ttm-80) REVERT: K 102 GLU cc_start: 0.7187 (pm20) cc_final: 0.6875 (pm20) REVERT: K 296 SER cc_start: 0.8624 (m) cc_final: 0.8398 (t) REVERT: K 379 SER cc_start: 0.8802 (m) cc_final: 0.8343 (t) REVERT: K 386 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: K 398 GLU cc_start: 0.7592 (tp30) cc_final: 0.7118 (tp30) REVERT: L 54 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: L 63 LEU cc_start: 0.8098 (tp) cc_final: 0.7672 (tp) REVERT: L 70 VAL cc_start: 0.8548 (t) cc_final: 0.8180 (p) REVERT: L 233 TYR cc_start: 0.8142 (p90) cc_final: 0.7830 (p90) REVERT: L 293 GLU cc_start: 0.7605 (tt0) cc_final: 0.7386 (tt0) REVERT: L 374 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8363 (mtmm) REVERT: M 50 ASP cc_start: 0.8173 (m-30) cc_final: 0.7765 (m-30) REVERT: M 212 TYR cc_start: 0.8526 (m-80) cc_final: 0.8256 (m-80) REVERT: M 271 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7574 (ttm-80) REVERT: M 318 ASN cc_start: 0.8481 (t0) cc_final: 0.8181 (t0) REVERT: M 327 ASP cc_start: 0.8004 (t0) cc_final: 0.7702 (t0) REVERT: M 386 GLU cc_start: 0.7849 (tp30) cc_final: 0.7306 (tp30) REVERT: M 444 ASP cc_start: 0.7915 (m-30) cc_final: 0.7715 (m-30) REVERT: M 478 GLU cc_start: 0.8115 (mp0) cc_final: 0.7606 (mp0) REVERT: M 503 GLU cc_start: 0.7719 (mp0) cc_final: 0.7387 (mp0) REVERT: M 574 SER cc_start: 0.8300 (p) cc_final: 0.8001 (t) REVERT: N 29 GLU cc_start: 0.6820 (mp0) cc_final: 0.6616 (mp0) REVERT: N 249 GLU cc_start: 0.7242 (pt0) cc_final: 0.6692 (pm20) REVERT: N 301 GLU cc_start: 0.7709 (tt0) cc_final: 0.7399 (tt0) REVERT: N 311 TYR cc_start: 0.8465 (m-80) cc_final: 0.8262 (m-80) REVERT: N 336 ARG cc_start: 0.8374 (ptp90) cc_final: 0.8036 (mtm-85) REVERT: N 355 CYS cc_start: 0.7844 (p) cc_final: 0.7513 (p) REVERT: N 383 GLN cc_start: 0.7971 (mt0) cc_final: 0.7707 (mm-40) REVERT: N 394 VAL cc_start: 0.8868 (t) cc_final: 0.8421 (p) REVERT: N 401 GLU cc_start: 0.7219 (mp0) cc_final: 0.6999 (mp0) REVERT: N 427 GLN cc_start: 0.7929 (mp10) cc_final: 0.7607 (mp10) REVERT: N 506 LYS cc_start: 0.8684 (mttm) cc_final: 0.8309 (mtpp) REVERT: O 19 GLU cc_start: 0.7559 (mp0) cc_final: 0.7242 (mp0) REVERT: O 107 ASN cc_start: 0.7727 (t0) cc_final: 0.7418 (t0) REVERT: O 115 ASP cc_start: 0.8072 (p0) cc_final: 0.7669 (p0) REVERT: O 171 ARG cc_start: 0.7609 (mmm-85) cc_final: 0.7355 (mmm-85) REVERT: O 312 ASP cc_start: 0.7808 (p0) cc_final: 0.7565 (p0) REVERT: O 366 ARG cc_start: 0.7763 (ptp-170) cc_final: 0.7483 (ptp-170) REVERT: O 416 GLU cc_start: 0.8011 (tp30) cc_final: 0.7759 (tm-30) REVERT: O 559 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8509 (mtpp) REVERT: P 19 GLU cc_start: 0.7371 (mp0) cc_final: 0.7076 (mp0) REVERT: P 50 ASP cc_start: 0.7860 (m-30) cc_final: 0.7631 (m-30) REVERT: P 158 THR cc_start: 0.8783 (p) cc_final: 0.8494 (t) REVERT: P 239 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7421 (tmtt) REVERT: P 349 LEU cc_start: 0.8964 (mm) cc_final: 0.8684 (mt) REVERT: P 401 GLU cc_start: 0.8010 (mp0) cc_final: 0.7707 (mp0) REVERT: P 411 LYS cc_start: 0.7593 (mtmt) cc_final: 0.7371 (mtmt) REVERT: P 423 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7979 (mtmm) REVERT: P 444 ASP cc_start: 0.7440 (t0) cc_final: 0.7037 (t0) REVERT: P 459 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7641 (mm-30) REVERT: P 516 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8126 (pt0) REVERT: P 559 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8216 (mtmm) REVERT: Q 67 ASP cc_start: 0.7700 (m-30) cc_final: 0.7448 (m-30) REVERT: Q 159 VAL cc_start: 0.8889 (m) cc_final: 0.8439 (p) REVERT: Q 209 ASN cc_start: 0.8615 (m110) cc_final: 0.8073 (m-40) REVERT: Q 268 LYS cc_start: 0.8804 (tttm) cc_final: 0.8539 (ttmm) REVERT: Q 282 ARG cc_start: 0.8711 (mmm-85) cc_final: 0.8315 (mtp180) REVERT: Q 283 ASN cc_start: 0.8980 (m-40) cc_final: 0.8509 (m-40) REVERT: Q 288 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8659 (tt) REVERT: Q 297 ASN cc_start: 0.6913 (t0) cc_final: 0.6627 (t0) REVERT: Q 306 GLU cc_start: 0.7538 (tm-30) cc_final: 0.6935 (tm-30) REVERT: Q 308 PHE cc_start: 0.7728 (t80) cc_final: 0.7197 (t80) REVERT: Q 327 ASP cc_start: 0.7451 (t0) cc_final: 0.7226 (t0) REVERT: Q 380 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8680 (tt) REVERT: Q 418 ASP cc_start: 0.8153 (m-30) cc_final: 0.7946 (t0) REVERT: Q 544 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7792 (tp-100) REVERT: R 24 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7409 (mtp85) REVERT: R 140 ASP cc_start: 0.6441 (m-30) cc_final: 0.6179 (m-30) REVERT: R 158 THR cc_start: 0.6823 (p) cc_final: 0.6307 (p) REVERT: R 159 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8148 (t) REVERT: R 160 LYS cc_start: 0.7969 (mppt) cc_final: 0.7698 (mppt) REVERT: R 192 ARG cc_start: 0.7306 (tpp80) cc_final: 0.6001 (tpp80) REVERT: R 245 LEU cc_start: 0.7462 (pp) cc_final: 0.6903 (mt) REVERT: R 270 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6982 (tt) REVERT: R 283 ASN cc_start: 0.7658 (m110) cc_final: 0.7328 (m-40) REVERT: R 294 LYS cc_start: 0.8159 (tppt) cc_final: 0.7397 (mptt) REVERT: R 427 GLN cc_start: 0.7067 (mp10) cc_final: 0.6401 (mp10) REVERT: R 497 TYR cc_start: 0.7757 (t80) cc_final: 0.7554 (t80) REVERT: R 508 LYS cc_start: 0.7949 (mttp) cc_final: 0.7718 (mttp) REVERT: R 550 MET cc_start: 0.8149 (ppp) cc_final: 0.7485 (ppp) REVERT: R 559 LYS cc_start: 0.8494 (mtmt) cc_final: 0.7920 (mtmt) outliers start: 135 outliers final: 92 residues processed: 1681 average time/residue: 0.6643 time to fit residues: 1819.5540 Evaluate side-chains 1702 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1597 time to evaluate : 5.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 477 GLU Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 353 PHE Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain O residue 578 LEU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 267 ILE Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 413 MET Chi-restraints excluded: chain P residue 516 GLN Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 394 VAL Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 515 THR Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 258 optimal weight: 0.9980 chunk 692 optimal weight: 0.0060 chunk 152 optimal weight: 4.9990 chunk 451 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 770 optimal weight: 8.9990 chunk 639 optimal weight: 2.9990 chunk 356 optimal weight: 0.2980 chunk 64 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 404 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN D 234 GLN H 129 GLN I 365 GLN M 466 GLN P 214 GLN R 277 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 66064 Z= 0.150 Angle : 0.502 17.314 89371 Z= 0.255 Chirality : 0.040 0.162 9710 Planarity : 0.003 0.052 11449 Dihedral : 8.744 161.944 9438 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.91 % Allowed : 15.17 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.09), residues: 7933 helix: 1.04 (0.10), residues: 3101 sheet: 0.84 (0.16), residues: 1020 loop : -1.55 (0.09), residues: 3812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 409 HIS 0.004 0.001 HIS Q 434 PHE 0.018 0.001 PHE K 262 TYR 0.027 0.001 TYR R 258 ARG 0.013 0.000 ARG M 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1723 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1592 time to evaluate : 5.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8014 (m-30) cc_final: 0.7642 (m-30) REVERT: A 58 GLU cc_start: 0.7575 (mp0) cc_final: 0.7290 (mp0) REVERT: A 74 ASP cc_start: 0.7985 (m-30) cc_final: 0.7668 (m-30) REVERT: A 170 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7329 (p0) REVERT: B 67 TYR cc_start: 0.8505 (m-80) cc_final: 0.8172 (m-80) REVERT: B 70 VAL cc_start: 0.8820 (t) cc_final: 0.8541 (m) REVERT: B 97 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8175 (ttmt) REVERT: B 99 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7665 (ttm-80) REVERT: B 102 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7564 (mm-30) REVERT: B 132 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7345 (mp0) REVERT: B 179 ASP cc_start: 0.8298 (t0) cc_final: 0.7958 (t0) REVERT: B 202 ASP cc_start: 0.8379 (m-30) cc_final: 0.8092 (m-30) REVERT: B 233 TYR cc_start: 0.8081 (p90) cc_final: 0.7793 (p90) REVERT: B 257 ILE cc_start: 0.8502 (mm) cc_final: 0.8177 (mt) REVERT: B 258 ASN cc_start: 0.8261 (m-40) cc_final: 0.7806 (m-40) REVERT: B 374 LYS cc_start: 0.8604 (mtmt) cc_final: 0.8302 (mttp) REVERT: B 382 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7570 (tp30) REVERT: C 16 ARG cc_start: 0.8079 (ttm170) cc_final: 0.7767 (mtt90) REVERT: C 58 GLU cc_start: 0.7899 (pm20) cc_final: 0.7660 (pm20) REVERT: C 102 GLU cc_start: 0.7973 (tp30) cc_final: 0.7734 (tp30) REVERT: C 104 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7552 (mm-30) REVERT: C 286 GLU cc_start: 0.8107 (tp30) cc_final: 0.7906 (tp30) REVERT: C 316 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7561 (ttp-170) REVERT: D 109 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7250 (mtt-85) REVERT: D 128 GLU cc_start: 0.8088 (mp0) cc_final: 0.7880 (mp0) REVERT: D 129 GLN cc_start: 0.8414 (mm110) cc_final: 0.8056 (mm-40) REVERT: D 131 ARG cc_start: 0.8373 (ptm-80) cc_final: 0.8087 (ptm160) REVERT: D 132 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7370 (mm-30) REVERT: D 182 ILE cc_start: 0.8631 (mm) cc_final: 0.8364 (mt) REVERT: D 238 LEU cc_start: 0.4854 (OUTLIER) cc_final: 0.4570 (tt) REVERT: D 290 ARG cc_start: 0.8176 (mmt-90) cc_final: 0.7835 (mmt-90) REVERT: D 343 VAL cc_start: 0.8216 (t) cc_final: 0.7992 (t) REVERT: E 77 ASN cc_start: 0.7586 (m-40) cc_final: 0.7343 (m-40) REVERT: E 79 LEU cc_start: 0.8654 (mm) cc_final: 0.8448 (mm) REVERT: E 98 THR cc_start: 0.8061 (m) cc_final: 0.7794 (m) REVERT: E 118 GLU cc_start: 0.8073 (tp30) cc_final: 0.7867 (tp30) REVERT: E 133 LYS cc_start: 0.8659 (mttm) cc_final: 0.8443 (mttt) REVERT: E 195 GLN cc_start: 0.7876 (mm110) cc_final: 0.7660 (mm-40) REVERT: E 289 ARG cc_start: 0.8426 (ttp80) cc_final: 0.8199 (ttp80) REVERT: E 300 THR cc_start: 0.8367 (m) cc_final: 0.8095 (p) REVERT: E 361 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7010 (mpp) REVERT: E 405 ASN cc_start: 0.8091 (t0) cc_final: 0.7815 (t0) REVERT: F 17 SER cc_start: 0.8308 (m) cc_final: 0.8065 (t) REVERT: F 45 MET cc_start: 0.8407 (tpp) cc_final: 0.7900 (mmt) REVERT: F 65 ASP cc_start: 0.7584 (m-30) cc_final: 0.7239 (m-30) REVERT: F 76 ASP cc_start: 0.7208 (m-30) cc_final: 0.6614 (m-30) REVERT: F 97 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8544 (ttmm) REVERT: F 114 SER cc_start: 0.8734 (m) cc_final: 0.8234 (p) REVERT: F 137 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8212 (ttmm) REVERT: F 233 TYR cc_start: 0.7525 (p90) cc_final: 0.6855 (p90) REVERT: F 296 SER cc_start: 0.8939 (m) cc_final: 0.8553 (t) REVERT: G 47 ASP cc_start: 0.8449 (m-30) cc_final: 0.8236 (m-30) REVERT: G 51 SER cc_start: 0.8535 (m) cc_final: 0.7969 (p) REVERT: G 107 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7599 (tm-30) REVERT: G 166 THR cc_start: 0.8792 (t) cc_final: 0.8558 (m) REVERT: G 199 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8270 (mt0) REVERT: G 202 ASP cc_start: 0.7661 (m-30) cc_final: 0.7368 (m-30) REVERT: G 255 ASP cc_start: 0.7862 (t0) cc_final: 0.7421 (t0) REVERT: G 275 LYS cc_start: 0.8389 (mttt) cc_final: 0.8144 (mtpp) REVERT: G 353 LYS cc_start: 0.8465 (mttt) cc_final: 0.8239 (mttt) REVERT: G 403 ILE cc_start: 0.8234 (mt) cc_final: 0.8028 (mt) REVERT: H 43 LYS cc_start: 0.8259 (mtpp) cc_final: 0.7981 (mttm) REVERT: H 46 LYS cc_start: 0.8255 (mttt) cc_final: 0.7927 (mtpp) REVERT: H 65 ASP cc_start: 0.7088 (m-30) cc_final: 0.6829 (m-30) REVERT: H 107 GLU cc_start: 0.8140 (tp30) cc_final: 0.7901 (tt0) REVERT: H 110 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8252 (ttmm) REVERT: H 286 GLU cc_start: 0.7869 (tp30) cc_final: 0.7575 (tp30) REVERT: H 388 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8231 (m) REVERT: I 50 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8084 (ttpp) REVERT: I 74 ASP cc_start: 0.7759 (m-30) cc_final: 0.7231 (m-30) REVERT: I 76 ASP cc_start: 0.7590 (m-30) cc_final: 0.6997 (m-30) REVERT: I 77 ASN cc_start: 0.7480 (t0) cc_final: 0.7126 (t0) REVERT: I 107 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: I 142 LYS cc_start: 0.8906 (tttt) cc_final: 0.8618 (ttmt) REVERT: I 266 GLN cc_start: 0.7793 (pp30) cc_final: 0.7508 (pp30) REVERT: I 358 LEU cc_start: 0.8402 (tp) cc_final: 0.8154 (mp) REVERT: J 17 SER cc_start: 0.8016 (m) cc_final: 0.7729 (t) REVERT: J 74 ASP cc_start: 0.7755 (m-30) cc_final: 0.7429 (t0) REVERT: J 99 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7150 (ttm-80) REVERT: J 233 TYR cc_start: 0.7778 (p90) cc_final: 0.7545 (p90) REVERT: J 242 GLU cc_start: 0.7748 (tt0) cc_final: 0.7525 (tt0) REVERT: J 300 THR cc_start: 0.8889 (m) cc_final: 0.8595 (p) REVERT: K 14 ASP cc_start: 0.7074 (m-30) cc_final: 0.6671 (m-30) REVERT: K 68 LEU cc_start: 0.8896 (mp) cc_final: 0.8687 (mt) REVERT: K 102 GLU cc_start: 0.7158 (pm20) cc_final: 0.6897 (pm20) REVERT: K 202 ASP cc_start: 0.8427 (m-30) cc_final: 0.8223 (m-30) REVERT: K 296 SER cc_start: 0.8583 (m) cc_final: 0.8361 (t) REVERT: K 379 SER cc_start: 0.8793 (m) cc_final: 0.8317 (t) REVERT: K 386 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: K 398 GLU cc_start: 0.7588 (tp30) cc_final: 0.7103 (tp30) REVERT: L 54 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: L 63 LEU cc_start: 0.8065 (tp) cc_final: 0.7630 (tp) REVERT: L 70 VAL cc_start: 0.8547 (t) cc_final: 0.8192 (p) REVERT: L 233 TYR cc_start: 0.8101 (p90) cc_final: 0.7843 (p90) REVERT: L 293 GLU cc_start: 0.7597 (tt0) cc_final: 0.7379 (tt0) REVERT: L 374 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8362 (mtmm) REVERT: M 50 ASP cc_start: 0.8197 (m-30) cc_final: 0.7791 (m-30) REVERT: M 212 TYR cc_start: 0.8547 (m-80) cc_final: 0.8281 (m-80) REVERT: M 259 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8497 (pm20) REVERT: M 271 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7574 (ttm-80) REVERT: M 318 ASN cc_start: 0.8479 (t0) cc_final: 0.8181 (t0) REVERT: M 327 ASP cc_start: 0.7971 (t0) cc_final: 0.7644 (t0) REVERT: M 386 GLU cc_start: 0.7858 (tp30) cc_final: 0.7245 (tp30) REVERT: M 462 PHE cc_start: 0.8342 (t80) cc_final: 0.8044 (t80) REVERT: M 478 GLU cc_start: 0.8112 (mp0) cc_final: 0.7636 (mp0) REVERT: M 506 LYS cc_start: 0.7966 (tmtt) cc_final: 0.7748 (ptmm) REVERT: M 507 PHE cc_start: 0.8199 (m-10) cc_final: 0.7964 (m-10) REVERT: M 574 SER cc_start: 0.8289 (p) cc_final: 0.7944 (t) REVERT: N 14 TYR cc_start: 0.8753 (p90) cc_final: 0.8301 (p90) REVERT: N 29 GLU cc_start: 0.6814 (mp0) cc_final: 0.6601 (mp0) REVERT: N 143 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7427 (mt-10) REVERT: N 249 GLU cc_start: 0.7246 (pt0) cc_final: 0.6652 (pm20) REVERT: N 301 GLU cc_start: 0.7658 (tt0) cc_final: 0.7349 (tt0) REVERT: N 336 ARG cc_start: 0.8359 (ptp90) cc_final: 0.8062 (mtm-85) REVERT: N 355 CYS cc_start: 0.7834 (p) cc_final: 0.7532 (p) REVERT: N 383 GLN cc_start: 0.7951 (mt0) cc_final: 0.7699 (mm-40) REVERT: N 394 VAL cc_start: 0.8847 (t) cc_final: 0.8384 (p) REVERT: N 401 GLU cc_start: 0.7225 (mp0) cc_final: 0.7006 (mp0) REVERT: N 427 GLN cc_start: 0.7895 (mp10) cc_final: 0.7672 (mp10) REVERT: N 457 PHE cc_start: 0.8638 (t80) cc_final: 0.8426 (t80) REVERT: N 478 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7644 (mm-30) REVERT: N 506 LYS cc_start: 0.8690 (mttm) cc_final: 0.8301 (mtpp) REVERT: O 107 ASN cc_start: 0.7689 (t0) cc_final: 0.7398 (t0) REVERT: O 115 ASP cc_start: 0.8087 (p0) cc_final: 0.7638 (p0) REVERT: O 171 ARG cc_start: 0.7593 (mmm-85) cc_final: 0.7315 (mmm-85) REVERT: O 300 LEU cc_start: 0.8332 (mt) cc_final: 0.7997 (mp) REVERT: O 312 ASP cc_start: 0.7843 (p0) cc_final: 0.7604 (p0) REVERT: O 366 ARG cc_start: 0.7715 (ptp-170) cc_final: 0.7421 (ptp-170) REVERT: O 387 ASP cc_start: 0.7685 (t0) cc_final: 0.7351 (t0) REVERT: O 391 LYS cc_start: 0.8064 (ptpp) cc_final: 0.7830 (ptpp) REVERT: O 416 GLU cc_start: 0.7997 (tp30) cc_final: 0.7755 (tm-30) REVERT: O 559 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8481 (mtpp) REVERT: P 19 GLU cc_start: 0.7391 (mp0) cc_final: 0.7081 (mp0) REVERT: P 40 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8517 (mmtp) REVERT: P 50 ASP cc_start: 0.7857 (m-30) cc_final: 0.7635 (m-30) REVERT: P 103 LYS cc_start: 0.8623 (pttt) cc_final: 0.8395 (pttp) REVERT: P 158 THR cc_start: 0.8773 (p) cc_final: 0.8495 (t) REVERT: P 239 LYS cc_start: 0.8083 (mtmm) cc_final: 0.7482 (tmtt) REVERT: P 349 LEU cc_start: 0.8958 (mm) cc_final: 0.8661 (mt) REVERT: P 382 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: P 401 GLU cc_start: 0.8025 (mp0) cc_final: 0.7739 (mp0) REVERT: P 411 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7365 (mtmt) REVERT: P 423 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7966 (mtmm) REVERT: P 444 ASP cc_start: 0.7324 (t0) cc_final: 0.6956 (t0) REVERT: P 459 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7609 (mm-30) REVERT: P 516 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: P 559 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8213 (mtmm) REVERT: Q 67 ASP cc_start: 0.7713 (m-30) cc_final: 0.7446 (m-30) REVERT: Q 209 ASN cc_start: 0.8591 (m110) cc_final: 0.8319 (m-40) REVERT: Q 266 LEU cc_start: 0.8687 (mt) cc_final: 0.8472 (mt) REVERT: Q 268 LYS cc_start: 0.8812 (tttm) cc_final: 0.8549 (ttmm) REVERT: Q 282 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8314 (mtp180) REVERT: Q 283 ASN cc_start: 0.8952 (m-40) cc_final: 0.8516 (m-40) REVERT: Q 297 ASN cc_start: 0.6903 (t0) cc_final: 0.6598 (t0) REVERT: Q 306 GLU cc_start: 0.7547 (tm-30) cc_final: 0.6929 (tm-30) REVERT: Q 308 PHE cc_start: 0.7695 (t80) cc_final: 0.7159 (t80) REVERT: Q 327 ASP cc_start: 0.7445 (t0) cc_final: 0.7241 (t0) REVERT: Q 377 LEU cc_start: 0.8998 (tt) cc_final: 0.8755 (tp) REVERT: Q 380 ILE cc_start: 0.8898 (mt) cc_final: 0.8675 (tt) REVERT: Q 477 GLU cc_start: 0.7595 (tp30) cc_final: 0.7329 (tp30) REVERT: Q 514 SER cc_start: 0.8673 (t) cc_final: 0.8442 (p) REVERT: Q 544 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7760 (tp-100) REVERT: Q 601 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8147 (mm-30) REVERT: R 24 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7404 (mtp85) REVERT: R 140 ASP cc_start: 0.6405 (m-30) cc_final: 0.6151 (m-30) REVERT: R 158 THR cc_start: 0.6759 (p) cc_final: 0.6251 (p) REVERT: R 160 LYS cc_start: 0.7923 (mppt) cc_final: 0.7690 (mppt) REVERT: R 192 ARG cc_start: 0.7318 (tpp80) cc_final: 0.5982 (tpp80) REVERT: R 245 LEU cc_start: 0.7458 (pp) cc_final: 0.6894 (mt) REVERT: R 270 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6913 (tt) REVERT: R 283 ASN cc_start: 0.7636 (m110) cc_final: 0.7296 (m110) REVERT: R 417 VAL cc_start: 0.8358 (p) cc_final: 0.8079 (m) REVERT: R 427 GLN cc_start: 0.7164 (mp10) cc_final: 0.6949 (mp10) REVERT: R 475 LEU cc_start: 0.8630 (tp) cc_final: 0.8379 (tt) REVERT: R 497 TYR cc_start: 0.7762 (t80) cc_final: 0.7501 (t80) REVERT: R 508 LYS cc_start: 0.7924 (mttp) cc_final: 0.7684 (mttp) REVERT: R 536 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7382 (ttt90) REVERT: R 550 MET cc_start: 0.8113 (ppp) cc_final: 0.7512 (ppp) REVERT: R 559 LYS cc_start: 0.8500 (mtmt) cc_final: 0.7921 (mtmt) outliers start: 131 outliers final: 93 residues processed: 1644 average time/residue: 0.7232 time to fit residues: 1948.4481 Evaluate side-chains 1672 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1567 time to evaluate : 5.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 361 MET Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 259 GLN Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 388 ILE Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 477 GLU Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 348 THR Chi-restraints excluded: chain P residue 380 ILE Chi-restraints excluded: chain P residue 382 GLN Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 413 MET Chi-restraints excluded: chain P residue 516 GLN Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 383 GLN Chi-restraints excluded: chain Q residue 394 VAL Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 515 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 742 optimal weight: 0.0670 chunk 86 optimal weight: 0.9980 chunk 438 optimal weight: 0.4980 chunk 562 optimal weight: 0.3980 chunk 435 optimal weight: 0.9990 chunk 648 optimal weight: 6.9990 chunk 430 optimal weight: 0.9980 chunk 767 optimal weight: 9.9990 chunk 480 optimal weight: 0.0000 chunk 467 optimal weight: 2.9990 chunk 354 optimal weight: 0.9990 overall best weight: 0.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 315 ASN D 234 GLN H 129 GLN P 214 GLN P 240 GLN Q 443 GLN R 277 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 66064 Z= 0.129 Angle : 0.482 16.133 89371 Z= 0.244 Chirality : 0.040 0.169 9710 Planarity : 0.003 0.049 11449 Dihedral : 8.505 161.686 9438 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.84 % Allowed : 15.84 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.10), residues: 7933 helix: 1.20 (0.10), residues: 3090 sheet: 0.96 (0.16), residues: 1003 loop : -1.48 (0.10), residues: 3840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 409 HIS 0.003 0.000 HIS J 313 PHE 0.018 0.001 PHE N 293 TYR 0.026 0.001 TYR R 258 ARG 0.014 0.000 ARG J 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1705 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1579 time to evaluate : 5.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7518 (mp0) cc_final: 0.7230 (mp0) REVERT: A 74 ASP cc_start: 0.7985 (m-30) cc_final: 0.7644 (m-30) REVERT: B 67 TYR cc_start: 0.8497 (m-80) cc_final: 0.8169 (m-80) REVERT: B 70 VAL cc_start: 0.8762 (t) cc_final: 0.8473 (m) REVERT: B 97 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8178 (ttmt) REVERT: B 99 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7463 (ttm-80) REVERT: B 102 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7540 (mm-30) REVERT: B 132 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7245 (mp0) REVERT: B 179 ASP cc_start: 0.8264 (t0) cc_final: 0.7915 (t0) REVERT: B 202 ASP cc_start: 0.8401 (m-30) cc_final: 0.8122 (m-30) REVERT: B 257 ILE cc_start: 0.8467 (mm) cc_final: 0.8184 (mt) REVERT: B 258 ASN cc_start: 0.8241 (m-40) cc_final: 0.7860 (m110) REVERT: B 374 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8296 (mttp) REVERT: B 382 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7579 (tp30) REVERT: C 16 ARG cc_start: 0.8052 (ttm170) cc_final: 0.7751 (mtt90) REVERT: C 58 GLU cc_start: 0.7811 (pm20) cc_final: 0.7590 (pm20) REVERT: C 102 GLU cc_start: 0.7946 (tp30) cc_final: 0.7700 (tp30) REVERT: C 104 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7550 (mm-30) REVERT: C 132 GLU cc_start: 0.7707 (mp0) cc_final: 0.7310 (mp0) REVERT: C 286 GLU cc_start: 0.8118 (tp30) cc_final: 0.7912 (tp30) REVERT: C 316 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7540 (ttp-170) REVERT: D 128 GLU cc_start: 0.8082 (mp0) cc_final: 0.7868 (mp0) REVERT: D 129 GLN cc_start: 0.8425 (mm110) cc_final: 0.8074 (mm-40) REVERT: D 131 ARG cc_start: 0.8406 (ptm-80) cc_final: 0.8117 (ptm160) REVERT: D 182 ILE cc_start: 0.8621 (mm) cc_final: 0.8366 (mt) REVERT: D 238 LEU cc_start: 0.4830 (OUTLIER) cc_final: 0.4563 (tt) REVERT: D 290 ARG cc_start: 0.8184 (mmt-90) cc_final: 0.7854 (mmt-90) REVERT: D 343 VAL cc_start: 0.8152 (t) cc_final: 0.7916 (t) REVERT: E 77 ASN cc_start: 0.7545 (m-40) cc_final: 0.7278 (m-40) REVERT: E 83 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: E 98 THR cc_start: 0.7994 (m) cc_final: 0.7696 (m) REVERT: E 99 ARG cc_start: 0.8609 (ttm-80) cc_final: 0.8290 (ttp-170) REVERT: E 118 GLU cc_start: 0.8088 (tp30) cc_final: 0.7725 (tp30) REVERT: E 283 VAL cc_start: 0.7328 (OUTLIER) cc_final: 0.6955 (m) REVERT: E 289 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8219 (ttp80) REVERT: E 361 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7231 (mpp) REVERT: E 405 ASN cc_start: 0.8222 (t0) cc_final: 0.7927 (t0) REVERT: F 17 SER cc_start: 0.8303 (m) cc_final: 0.8055 (t) REVERT: F 45 MET cc_start: 0.8179 (tpp) cc_final: 0.7957 (mmt) REVERT: F 65 ASP cc_start: 0.7579 (m-30) cc_final: 0.7256 (m-30) REVERT: F 76 ASP cc_start: 0.7185 (m-30) cc_final: 0.6590 (m-30) REVERT: F 97 LYS cc_start: 0.8834 (ttmm) cc_final: 0.8533 (ttmm) REVERT: F 114 SER cc_start: 0.8726 (m) cc_final: 0.8229 (p) REVERT: F 137 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8178 (ttmm) REVERT: F 233 TYR cc_start: 0.7411 (p90) cc_final: 0.6752 (p90) REVERT: F 296 SER cc_start: 0.8868 (m) cc_final: 0.8500 (t) REVERT: G 47 ASP cc_start: 0.8425 (m-30) cc_final: 0.8197 (m-30) REVERT: G 51 SER cc_start: 0.8508 (m) cc_final: 0.8108 (p) REVERT: G 53 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7595 (mttt) REVERT: G 107 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7589 (tm-30) REVERT: G 199 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8245 (mt0) REVERT: G 202 ASP cc_start: 0.7642 (m-30) cc_final: 0.7357 (m-30) REVERT: G 255 ASP cc_start: 0.7924 (t0) cc_final: 0.7460 (t0) REVERT: G 275 LYS cc_start: 0.8387 (mttt) cc_final: 0.8145 (mtpp) REVERT: G 353 LYS cc_start: 0.8490 (mttt) cc_final: 0.8231 (mttt) REVERT: G 398 GLU cc_start: 0.7781 (pm20) cc_final: 0.7528 (pm20) REVERT: H 46 LYS cc_start: 0.8246 (mttt) cc_final: 0.7922 (mtpp) REVERT: H 65 ASP cc_start: 0.7126 (m-30) cc_final: 0.6847 (m-30) REVERT: H 107 GLU cc_start: 0.8119 (tp30) cc_final: 0.7892 (tt0) REVERT: H 110 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8243 (ttmm) REVERT: H 250 ASP cc_start: 0.8172 (m-30) cc_final: 0.7971 (m-30) REVERT: H 286 GLU cc_start: 0.7823 (tp30) cc_final: 0.7538 (tp30) REVERT: H 388 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8244 (m) REVERT: I 74 ASP cc_start: 0.7712 (m-30) cc_final: 0.7171 (m-30) REVERT: I 76 ASP cc_start: 0.7628 (m-30) cc_final: 0.7042 (m-30) REVERT: I 77 ASN cc_start: 0.7433 (t0) cc_final: 0.7165 (t0) REVERT: I 107 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: I 142 LYS cc_start: 0.8894 (tttt) cc_final: 0.8613 (ttmt) REVERT: I 266 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7501 (pp30) REVERT: I 358 LEU cc_start: 0.8408 (tp) cc_final: 0.8152 (mp) REVERT: J 17 SER cc_start: 0.8019 (m) cc_final: 0.7711 (t) REVERT: J 74 ASP cc_start: 0.7744 (m-30) cc_final: 0.7428 (t0) REVERT: J 79 LEU cc_start: 0.8462 (mt) cc_final: 0.8026 (mt) REVERT: J 300 THR cc_start: 0.8849 (m) cc_final: 0.8577 (p) REVERT: K 14 ASP cc_start: 0.7033 (m-30) cc_final: 0.6626 (m-30) REVERT: K 68 LEU cc_start: 0.8893 (mp) cc_final: 0.8685 (mt) REVERT: K 76 ASP cc_start: 0.8410 (m-30) cc_final: 0.8047 (m-30) REVERT: K 102 GLU cc_start: 0.7168 (pm20) cc_final: 0.6959 (pm20) REVERT: K 104 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7343 (mt-10) REVERT: K 202 ASP cc_start: 0.8415 (m-30) cc_final: 0.8209 (m-30) REVERT: K 259 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7877 (mttt) REVERT: K 296 SER cc_start: 0.8541 (m) cc_final: 0.8334 (t) REVERT: K 379 SER cc_start: 0.8777 (m) cc_final: 0.8316 (t) REVERT: K 386 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.7026 (m-80) REVERT: K 398 GLU cc_start: 0.7574 (tp30) cc_final: 0.7058 (tp30) REVERT: L 9 LYS cc_start: 0.8319 (ttmm) cc_final: 0.8102 (ttmm) REVERT: L 63 LEU cc_start: 0.8002 (tp) cc_final: 0.7746 (tp) REVERT: L 70 VAL cc_start: 0.8554 (t) cc_final: 0.8222 (p) REVERT: L 293 GLU cc_start: 0.7585 (tt0) cc_final: 0.7342 (tt0) REVERT: L 374 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8360 (mtmm) REVERT: M 50 ASP cc_start: 0.8168 (m-30) cc_final: 0.7729 (m-30) REVERT: M 212 TYR cc_start: 0.8543 (m-80) cc_final: 0.8287 (m-80) REVERT: M 271 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7502 (ttm-80) REVERT: M 318 ASN cc_start: 0.8471 (t0) cc_final: 0.8164 (t0) REVERT: M 327 ASP cc_start: 0.7951 (t0) cc_final: 0.7619 (t0) REVERT: M 386 GLU cc_start: 0.7894 (tp30) cc_final: 0.7321 (tp30) REVERT: M 462 PHE cc_start: 0.8326 (t80) cc_final: 0.8116 (t80) REVERT: M 478 GLU cc_start: 0.8099 (mp0) cc_final: 0.7801 (mp0) REVERT: M 574 SER cc_start: 0.8277 (p) cc_final: 0.7944 (t) REVERT: N 14 TYR cc_start: 0.8762 (p90) cc_final: 0.8313 (p90) REVERT: N 29 GLU cc_start: 0.6778 (mp0) cc_final: 0.6566 (mp0) REVERT: N 143 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7401 (mt-10) REVERT: N 187 ASN cc_start: 0.8609 (m110) cc_final: 0.8296 (m110) REVERT: N 249 GLU cc_start: 0.7230 (pt0) cc_final: 0.6641 (pm20) REVERT: N 301 GLU cc_start: 0.7584 (tt0) cc_final: 0.7275 (tt0) REVERT: N 302 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7830 (mttt) REVERT: N 336 ARG cc_start: 0.8332 (ptp90) cc_final: 0.8058 (mtm-85) REVERT: N 355 CYS cc_start: 0.7830 (p) cc_final: 0.7542 (p) REVERT: N 383 GLN cc_start: 0.7940 (mt0) cc_final: 0.7702 (mm-40) REVERT: N 394 VAL cc_start: 0.8820 (t) cc_final: 0.8349 (p) REVERT: N 401 GLU cc_start: 0.7230 (mp0) cc_final: 0.6992 (mp0) REVERT: N 478 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7501 (mm-30) REVERT: N 498 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7217 (mm-30) REVERT: N 506 LYS cc_start: 0.8701 (mttm) cc_final: 0.8304 (mtpp) REVERT: O 19 GLU cc_start: 0.7466 (mp0) cc_final: 0.7135 (mp0) REVERT: O 107 ASN cc_start: 0.7655 (t0) cc_final: 0.7414 (t0) REVERT: O 115 ASP cc_start: 0.8002 (p0) cc_final: 0.7538 (p0) REVERT: O 299 TYR cc_start: 0.8377 (p90) cc_final: 0.8004 (p90) REVERT: O 300 LEU cc_start: 0.8312 (mt) cc_final: 0.7948 (mp) REVERT: O 387 ASP cc_start: 0.7593 (t0) cc_final: 0.7264 (t0) REVERT: O 391 LYS cc_start: 0.8048 (ptpp) cc_final: 0.7725 (ptpp) REVERT: O 416 GLU cc_start: 0.7985 (tp30) cc_final: 0.7699 (tm-30) REVERT: O 559 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8474 (mtpp) REVERT: P 19 GLU cc_start: 0.7298 (mp0) cc_final: 0.6992 (mp0) REVERT: P 40 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8507 (mmtp) REVERT: P 50 ASP cc_start: 0.7849 (m-30) cc_final: 0.7631 (m-30) REVERT: P 239 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7487 (tmtt) REVERT: P 283 ASN cc_start: 0.8473 (m-40) cc_final: 0.8181 (m110) REVERT: P 349 LEU cc_start: 0.8934 (mm) cc_final: 0.8650 (mt) REVERT: P 401 GLU cc_start: 0.7982 (mp0) cc_final: 0.7701 (mp0) REVERT: P 411 LYS cc_start: 0.7576 (mtmt) cc_final: 0.7353 (mtmt) REVERT: P 423 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7976 (mtmm) REVERT: P 444 ASP cc_start: 0.7332 (t0) cc_final: 0.6967 (t0) REVERT: P 559 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8160 (mtmm) REVERT: Q 67 ASP cc_start: 0.7695 (m-30) cc_final: 0.7423 (m-30) REVERT: Q 209 ASN cc_start: 0.8546 (m110) cc_final: 0.8022 (m-40) REVERT: Q 211 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7322 (mp0) REVERT: Q 268 LYS cc_start: 0.8777 (tttm) cc_final: 0.8540 (ttmm) REVERT: Q 281 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8434 (tp) REVERT: Q 283 ASN cc_start: 0.8892 (m-40) cc_final: 0.8497 (m-40) REVERT: Q 297 ASN cc_start: 0.6915 (t0) cc_final: 0.6608 (t0) REVERT: Q 306 GLU cc_start: 0.7541 (tm-30) cc_final: 0.6922 (tm-30) REVERT: Q 308 PHE cc_start: 0.7667 (t80) cc_final: 0.7070 (t80) REVERT: Q 327 ASP cc_start: 0.7446 (t0) cc_final: 0.7234 (t0) REVERT: Q 380 ILE cc_start: 0.8887 (mt) cc_final: 0.8671 (tt) REVERT: Q 418 ASP cc_start: 0.8265 (t0) cc_final: 0.7990 (t0) REVERT: Q 544 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7709 (tp-100) REVERT: Q 566 ARG cc_start: 0.7427 (ttp80) cc_final: 0.7151 (ttt90) REVERT: R 24 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7405 (mtp85) REVERT: R 140 ASP cc_start: 0.6361 (m-30) cc_final: 0.6116 (m-30) REVERT: R 192 ARG cc_start: 0.7298 (tpp80) cc_final: 0.5979 (tpp80) REVERT: R 240 GLN cc_start: 0.7305 (mp10) cc_final: 0.6542 (mt0) REVERT: R 245 LEU cc_start: 0.7489 (pp) cc_final: 0.6913 (mt) REVERT: R 270 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6847 (tt) REVERT: R 282 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.8068 (mtp180) REVERT: R 283 ASN cc_start: 0.7626 (m110) cc_final: 0.7293 (m110) REVERT: R 416 GLU cc_start: 0.7238 (mm-30) cc_final: 0.7035 (mm-30) REVERT: R 427 GLN cc_start: 0.7247 (mp10) cc_final: 0.6996 (mp10) REVERT: R 497 TYR cc_start: 0.7747 (t80) cc_final: 0.7464 (t80) REVERT: R 508 LYS cc_start: 0.7913 (mttp) cc_final: 0.7706 (mttp) REVERT: R 536 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.7371 (ttt90) REVERT: R 550 MET cc_start: 0.8074 (ppp) cc_final: 0.7551 (ppp) REVERT: R 559 LYS cc_start: 0.8500 (mtmt) cc_final: 0.7977 (mtmt) outliers start: 126 outliers final: 84 residues processed: 1628 average time/residue: 0.6669 time to fit residues: 1766.2887 Evaluate side-chains 1644 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1550 time to evaluate : 5.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 361 MET Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 326 SER Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 387 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 388 ILE Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 353 PHE Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 348 THR Chi-restraints excluded: chain P residue 380 ILE Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 413 MET Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 242 LYS Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 394 VAL Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 444 ASP Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 469 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 474 optimal weight: 2.9990 chunk 306 optimal weight: 3.9990 chunk 458 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 487 optimal weight: 2.9990 chunk 522 optimal weight: 0.8980 chunk 379 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 603 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 234 GLN E 154 ASN F 324 ASN H 129 GLN M 466 GLN Q 443 GLN R 277 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 66064 Z= 0.155 Angle : 0.501 16.537 89371 Z= 0.252 Chirality : 0.040 0.158 9710 Planarity : 0.003 0.048 11449 Dihedral : 8.501 160.115 9438 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.59 % Allowed : 16.66 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.10), residues: 7933 helix: 1.23 (0.10), residues: 3093 sheet: 1.01 (0.17), residues: 1002 loop : -1.47 (0.10), residues: 3838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 409 HIS 0.004 0.001 HIS Q 434 PHE 0.021 0.001 PHE N 293 TYR 0.027 0.001 TYR R 258 ARG 0.010 0.000 ARG M 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1690 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1581 time to evaluate : 5.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7529 (mp0) cc_final: 0.7175 (mp0) REVERT: A 74 ASP cc_start: 0.8000 (m-30) cc_final: 0.7657 (m-30) REVERT: B 67 TYR cc_start: 0.8499 (m-80) cc_final: 0.8171 (m-80) REVERT: B 70 VAL cc_start: 0.8757 (t) cc_final: 0.8459 (m) REVERT: B 99 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.7490 (ttm-80) REVERT: B 102 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 132 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7221 (mp0) REVERT: B 179 ASP cc_start: 0.8279 (t0) cc_final: 0.7979 (t0) REVERT: B 257 ILE cc_start: 0.8463 (mm) cc_final: 0.8174 (mt) REVERT: B 258 ASN cc_start: 0.8272 (m-40) cc_final: 0.7897 (m110) REVERT: B 374 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8319 (mttp) REVERT: B 382 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7575 (tp30) REVERT: C 58 GLU cc_start: 0.7814 (pm20) cc_final: 0.7587 (pm20) REVERT: C 102 GLU cc_start: 0.7952 (tp30) cc_final: 0.7705 (tp30) REVERT: C 104 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7553 (mm-30) REVERT: C 132 GLU cc_start: 0.7734 (mp0) cc_final: 0.7311 (mp0) REVERT: C 286 GLU cc_start: 0.8083 (tp30) cc_final: 0.7882 (tp30) REVERT: C 316 ARG cc_start: 0.7767 (ttp-170) cc_final: 0.7542 (ttp-170) REVERT: D 128 GLU cc_start: 0.8090 (mp0) cc_final: 0.7877 (mp0) REVERT: D 129 GLN cc_start: 0.8420 (mm110) cc_final: 0.8052 (mm-40) REVERT: D 131 ARG cc_start: 0.8417 (ptm-80) cc_final: 0.8130 (ptm160) REVERT: D 132 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7057 (mm-30) REVERT: D 182 ILE cc_start: 0.8632 (mm) cc_final: 0.8376 (mt) REVERT: D 238 LEU cc_start: 0.4841 (OUTLIER) cc_final: 0.4578 (tt) REVERT: D 290 ARG cc_start: 0.8194 (mmt-90) cc_final: 0.7852 (mmt-90) REVERT: D 343 VAL cc_start: 0.8180 (t) cc_final: 0.7936 (t) REVERT: E 60 LEU cc_start: 0.8224 (tp) cc_final: 0.7933 (mp) REVERT: E 77 ASN cc_start: 0.7576 (m-40) cc_final: 0.7340 (m-40) REVERT: E 83 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: E 99 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8301 (ttp-170) REVERT: E 118 GLU cc_start: 0.8103 (tp30) cc_final: 0.7740 (tp30) REVERT: E 133 LYS cc_start: 0.8645 (mttm) cc_final: 0.8386 (mttp) REVERT: E 283 VAL cc_start: 0.7457 (OUTLIER) cc_final: 0.7039 (m) REVERT: E 289 ARG cc_start: 0.8432 (ttp80) cc_final: 0.8185 (ttp80) REVERT: E 361 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7261 (mpp) REVERT: E 405 ASN cc_start: 0.8211 (t0) cc_final: 0.7932 (t0) REVERT: F 17 SER cc_start: 0.8301 (m) cc_final: 0.8055 (t) REVERT: F 45 MET cc_start: 0.8179 (tpp) cc_final: 0.7940 (mmt) REVERT: F 65 ASP cc_start: 0.7590 (m-30) cc_final: 0.7267 (m-30) REVERT: F 76 ASP cc_start: 0.7195 (m-30) cc_final: 0.6600 (m-30) REVERT: F 114 SER cc_start: 0.8728 (m) cc_final: 0.8236 (p) REVERT: F 137 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8169 (ttmm) REVERT: F 233 TYR cc_start: 0.7408 (p90) cc_final: 0.6738 (p90) REVERT: F 296 SER cc_start: 0.8881 (m) cc_final: 0.8518 (t) REVERT: G 47 ASP cc_start: 0.8449 (m-30) cc_final: 0.8233 (m-30) REVERT: G 51 SER cc_start: 0.8459 (m) cc_final: 0.8192 (p) REVERT: G 53 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7597 (mttt) REVERT: G 107 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7470 (tm-30) REVERT: G 199 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8239 (mt0) REVERT: G 202 ASP cc_start: 0.7666 (m-30) cc_final: 0.7373 (m-30) REVERT: G 255 ASP cc_start: 0.7935 (t0) cc_final: 0.7459 (t0) REVERT: G 275 LYS cc_start: 0.8438 (mttt) cc_final: 0.8188 (mtpp) REVERT: G 353 LYS cc_start: 0.8488 (mttt) cc_final: 0.8235 (mttt) REVERT: H 46 LYS cc_start: 0.8258 (mttt) cc_final: 0.7919 (mtpp) REVERT: H 65 ASP cc_start: 0.7164 (m-30) cc_final: 0.6883 (m-30) REVERT: H 107 GLU cc_start: 0.8125 (tp30) cc_final: 0.7635 (tp30) REVERT: H 110 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8223 (ttmm) REVERT: H 250 ASP cc_start: 0.8146 (m-30) cc_final: 0.7940 (m-30) REVERT: H 286 GLU cc_start: 0.7829 (tp30) cc_final: 0.7540 (tp30) REVERT: H 388 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8211 (m) REVERT: I 74 ASP cc_start: 0.7727 (m-30) cc_final: 0.7191 (m-30) REVERT: I 76 ASP cc_start: 0.7637 (m-30) cc_final: 0.7053 (m-30) REVERT: I 77 ASN cc_start: 0.7466 (t0) cc_final: 0.7223 (t0) REVERT: I 107 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: I 142 LYS cc_start: 0.8904 (tttt) cc_final: 0.8620 (ttmt) REVERT: I 266 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7492 (pp30) REVERT: J 17 SER cc_start: 0.8025 (m) cc_final: 0.7722 (t) REVERT: J 74 ASP cc_start: 0.7750 (m-30) cc_final: 0.7430 (t0) REVERT: J 79 LEU cc_start: 0.8480 (mt) cc_final: 0.8025 (mt) REVERT: J 99 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.7101 (ttm-80) REVERT: J 146 GLU cc_start: 0.7843 (tt0) cc_final: 0.7628 (tt0) REVERT: J 300 THR cc_start: 0.8869 (m) cc_final: 0.8618 (p) REVERT: K 14 ASP cc_start: 0.7079 (m-30) cc_final: 0.6668 (m-30) REVERT: K 68 LEU cc_start: 0.8893 (mp) cc_final: 0.8691 (mt) REVERT: K 76 ASP cc_start: 0.8425 (m-30) cc_final: 0.8051 (m-30) REVERT: K 102 GLU cc_start: 0.7216 (pm20) cc_final: 0.6989 (pm20) REVERT: K 104 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7282 (mt-10) REVERT: K 202 ASP cc_start: 0.8419 (m-30) cc_final: 0.8216 (m-30) REVERT: K 296 SER cc_start: 0.8562 (m) cc_final: 0.8357 (t) REVERT: K 379 SER cc_start: 0.8773 (m) cc_final: 0.8318 (t) REVERT: K 386 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: K 398 GLU cc_start: 0.7574 (tp30) cc_final: 0.7056 (tp30) REVERT: L 63 LEU cc_start: 0.7982 (tp) cc_final: 0.7744 (tp) REVERT: L 70 VAL cc_start: 0.8555 (t) cc_final: 0.8235 (p) REVERT: L 116 TYR cc_start: 0.8578 (m-80) cc_final: 0.8218 (m-80) REVERT: L 293 GLU cc_start: 0.7570 (tt0) cc_final: 0.7340 (tt0) REVERT: L 374 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8351 (mtmm) REVERT: M 50 ASP cc_start: 0.8188 (m-30) cc_final: 0.7778 (m-30) REVERT: M 212 TYR cc_start: 0.8526 (m-80) cc_final: 0.8261 (m-80) REVERT: M 271 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7566 (ttm-80) REVERT: M 318 ASN cc_start: 0.8478 (t0) cc_final: 0.8166 (t0) REVERT: M 327 ASP cc_start: 0.7985 (t0) cc_final: 0.7652 (t0) REVERT: M 386 GLU cc_start: 0.7894 (tp30) cc_final: 0.7318 (tp30) REVERT: M 421 PHE cc_start: 0.7305 (m-10) cc_final: 0.6987 (m-80) REVERT: M 462 PHE cc_start: 0.8343 (t80) cc_final: 0.8027 (t80) REVERT: M 478 GLU cc_start: 0.8120 (mp0) cc_final: 0.7818 (mp0) REVERT: M 507 PHE cc_start: 0.8162 (m-10) cc_final: 0.7902 (m-10) REVERT: M 574 SER cc_start: 0.8289 (p) cc_final: 0.7958 (t) REVERT: N 14 TYR cc_start: 0.8775 (p90) cc_final: 0.8315 (p90) REVERT: N 29 GLU cc_start: 0.6798 (mp0) cc_final: 0.6574 (mp0) REVERT: N 143 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7415 (mt-10) REVERT: N 187 ASN cc_start: 0.8622 (m110) cc_final: 0.8325 (m110) REVERT: N 249 GLU cc_start: 0.7248 (pt0) cc_final: 0.6656 (pm20) REVERT: N 301 GLU cc_start: 0.7606 (tt0) cc_final: 0.7284 (tt0) REVERT: N 302 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7822 (mttt) REVERT: N 336 ARG cc_start: 0.8347 (ptp90) cc_final: 0.8075 (mtm-85) REVERT: N 355 CYS cc_start: 0.7939 (p) cc_final: 0.7682 (p) REVERT: N 383 GLN cc_start: 0.7945 (mt0) cc_final: 0.7715 (mm-40) REVERT: N 394 VAL cc_start: 0.8820 (t) cc_final: 0.8352 (p) REVERT: N 401 GLU cc_start: 0.7243 (mp0) cc_final: 0.7009 (mp0) REVERT: N 478 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7521 (mm-30) REVERT: N 506 LYS cc_start: 0.8702 (mttm) cc_final: 0.8306 (mtpp) REVERT: N 578 LEU cc_start: 0.8469 (pt) cc_final: 0.8236 (mp) REVERT: O 19 GLU cc_start: 0.7466 (mp0) cc_final: 0.7130 (mp0) REVERT: O 107 ASN cc_start: 0.7698 (t0) cc_final: 0.7445 (t0) REVERT: O 115 ASP cc_start: 0.7992 (p0) cc_final: 0.7570 (p0) REVERT: O 299 TYR cc_start: 0.8379 (p90) cc_final: 0.8008 (p90) REVERT: O 300 LEU cc_start: 0.8315 (mt) cc_final: 0.7947 (mp) REVERT: O 387 ASP cc_start: 0.7612 (t0) cc_final: 0.7297 (t0) REVERT: O 391 LYS cc_start: 0.8162 (ptpp) cc_final: 0.7837 (ptpp) REVERT: O 416 GLU cc_start: 0.8004 (tp30) cc_final: 0.7736 (tm-30) REVERT: O 559 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8464 (mtpp) REVERT: P 19 GLU cc_start: 0.7301 (mp0) cc_final: 0.6988 (mp0) REVERT: P 40 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8506 (mmtp) REVERT: P 50 ASP cc_start: 0.7854 (m-30) cc_final: 0.7634 (m-30) REVERT: P 239 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7505 (tmtt) REVERT: P 283 ASN cc_start: 0.8485 (m-40) cc_final: 0.8183 (m110) REVERT: P 349 LEU cc_start: 0.8936 (mm) cc_final: 0.8671 (mt) REVERT: P 401 GLU cc_start: 0.7993 (mp0) cc_final: 0.7720 (mp0) REVERT: P 411 LYS cc_start: 0.7576 (mtmt) cc_final: 0.7357 (mtmt) REVERT: P 423 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7990 (mtmm) REVERT: P 444 ASP cc_start: 0.7351 (t0) cc_final: 0.6989 (t0) REVERT: P 559 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8165 (mtmm) REVERT: Q 67 ASP cc_start: 0.7683 (m-30) cc_final: 0.7417 (m-30) REVERT: Q 209 ASN cc_start: 0.8518 (m110) cc_final: 0.8009 (m-40) REVERT: Q 211 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7337 (mp0) REVERT: Q 268 LYS cc_start: 0.8786 (tttm) cc_final: 0.8549 (ttmm) REVERT: Q 283 ASN cc_start: 0.8911 (m-40) cc_final: 0.8508 (m-40) REVERT: Q 297 ASN cc_start: 0.6911 (t0) cc_final: 0.6585 (t0) REVERT: Q 308 PHE cc_start: 0.7664 (t80) cc_final: 0.7088 (t80) REVERT: Q 327 ASP cc_start: 0.7453 (t0) cc_final: 0.7241 (t0) REVERT: Q 380 ILE cc_start: 0.8900 (mt) cc_final: 0.8678 (tt) REVERT: Q 418 ASP cc_start: 0.8230 (t0) cc_final: 0.7978 (t0) REVERT: Q 477 GLU cc_start: 0.7580 (tp30) cc_final: 0.7258 (tp30) REVERT: Q 544 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7743 (tp-100) REVERT: Q 601 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8273 (mm-30) REVERT: R 24 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7414 (mtp85) REVERT: R 140 ASP cc_start: 0.6349 (m-30) cc_final: 0.6072 (m-30) REVERT: R 192 ARG cc_start: 0.7337 (tpp80) cc_final: 0.6012 (tpp80) REVERT: R 240 GLN cc_start: 0.7454 (mp10) cc_final: 0.6503 (mt0) REVERT: R 245 LEU cc_start: 0.7481 (pp) cc_final: 0.6915 (mt) REVERT: R 270 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6859 (tt) REVERT: R 282 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.8089 (mtp180) REVERT: R 283 ASN cc_start: 0.7638 (m110) cc_final: 0.7316 (m110) REVERT: R 427 GLN cc_start: 0.7281 (mp10) cc_final: 0.7020 (mp10) REVERT: R 497 TYR cc_start: 0.7764 (t80) cc_final: 0.7487 (t80) REVERT: R 508 LYS cc_start: 0.7917 (mttp) cc_final: 0.7697 (mttp) REVERT: R 550 MET cc_start: 0.8104 (ppp) cc_final: 0.7536 (ppp) REVERT: R 559 LYS cc_start: 0.8476 (mtmt) cc_final: 0.7970 (mtmt) outliers start: 109 outliers final: 87 residues processed: 1627 average time/residue: 0.6574 time to fit residues: 1735.4098 Evaluate side-chains 1665 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1569 time to evaluate : 5.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 361 MET Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 295 ILE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 388 ILE Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 353 PHE Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 348 THR Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 413 MET Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 394 VAL Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 444 ASP Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 469 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 697 optimal weight: 2.9990 chunk 735 optimal weight: 0.7980 chunk 670 optimal weight: 7.9990 chunk 714 optimal weight: 6.9990 chunk 734 optimal weight: 1.9990 chunk 430 optimal weight: 0.9990 chunk 311 optimal weight: 5.9990 chunk 561 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 646 optimal weight: 0.6980 chunk 676 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS E 154 ASN E 195 GLN H 129 GLN I 365 GLN P 382 GLN Q 214 GLN Q 443 GLN R 277 GLN ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 66064 Z= 0.248 Angle : 0.553 18.038 89371 Z= 0.280 Chirality : 0.042 0.203 9710 Planarity : 0.004 0.050 11449 Dihedral : 8.692 157.591 9438 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.90 % Allowed : 16.69 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.09), residues: 7933 helix: 1.12 (0.10), residues: 3107 sheet: 0.94 (0.16), residues: 1009 loop : -1.53 (0.09), residues: 3817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 49 HIS 0.006 0.001 HIS Q 434 PHE 0.025 0.001 PHE K 262 TYR 0.028 0.001 TYR R 258 ARG 0.011 0.000 ARG R 505 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1730 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1600 time to evaluate : 5.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8036 (m-30) cc_final: 0.7667 (m-30) REVERT: A 58 GLU cc_start: 0.7588 (mp0) cc_final: 0.7226 (mp0) REVERT: A 74 ASP cc_start: 0.8016 (m-30) cc_final: 0.7682 (m-30) REVERT: B 67 TYR cc_start: 0.8538 (m-80) cc_final: 0.8250 (m-80) REVERT: B 70 VAL cc_start: 0.8809 (t) cc_final: 0.8526 (m) REVERT: B 99 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7601 (ttm-80) REVERT: B 102 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 132 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7255 (mp0) REVERT: B 179 ASP cc_start: 0.8314 (t0) cc_final: 0.8043 (t0) REVERT: B 257 ILE cc_start: 0.8504 (mm) cc_final: 0.8221 (mt) REVERT: B 258 ASN cc_start: 0.8351 (m-40) cc_final: 0.7972 (m110) REVERT: B 374 LYS cc_start: 0.8601 (mtmt) cc_final: 0.8318 (mttp) REVERT: B 382 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7560 (tp30) REVERT: C 58 GLU cc_start: 0.7916 (pm20) cc_final: 0.7575 (pm20) REVERT: C 102 GLU cc_start: 0.7941 (tp30) cc_final: 0.7736 (tp30) REVERT: C 104 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7577 (mm-30) REVERT: C 286 GLU cc_start: 0.8126 (tp30) cc_final: 0.7897 (tp30) REVERT: C 290 ARG cc_start: 0.8883 (mmt180) cc_final: 0.8591 (mmt180) REVERT: C 316 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7533 (ttp-170) REVERT: D 109 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7223 (mtt-85) REVERT: D 128 GLU cc_start: 0.8122 (mp0) cc_final: 0.7891 (mp0) REVERT: D 129 GLN cc_start: 0.8472 (mm110) cc_final: 0.8111 (mm-40) REVERT: D 131 ARG cc_start: 0.8408 (ptm-80) cc_final: 0.8130 (ptm160) REVERT: D 132 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7082 (mm-30) REVERT: D 182 ILE cc_start: 0.8637 (mm) cc_final: 0.8424 (mt) REVERT: D 238 LEU cc_start: 0.4629 (OUTLIER) cc_final: 0.4365 (tt) REVERT: D 290 ARG cc_start: 0.8191 (mmt-90) cc_final: 0.7843 (mmt-90) REVERT: D 343 VAL cc_start: 0.8228 (t) cc_final: 0.7988 (t) REVERT: D 358 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8149 (mp) REVERT: E 60 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7955 (mp) REVERT: E 77 ASN cc_start: 0.7617 (m-40) cc_final: 0.7416 (m-40) REVERT: E 83 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: E 99 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.8446 (ttp-170) REVERT: E 118 GLU cc_start: 0.8113 (tp30) cc_final: 0.7764 (tp30) REVERT: E 155 ARG cc_start: 0.9017 (mmm160) cc_final: 0.8666 (mmm160) REVERT: E 283 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7393 (t) REVERT: E 361 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7332 (mpp) REVERT: E 405 ASN cc_start: 0.8243 (t0) cc_final: 0.7949 (t0) REVERT: F 45 MET cc_start: 0.8264 (tpp) cc_final: 0.8023 (mmt) REVERT: F 53 LYS cc_start: 0.8599 (ptmm) cc_final: 0.8397 (ttpp) REVERT: F 65 ASP cc_start: 0.7582 (m-30) cc_final: 0.7284 (m-30) REVERT: F 76 ASP cc_start: 0.7265 (m-30) cc_final: 0.6663 (m-30) REVERT: F 114 SER cc_start: 0.8719 (m) cc_final: 0.8225 (p) REVERT: F 137 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8205 (ttmm) REVERT: F 154 ASN cc_start: 0.7542 (m-40) cc_final: 0.7125 (m110) REVERT: F 233 TYR cc_start: 0.7506 (p90) cc_final: 0.6829 (p90) REVERT: F 296 SER cc_start: 0.8953 (m) cc_final: 0.8572 (t) REVERT: G 51 SER cc_start: 0.8584 (m) cc_final: 0.8258 (p) REVERT: G 53 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7616 (mttt) REVERT: G 107 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7438 (tm-30) REVERT: G 199 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8249 (mt0) REVERT: G 255 ASP cc_start: 0.7871 (t0) cc_final: 0.7376 (t0) REVERT: G 275 LYS cc_start: 0.8445 (mttt) cc_final: 0.8181 (mtpp) REVERT: G 353 LYS cc_start: 0.8488 (mttt) cc_final: 0.8238 (mttt) REVERT: G 405 ASN cc_start: 0.7697 (t0) cc_final: 0.7334 (m110) REVERT: H 46 LYS cc_start: 0.8250 (mttt) cc_final: 0.7925 (mtpp) REVERT: H 59 LEU cc_start: 0.8685 (mt) cc_final: 0.8417 (mm) REVERT: H 65 ASP cc_start: 0.7153 (m-30) cc_final: 0.6882 (m-30) REVERT: H 110 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8217 (ttmm) REVERT: H 118 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7716 (mm-30) REVERT: H 199 GLN cc_start: 0.7719 (mp10) cc_final: 0.7474 (mt0) REVERT: H 286 GLU cc_start: 0.7878 (tp30) cc_final: 0.7563 (tp30) REVERT: H 388 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8267 (m) REVERT: I 50 LYS cc_start: 0.8385 (ptmt) cc_final: 0.8059 (ttpp) REVERT: I 74 ASP cc_start: 0.7741 (m-30) cc_final: 0.7146 (m-30) REVERT: I 76 ASP cc_start: 0.7603 (m-30) cc_final: 0.7008 (m-30) REVERT: I 77 ASN cc_start: 0.7544 (t0) cc_final: 0.7143 (t0) REVERT: I 107 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: I 142 LYS cc_start: 0.8907 (tttt) cc_final: 0.8620 (ttmt) REVERT: I 266 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7404 (pp30) REVERT: J 17 SER cc_start: 0.8035 (m) cc_final: 0.7735 (t) REVERT: J 74 ASP cc_start: 0.7775 (m-30) cc_final: 0.7455 (t0) REVERT: J 300 THR cc_start: 0.8901 (m) cc_final: 0.8615 (p) REVERT: K 14 ASP cc_start: 0.7160 (m-30) cc_final: 0.6753 (m-30) REVERT: K 68 LEU cc_start: 0.8904 (mp) cc_final: 0.8702 (mt) REVERT: K 102 GLU cc_start: 0.7299 (pm20) cc_final: 0.7036 (pm20) REVERT: K 202 ASP cc_start: 0.8478 (m-30) cc_final: 0.8270 (m-30) REVERT: K 296 SER cc_start: 0.8644 (m) cc_final: 0.8425 (t) REVERT: K 379 SER cc_start: 0.8762 (m) cc_final: 0.8328 (t) REVERT: K 386 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.6866 (m-80) REVERT: K 398 GLU cc_start: 0.7576 (tp30) cc_final: 0.7076 (tp30) REVERT: L 63 LEU cc_start: 0.8067 (tp) cc_final: 0.7646 (tp) REVERT: L 70 VAL cc_start: 0.8559 (t) cc_final: 0.8260 (p) REVERT: L 116 TYR cc_start: 0.8605 (m-80) cc_final: 0.8234 (m-80) REVERT: L 374 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8349 (mtmm) REVERT: M 50 ASP cc_start: 0.8215 (m-30) cc_final: 0.7829 (m-30) REVERT: M 259 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8497 (pm20) REVERT: M 271 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7586 (ttm-80) REVERT: M 318 ASN cc_start: 0.8492 (t0) cc_final: 0.8179 (t0) REVERT: M 327 ASP cc_start: 0.8063 (t0) cc_final: 0.7747 (t0) REVERT: M 386 GLU cc_start: 0.7904 (tp30) cc_final: 0.7374 (tp30) REVERT: M 462 PHE cc_start: 0.8378 (t80) cc_final: 0.8125 (t80) REVERT: M 478 GLU cc_start: 0.8138 (mp0) cc_final: 0.7802 (mp0) REVERT: M 574 SER cc_start: 0.8318 (p) cc_final: 0.8021 (t) REVERT: N 249 GLU cc_start: 0.7264 (pt0) cc_final: 0.6676 (pm20) REVERT: N 301 GLU cc_start: 0.7671 (tt0) cc_final: 0.7353 (tt0) REVERT: N 302 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7692 (mttm) REVERT: N 336 ARG cc_start: 0.8387 (ptp90) cc_final: 0.8128 (mtm-85) REVERT: N 355 CYS cc_start: 0.8002 (p) cc_final: 0.7713 (p) REVERT: N 383 GLN cc_start: 0.7958 (mt0) cc_final: 0.7730 (mm-40) REVERT: N 394 VAL cc_start: 0.8855 (t) cc_final: 0.8401 (p) REVERT: N 401 GLU cc_start: 0.7243 (mp0) cc_final: 0.7012 (mp0) REVERT: N 478 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7573 (mm-30) REVERT: N 506 LYS cc_start: 0.8710 (mttm) cc_final: 0.8303 (mtpp) REVERT: O 107 ASN cc_start: 0.7822 (t0) cc_final: 0.7559 (t0) REVERT: O 115 ASP cc_start: 0.7982 (p0) cc_final: 0.7557 (p0) REVERT: O 171 ARG cc_start: 0.7669 (mmm-85) cc_final: 0.7379 (mmm-85) REVERT: O 416 GLU cc_start: 0.8032 (tp30) cc_final: 0.7783 (tm-30) REVERT: O 428 GLU cc_start: 0.7537 (tp30) cc_final: 0.7336 (tm-30) REVERT: O 559 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8520 (mtpp) REVERT: P 19 GLU cc_start: 0.7320 (mp0) cc_final: 0.7013 (mp0) REVERT: P 50 ASP cc_start: 0.7858 (m-30) cc_final: 0.7638 (m-30) REVERT: P 239 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7563 (tmtt) REVERT: P 283 ASN cc_start: 0.8553 (m-40) cc_final: 0.8220 (m110) REVERT: P 349 LEU cc_start: 0.8967 (mm) cc_final: 0.8708 (mt) REVERT: P 401 GLU cc_start: 0.8034 (mp0) cc_final: 0.7754 (mp0) REVERT: P 411 LYS cc_start: 0.7603 (mtmt) cc_final: 0.7379 (mtmt) REVERT: P 423 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7978 (mtmm) REVERT: P 444 ASP cc_start: 0.7440 (t0) cc_final: 0.7060 (t0) REVERT: P 459 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7637 (mm-30) REVERT: P 559 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8180 (mtmm) REVERT: Q 67 ASP cc_start: 0.7687 (m-30) cc_final: 0.7420 (m-30) REVERT: Q 209 ASN cc_start: 0.8500 (m110) cc_final: 0.8021 (m-40) REVERT: Q 211 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7360 (mp0) REVERT: Q 268 LYS cc_start: 0.8785 (tttm) cc_final: 0.8554 (ttmm) REVERT: Q 283 ASN cc_start: 0.8958 (m-40) cc_final: 0.8505 (m-40) REVERT: Q 297 ASN cc_start: 0.6936 (t0) cc_final: 0.6605 (t0) REVERT: Q 308 PHE cc_start: 0.7673 (t80) cc_final: 0.7117 (t80) REVERT: Q 327 ASP cc_start: 0.7481 (t0) cc_final: 0.7270 (t0) REVERT: Q 380 ILE cc_start: 0.8945 (mt) cc_final: 0.8716 (tt) REVERT: Q 477 GLU cc_start: 0.7749 (tp30) cc_final: 0.7388 (tp30) REVERT: Q 544 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7642 (tm-30) REVERT: Q 578 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7735 (pp) REVERT: Q 601 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8126 (mm-30) REVERT: R 24 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7463 (mtp85) REVERT: R 140 ASP cc_start: 0.6434 (m-30) cc_final: 0.6135 (m-30) REVERT: R 192 ARG cc_start: 0.7350 (tpp80) cc_final: 0.6017 (tpp80) REVERT: R 240 GLN cc_start: 0.7843 (mp10) cc_final: 0.6800 (mt0) REVERT: R 245 LEU cc_start: 0.7443 (pp) cc_final: 0.6821 (mt) REVERT: R 270 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6908 (tt) REVERT: R 282 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.8067 (mtp180) REVERT: R 283 ASN cc_start: 0.7626 (m110) cc_final: 0.7313 (m110) REVERT: R 427 GLN cc_start: 0.7419 (mp10) cc_final: 0.7142 (mp10) REVERT: R 497 TYR cc_start: 0.7826 (t80) cc_final: 0.7524 (t80) REVERT: R 508 LYS cc_start: 0.7985 (mttp) cc_final: 0.7771 (mttp) REVERT: R 517 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7394 (mtp180) REVERT: R 536 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7345 (ttt90) REVERT: R 559 LYS cc_start: 0.8484 (mtmt) cc_final: 0.7924 (mtmt) outliers start: 130 outliers final: 101 residues processed: 1656 average time/residue: 0.6588 time to fit residues: 1771.1901 Evaluate side-chains 1705 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1590 time to evaluate : 5.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 361 MET Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 259 GLN Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 297 ASN Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 353 PHE Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 382 GLN Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 348 THR Chi-restraints excluded: chain P residue 382 GLN Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 413 MET Chi-restraints excluded: chain P residue 466 GLN Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 394 VAL Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 444 ASP Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 578 LEU Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 517 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 712 optimal weight: 2.9990 chunk 469 optimal weight: 2.9990 chunk 756 optimal weight: 2.9990 chunk 461 optimal weight: 3.9990 chunk 358 optimal weight: 3.9990 chunk 525 optimal weight: 0.5980 chunk 793 optimal weight: 2.9990 chunk 729 optimal weight: 0.0980 chunk 631 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 487 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 234 GLN E 154 ASN H 129 GLN P 382 GLN R 277 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 66064 Z= 0.152 Angle : 0.525 17.396 89371 Z= 0.263 Chirality : 0.041 0.209 9710 Planarity : 0.003 0.059 11449 Dihedral : 8.550 159.085 9438 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.53 % Allowed : 17.17 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.10), residues: 7933 helix: 1.22 (0.10), residues: 3095 sheet: 0.97 (0.16), residues: 1002 loop : -1.49 (0.09), residues: 3836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 340 HIS 0.003 0.001 HIS J 313 PHE 0.032 0.001 PHE Q 293 TYR 0.027 0.001 TYR R 258 ARG 0.014 0.000 ARG M 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1691 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1586 time to evaluate : 5.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7532 (mp0) cc_final: 0.7182 (mp0) REVERT: A 74 ASP cc_start: 0.7987 (m-30) cc_final: 0.7659 (m-30) REVERT: A 374 LYS cc_start: 0.8237 (mttm) cc_final: 0.8008 (mttm) REVERT: B 67 TYR cc_start: 0.8516 (m-80) cc_final: 0.8173 (m-80) REVERT: B 70 VAL cc_start: 0.8751 (t) cc_final: 0.8453 (m) REVERT: B 99 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7506 (ttm-80) REVERT: B 102 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7632 (mm-30) REVERT: B 132 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7225 (mp0) REVERT: B 179 ASP cc_start: 0.8285 (t0) cc_final: 0.7992 (t0) REVERT: B 257 ILE cc_start: 0.8477 (mm) cc_final: 0.8186 (mt) REVERT: B 258 ASN cc_start: 0.8320 (m-40) cc_final: 0.7939 (m110) REVERT: B 374 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8304 (mttp) REVERT: B 382 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7558 (tp30) REVERT: C 58 GLU cc_start: 0.7849 (pm20) cc_final: 0.7603 (pm20) REVERT: C 102 GLU cc_start: 0.7923 (tp30) cc_final: 0.7721 (tp30) REVERT: C 104 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7585 (mm-30) REVERT: C 132 GLU cc_start: 0.7702 (mp0) cc_final: 0.7282 (mp0) REVERT: C 286 GLU cc_start: 0.8123 (tp30) cc_final: 0.7907 (tp30) REVERT: C 290 ARG cc_start: 0.8881 (mmt180) cc_final: 0.8594 (mmt180) REVERT: C 316 ARG cc_start: 0.7762 (ttp-170) cc_final: 0.7538 (ttp-170) REVERT: D 128 GLU cc_start: 0.8100 (mp0) cc_final: 0.7888 (mp0) REVERT: D 129 GLN cc_start: 0.8456 (mm110) cc_final: 0.8106 (mm-40) REVERT: D 131 ARG cc_start: 0.8384 (ptm-80) cc_final: 0.8104 (ptm160) REVERT: D 132 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7078 (mm-30) REVERT: D 182 ILE cc_start: 0.8619 (mm) cc_final: 0.8405 (mt) REVERT: D 238 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.4331 (tt) REVERT: D 290 ARG cc_start: 0.8172 (mmt-90) cc_final: 0.7822 (mmt-90) REVERT: D 343 VAL cc_start: 0.8168 (t) cc_final: 0.7927 (t) REVERT: E 60 LEU cc_start: 0.8272 (tp) cc_final: 0.7986 (mp) REVERT: E 83 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: E 99 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8301 (ttp-170) REVERT: E 118 GLU cc_start: 0.8100 (tp30) cc_final: 0.7739 (tp30) REVERT: E 133 LYS cc_start: 0.8565 (mttm) cc_final: 0.8338 (mttt) REVERT: E 155 ARG cc_start: 0.9009 (mmm160) cc_final: 0.8651 (mmm160) REVERT: E 185 PHE cc_start: 0.8658 (m-80) cc_final: 0.8359 (m-80) REVERT: E 283 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7073 (m) REVERT: E 289 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8217 (ttp80) REVERT: E 405 ASN cc_start: 0.8231 (t0) cc_final: 0.7937 (t0) REVERT: F 45 MET cc_start: 0.8187 (tpp) cc_final: 0.7958 (mmt) REVERT: F 53 LYS cc_start: 0.8605 (ptmm) cc_final: 0.8393 (ttpp) REVERT: F 65 ASP cc_start: 0.7573 (m-30) cc_final: 0.7266 (m-30) REVERT: F 76 ASP cc_start: 0.7255 (m-30) cc_final: 0.6646 (m-30) REVERT: F 97 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8503 (ttmm) REVERT: F 114 SER cc_start: 0.8699 (m) cc_final: 0.8212 (p) REVERT: F 137 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8189 (ttmm) REVERT: F 233 TYR cc_start: 0.7435 (p90) cc_final: 0.6786 (p90) REVERT: F 296 SER cc_start: 0.8886 (m) cc_final: 0.8504 (t) REVERT: G 51 SER cc_start: 0.8549 (m) cc_final: 0.8220 (p) REVERT: G 53 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7609 (mttt) REVERT: G 107 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7547 (tm-30) REVERT: G 199 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8234 (mt0) REVERT: G 225 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8454 (mtpt) REVERT: G 255 ASP cc_start: 0.7868 (t0) cc_final: 0.7371 (t0) REVERT: G 275 LYS cc_start: 0.8417 (mttt) cc_final: 0.8150 (mtpp) REVERT: G 338 GLU cc_start: 0.7648 (mp0) cc_final: 0.7394 (tp30) REVERT: G 353 LYS cc_start: 0.8489 (mttt) cc_final: 0.8235 (mttt) REVERT: H 46 LYS cc_start: 0.8235 (mttt) cc_final: 0.7920 (mtpp) REVERT: H 65 ASP cc_start: 0.7156 (m-30) cc_final: 0.6881 (m-30) REVERT: H 110 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8217 (ttmm) REVERT: H 118 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7648 (mm-30) REVERT: H 199 GLN cc_start: 0.7690 (mp10) cc_final: 0.7455 (mt0) REVERT: I 74 ASP cc_start: 0.7726 (m-30) cc_final: 0.7121 (m-30) REVERT: I 76 ASP cc_start: 0.7619 (m-30) cc_final: 0.7009 (m-30) REVERT: I 77 ASN cc_start: 0.7422 (t0) cc_final: 0.7173 (t0) REVERT: I 107 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: I 142 LYS cc_start: 0.8881 (tttt) cc_final: 0.8597 (ttmt) REVERT: I 266 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7437 (pp30) REVERT: J 17 SER cc_start: 0.8042 (m) cc_final: 0.7725 (t) REVERT: J 74 ASP cc_start: 0.7755 (m-30) cc_final: 0.7440 (t0) REVERT: J 202 ASP cc_start: 0.8106 (m-30) cc_final: 0.7883 (m-30) REVERT: J 300 THR cc_start: 0.8869 (m) cc_final: 0.8638 (p) REVERT: K 14 ASP cc_start: 0.7110 (m-30) cc_final: 0.6701 (m-30) REVERT: K 76 ASP cc_start: 0.8405 (m-30) cc_final: 0.8055 (m-30) REVERT: K 102 GLU cc_start: 0.7290 (pm20) cc_final: 0.7041 (pm20) REVERT: K 202 ASP cc_start: 0.8459 (m-30) cc_final: 0.8249 (m-30) REVERT: K 242 GLU cc_start: 0.8147 (tt0) cc_final: 0.7932 (tt0) REVERT: K 259 LYS cc_start: 0.8159 (mttt) cc_final: 0.7906 (mttt) REVERT: K 296 SER cc_start: 0.8582 (m) cc_final: 0.8367 (t) REVERT: K 379 SER cc_start: 0.8771 (m) cc_final: 0.8322 (t) REVERT: K 386 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: K 398 GLU cc_start: 0.7560 (tp30) cc_final: 0.7141 (tp30) REVERT: L 70 VAL cc_start: 0.8529 (t) cc_final: 0.8218 (p) REVERT: L 374 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8359 (mtmm) REVERT: M 50 ASP cc_start: 0.8185 (m-30) cc_final: 0.7761 (m-30) REVERT: M 259 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8477 (pm20) REVERT: M 271 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7550 (ttm-80) REVERT: M 318 ASN cc_start: 0.8470 (t0) cc_final: 0.8159 (t0) REVERT: M 327 ASP cc_start: 0.8008 (t0) cc_final: 0.7688 (t0) REVERT: M 386 GLU cc_start: 0.7882 (tp30) cc_final: 0.7359 (tp30) REVERT: M 421 PHE cc_start: 0.7281 (m-10) cc_final: 0.6955 (m-80) REVERT: M 462 PHE cc_start: 0.8330 (t80) cc_final: 0.8067 (t80) REVERT: M 478 GLU cc_start: 0.8115 (mp0) cc_final: 0.7801 (mp0) REVERT: M 574 SER cc_start: 0.8287 (p) cc_final: 0.7964 (t) REVERT: N 5 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8280 (mtpp) REVERT: N 14 TYR cc_start: 0.8757 (p90) cc_final: 0.8286 (p90) REVERT: N 187 ASN cc_start: 0.8624 (m110) cc_final: 0.8335 (m110) REVERT: N 249 GLU cc_start: 0.7249 (pt0) cc_final: 0.6652 (pm20) REVERT: N 301 GLU cc_start: 0.7622 (tt0) cc_final: 0.7309 (tt0) REVERT: N 302 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7833 (mttt) REVERT: N 336 ARG cc_start: 0.8342 (ptp90) cc_final: 0.8077 (mtm-85) REVERT: N 355 CYS cc_start: 0.7901 (p) cc_final: 0.7646 (p) REVERT: N 383 GLN cc_start: 0.7978 (mt0) cc_final: 0.7758 (mm-40) REVERT: N 394 VAL cc_start: 0.8846 (t) cc_final: 0.8383 (p) REVERT: N 401 GLU cc_start: 0.7237 (mp0) cc_final: 0.7004 (mp0) REVERT: N 478 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7541 (mm-30) REVERT: N 506 LYS cc_start: 0.8701 (mttm) cc_final: 0.8308 (mtpp) REVERT: O 19 GLU cc_start: 0.7467 (mp0) cc_final: 0.7140 (mp0) REVERT: O 115 ASP cc_start: 0.7964 (p0) cc_final: 0.7547 (p0) REVERT: O 391 LYS cc_start: 0.8196 (ptpp) cc_final: 0.7964 (pttm) REVERT: O 416 GLU cc_start: 0.8035 (tp30) cc_final: 0.7784 (tm-30) REVERT: O 559 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8491 (mtpp) REVERT: P 19 GLU cc_start: 0.7304 (mp0) cc_final: 0.6998 (mp0) REVERT: P 50 ASP cc_start: 0.7840 (m-30) cc_final: 0.7617 (m-30) REVERT: P 239 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7618 (tmtt) REVERT: P 283 ASN cc_start: 0.8505 (m-40) cc_final: 0.8219 (m110) REVERT: P 349 LEU cc_start: 0.8955 (mm) cc_final: 0.8692 (mt) REVERT: P 401 GLU cc_start: 0.8008 (mp0) cc_final: 0.7730 (mp0) REVERT: P 411 LYS cc_start: 0.7582 (mtmt) cc_final: 0.7365 (mtmt) REVERT: P 423 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7984 (mtmm) REVERT: P 444 ASP cc_start: 0.7305 (t0) cc_final: 0.6946 (t0) REVERT: P 559 LYS cc_start: 0.8463 (ttmt) cc_final: 0.8156 (mtmm) REVERT: Q 67 ASP cc_start: 0.7682 (m-30) cc_final: 0.7412 (m-30) REVERT: Q 209 ASN cc_start: 0.8481 (m110) cc_final: 0.8035 (m-40) REVERT: Q 211 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7328 (mp0) REVERT: Q 268 LYS cc_start: 0.8768 (tttm) cc_final: 0.8556 (ttmm) REVERT: Q 283 ASN cc_start: 0.8916 (m-40) cc_final: 0.8485 (m-40) REVERT: Q 297 ASN cc_start: 0.6883 (t0) cc_final: 0.6542 (t0) REVERT: Q 308 PHE cc_start: 0.7631 (t80) cc_final: 0.7095 (t80) REVERT: Q 327 ASP cc_start: 0.7472 (t0) cc_final: 0.7261 (t0) REVERT: Q 380 ILE cc_start: 0.8937 (mt) cc_final: 0.8736 (tt) REVERT: Q 416 GLU cc_start: 0.8176 (tp30) cc_final: 0.7931 (tp30) REVERT: Q 477 GLU cc_start: 0.7643 (tp30) cc_final: 0.7305 (tp30) REVERT: Q 544 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7734 (tp-100) REVERT: Q 578 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7661 (pp) REVERT: Q 601 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8060 (mt-10) REVERT: R 24 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7430 (mtp85) REVERT: R 140 ASP cc_start: 0.6386 (m-30) cc_final: 0.6100 (m-30) REVERT: R 192 ARG cc_start: 0.7313 (tpp80) cc_final: 0.5975 (tpp80) REVERT: R 240 GLN cc_start: 0.7788 (mp10) cc_final: 0.6981 (mt0) REVERT: R 245 LEU cc_start: 0.7449 (pp) cc_final: 0.6841 (mt) REVERT: R 270 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6669 (tt) REVERT: R 282 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.8043 (mtp180) REVERT: R 283 ASN cc_start: 0.7638 (m110) cc_final: 0.7308 (m110) REVERT: R 391 LYS cc_start: 0.8351 (mttt) cc_final: 0.8131 (mttp) REVERT: R 427 GLN cc_start: 0.7421 (mp10) cc_final: 0.7142 (mp10) REVERT: R 497 TYR cc_start: 0.7784 (t80) cc_final: 0.7450 (t80) REVERT: R 508 LYS cc_start: 0.7968 (mttp) cc_final: 0.7764 (mttp) REVERT: R 536 ARG cc_start: 0.7628 (ttm-80) cc_final: 0.7301 (ttt90) REVERT: R 559 LYS cc_start: 0.8477 (mtmt) cc_final: 0.7918 (mtmt) REVERT: R 580 VAL cc_start: 0.8518 (p) cc_final: 0.8268 (m) outliers start: 105 outliers final: 86 residues processed: 1632 average time/residue: 0.6639 time to fit residues: 1760.5079 Evaluate side-chains 1673 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1578 time to evaluate : 5.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain K residue 361 MET Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 259 GLN Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 382 GLN Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 348 THR Chi-restraints excluded: chain P residue 382 GLN Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 413 MET Chi-restraints excluded: chain P residue 448 MET Chi-restraints excluded: chain P residue 466 GLN Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 394 VAL Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 444 ASP Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 578 LEU Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 469 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 387 optimal weight: 2.9990 chunk 501 optimal weight: 0.0050 chunk 672 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 582 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 632 optimal weight: 2.9990 chunk 264 optimal weight: 0.6980 chunk 649 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 234 GLN E 154 ASN F 154 ASN H 129 GLN O 107 ASN Q 443 GLN ** R 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.103501 restraints weight = 96111.454| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.57 r_work: 0.3087 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 66064 Z= 0.149 Angle : 0.519 17.169 89371 Z= 0.260 Chirality : 0.040 0.180 9710 Planarity : 0.003 0.054 11449 Dihedral : 8.475 158.384 9438 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.64 % Allowed : 17.30 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.10), residues: 7933 helix: 1.28 (0.10), residues: 3089 sheet: 1.02 (0.17), residues: 1002 loop : -1.45 (0.10), residues: 3842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 49 HIS 0.003 0.001 HIS J 313 PHE 0.032 0.001 PHE M 507 TYR 0.027 0.001 TYR R 258 ARG 0.013 0.000 ARG M 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23544.85 seconds wall clock time: 406 minutes 49.61 seconds (24409.61 seconds total)