Starting phenix.real_space_refine on Thu Sep 26 14:11:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/09_2024/8sub_40763.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/09_2024/8sub_40763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/09_2024/8sub_40763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/09_2024/8sub_40763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/09_2024/8sub_40763.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/09_2024/8sub_40763.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 5 5.21 5 S 134 5.16 5 C 39110 2.51 5 N 10395 2.21 5 O 11548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 61226 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "B" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3186 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 1 Chain: "C" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "D" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3203 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 11, 'TRANS': 389} Chain breaks: 2 Chain: "E" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 388} Chain breaks: 1 Chain: "F" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3198 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 1 Chain: "G" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3119 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 379} Chain breaks: 2 Chain: "H" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3203 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 11, 'TRANS': 389} Chain breaks: 1 Chain: "I" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3145 Classifications: {'peptide': 394} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Chain breaks: 2 Chain: "J" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3199 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 2 Chain: "K" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3182 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 2 Chain: "L" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3199 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 1 Chain: "M" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4536 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 550} Chain breaks: 2 Chain: "N" Number of atoms: 4548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4548 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 551} Chain breaks: 2 Chain: "O" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4637 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain breaks: 1 Chain: "P" Number of atoms: 4346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4346 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 526} Chain breaks: 4 Chain: "Q" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4389 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 530} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.76, per 1000 atoms: 0.45 Number of scatterers: 61226 At special positions: 0 Unit cell: (187.59, 183.15, 220.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 134 16.00 P 34 15.00 Mg 5 11.99 O 11548 8.00 N 10395 7.00 C 39110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.01 Conformation dependent library (CDL) restraints added in 6.0 seconds 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14078 Finding SS restraints... Secondary structure from input PDB file: 362 helices and 65 sheets defined 47.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.33 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.538A pdb=" N ARG A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.887A pdb=" N SER A 37 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 38 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLY A 39 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS A 40 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 41 " --> pdb=" O VAL A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 41' Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 58 through 66 removed outlier: 4.544A pdb=" N ALA A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 81 through 99 removed outlier: 3.535A pdb=" N ASP A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 122 removed outlier: 3.809A pdb=" N GLU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.581A pdb=" N PHE A 130 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.648A pdb=" N LYS A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASP A 139 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA A 140 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.758A pdb=" N LYS A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.591A 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: 3.700A pdb=" N TYR A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.560A pdb=" N ALA A 321 " --> pdb=" O ILE A 317 " (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: 3.749A pdb=" N ALA A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.514A pdb=" N HIS A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.692A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.909A pdb=" N ARG B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 removed outlier: 3.620A pdb=" N SER B 37 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.606A pdb=" N VAL B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 removed outlier: 3.773A pdb=" N LEU B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 removed outlier: 3.752A pdb=" N ASP B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 99 removed outlier: 3.529A pdb=" N LEU B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 122 removed outlier: 3.673A pdb=" N GLU B 105 " --> pdb=" O CYS B 101 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 removed outlier: 3.950A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.798A pdb=" N LYS B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP B 139 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 140 " --> pdb=" O LYS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.510A pdb=" N LYS B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 181 Processing helix chain 'B' and resid 198 through 201 removed outlier: 4.004A pdb=" N PHE B 201 " --> pdb=" O PRO B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 252 through 260 removed outlier: 4.394A pdb=" N ASP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.864A pdb=" N GLU B 286 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.550A pdb=" N ASN B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.759A pdb=" N LEU B 323 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 3.528A 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 335 through 345 removed outlier: 3.726A pdb=" N ALA B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 360 removed outlier: 3.581A pdb=" N LYS B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.908A pdb=" N ALA B 375 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.784A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'C' and resid 11 through 23 removed outlier: 3.548A pdb=" N TYR C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 21 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 23 " --> pdb=" O VAL C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 38 removed outlier: 3.515A pdb=" N SER C 37 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 38 " --> pdb=" O GLY C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 34 through 38' Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 58 through 66 removed outlier: 4.202A pdb=" N ALA C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.540A pdb=" N SER C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 100 removed outlier: 3.519A pdb=" N LEU C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 122 removed outlier: 3.597A pdb=" N GLU C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 removed outlier: 3.561A pdb=" N GLN C 129 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 130 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG C 131 " --> pdb=" O GLU C 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 131' Processing helix chain 'C' and resid 134 through 140 removed outlier: 3.623A pdb=" N LYS C 137 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 138 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP C 139 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA C 140 " --> pdb=" O LYS C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 140' Processing helix chain 'C' and resid 141 through 153 removed outlier: 3.832A pdb=" N LYS C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 181 removed outlier: 3.611A pdb=" N ASP C 179 " --> pdb=" O TRP C 175 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.997A pdb=" N PHE C 201 " --> pdb=" O PRO C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 201' Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.584A pdb=" N ILE C 256 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 4.027A pdb=" N TYR C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 335 through 346 removed outlier: 3.863A pdb=" N ALA C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 360 removed outlier: 3.605A pdb=" N LEU C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.598A pdb=" N VAL C 381 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 396 through 407 removed outlier: 3.569A pdb=" N ALA C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.748A 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: 3.860A pdb=" N LEU D 60 " --> pdb=" O TYR D 56 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY D 61 " --> pdb=" O PRO D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 78 Processing helix chain 'D' and resid 81 through 99 removed outlier: 3.694A pdb=" N ASP D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 removed outlier: 3.695A pdb=" N LYS D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 132 removed outlier: 3.583A pdb=" N GLN D 129 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG D 131 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 removed outlier: 3.849A pdb=" N LYS D 137 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS D 138 " --> pdb=" O GLN D 135 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP D 139 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA D 140 " --> pdb=" O LYS D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 140' Processing helix chain 'D' and resid 141 through 154 removed outlier: 3.901A pdb=" N ASN D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 179 removed outlier: 3.545A pdb=" N ASP D 179 " --> pdb=" O TRP D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 removed outlier: 3.695A pdb=" N PHE D 201 " --> pdb=" O PRO D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.651A pdb=" N TYR D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 removed outlier: 3.683A pdb=" N ILE D 256 " --> pdb=" O TYR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.531A pdb=" N GLU D 286 " --> pdb=" O PHE D 282 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 293 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 295 " --> pdb=" O PHE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 321 removed outlier: 4.049A pdb=" N ILE D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 335 through 344 removed outlier: 4.034A pdb=" N ALA D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 360 removed outlier: 3.506A pdb=" N LYS D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 360 " --> pdb=" O VAL D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 375 removed outlier: 3.670A pdb=" N LYS D 374 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.770A pdb=" N LEU D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 407 removed outlier: 3.663A pdb=" N ALA D 404 " --> pdb=" O VAL D 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 23 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.658A pdb=" N VAL E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP E 49 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 66 removed outlier: 4.147A 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 81 through 100 removed outlier: 3.617A pdb=" N ILE E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 110 removed outlier: 3.617A pdb=" N GLU E 105 " --> pdb=" O CYS E 101 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 122 removed outlier: 4.025A pdb=" N LYS E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 132 removed outlier: 3.878A pdb=" N PHE E 130 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 140 removed outlier: 3.666A pdb=" N LYS E 137 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP E 139 " --> pdb=" O GLY E 136 " (cutoff:3.500A) removed outlier: 6.675A 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 154 removed outlier: 3.721A pdb=" N LYS E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 181 removed outlier: 3.633A pdb=" N ASP E 179 " --> pdb=" O TRP E 175 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 180 " --> pdb=" O ALA E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 201 removed outlier: 3.827A 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: 3.656A pdb=" N TYR E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE E 295 " --> pdb=" O PHE E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 321 Processing helix chain 'E' and resid 335 through 346 removed outlier: 3.902A pdb=" N THR E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS E 342 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 360 Processing helix chain 'E' and resid 371 through 375 Processing helix chain 'E' and resid 376 through 383 removed outlier: 3.634A pdb=" N VAL E 381 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU E 382 " --> pdb=" O ASN E 378 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 406 removed outlier: 3.535A pdb=" N LEU E 399 " --> pdb=" O ILE E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 23 removed outlier: 3.665A pdb=" N CYS F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 38 removed outlier: 3.846A pdb=" N SER F 37 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 56 removed outlier: 3.640A pdb=" N VAL F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP F 49 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 66 removed outlier: 4.080A pdb=" N LEU F 60 " --> pdb=" O TYR F 56 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 77 Processing helix chain 'F' and resid 82 through 99 removed outlier: 3.618A pdb=" N ASP F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG F 99 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 122 removed outlier: 3.684A pdb=" N GLU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 132 removed outlier: 3.882A pdb=" N ARG F 131 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 141 removed outlier: 3.768A pdb=" N LYS F 137 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP F 139 " --> pdb=" O GLY F 136 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA F 140 " --> pdb=" O LYS F 137 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE F 141 " --> pdb=" O LYS F 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 134 through 141' Processing helix chain 'F' and resid 142 through 154 removed outlier: 3.669A pdb=" N ASN F 154 " --> pdb=" O LYS F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 181 Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.706A pdb=" N PHE F 201 " --> pdb=" O PRO F 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 198 through 201' Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 252 through 258 Processing helix chain 'F' and resid 281 through 295 removed outlier: 4.283A pdb=" N GLY F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU F 286 " --> pdb=" O PHE F 282 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.537A pdb=" N ASN F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY F 320 " --> pdb=" O ARG F 316 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA F 321 " --> pdb=" O ILE F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.758A pdb=" N ALA F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 360 removed outlier: 3.610A pdb=" N ALA F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 375 removed outlier: 3.762A pdb=" N LYS F 374 " --> pdb=" O GLY F 371 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F 375 " --> pdb=" O GLY F 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 371 through 375' Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.520A pdb=" N GLU F 382 " --> pdb=" O ASN F 378 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS F 383 " --> pdb=" O SER F 379 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU F 384 " --> pdb=" O PHE F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 408 removed outlier: 4.249A pdb=" N LEU F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 24 removed outlier: 3.561A pdb=" N PHE G 15 " --> pdb=" O ASN G 11 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN G 24 " --> pdb=" O TYR G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 37 removed outlier: 3.515A pdb=" N ALA G 36 " --> pdb=" O GLY G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 54 Processing helix chain 'G' and resid 71 through 78 Processing helix chain 'G' and resid 83 through 100 Processing helix chain 'G' and resid 101 through 122 removed outlier: 3.912A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 132 removed outlier: 4.321A pdb=" N ARG G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 138 removed outlier: 3.969A pdb=" N LYS G 138 " --> pdb=" O GLN G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 141 No H-bonds generated for 'chain 'G' and resid 139 through 141' Processing helix chain 'G' and resid 142 through 155 removed outlier: 3.898A pdb=" N GLU G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 147 " --> pdb=" O TYR G 143 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 181 Processing helix chain 'G' and resid 198 through 201 removed outlier: 3.912A pdb=" N PHE G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 201' Processing helix chain 'G' and resid 244 through 252 Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.515A pdb=" N ILE G 256 " --> pdb=" O TYR G 252 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE G 257 " --> pdb=" O ILE G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 296 removed outlier: 3.746A pdb=" N TYR G 284 " --> pdb=" O ILE G 280 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU G 286 " --> pdb=" O PHE G 282 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET G 287 " --> pdb=" O VAL G 283 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 322 removed outlier: 4.018A pdb=" N ASN G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG G 316 " --> pdb=" O TYR G 312 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU G 322 " --> pdb=" O ILE G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 345 removed outlier: 3.748A pdb=" N LYS G 342 " --> pdb=" O GLU G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 360 Processing helix chain 'G' and resid 376 through 384 removed outlier: 3.582A pdb=" N LEU G 384 " --> pdb=" O PHE G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 406 Processing helix chain 'H' and resid 11 through 23 removed outlier: 3.630A pdb=" N CYS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 54 removed outlier: 3.546A pdb=" N GLN H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 66 Processing helix chain 'H' and resid 71 through 78 removed outlier: 3.536A pdb=" N SER H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP H 76 " --> pdb=" O GLN H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 99 Processing helix chain 'H' and resid 102 through 122 removed outlier: 3.614A pdb=" N ILE H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA H 122 " --> pdb=" O GLU H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 132 removed outlier: 3.561A pdb=" N GLN H 129 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE H 130 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG H 131 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU H 132 " --> pdb=" O GLN H 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 126 through 132' Processing helix chain 'H' and resid 134 through 140 removed outlier: 3.745A pdb=" N LYS H 138 " --> pdb=" O GLN H 135 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP H 139 " --> pdb=" O GLY H 136 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA H 140 " --> pdb=" O LYS H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 154 removed outlier: 3.821A pdb=" N ASN H 154 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 181 removed outlier: 3.680A pdb=" N ASP H 179 " --> pdb=" O TRP H 175 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.840A 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 281 through 295 removed outlier: 4.022A pdb=" N GLY H 285 " --> pdb=" O GLY H 281 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE H 295 " --> pdb=" O PHE H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 321 Processing helix chain 'H' and resid 322 through 324 No H-bonds generated for 'chain 'H' and resid 322 through 324' Processing helix chain 'H' and resid 335 through 345 removed outlier: 3.765A pdb=" N ALA H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS H 345 " --> pdb=" O THR H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 360 removed outlier: 3.930A pdb=" N ALA H 354 " --> pdb=" O GLU H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 384 removed outlier: 3.694A pdb=" N GLU H 382 " --> pdb=" O ASN H 378 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU H 384 " --> pdb=" O PHE H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 407 removed outlier: 4.056A pdb=" N SER H 407 " --> pdb=" O ILE H 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 23 removed outlier: 3.562A pdb=" N CYS I 23 " --> pdb=" O VAL I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 41 removed outlier: 3.590A pdb=" N SER I 37 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLY I 39 " --> pdb=" O ALA I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 56 removed outlier: 3.540A pdb=" N LYS I 50 " --> pdb=" O LYS I 46 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 66 removed outlier: 3.553A pdb=" N LEU I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 78 Processing helix chain 'I' and resid 81 through 100 removed outlier: 3.923A pdb=" N LYS I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 122 removed outlier: 3.860A pdb=" N LYS I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU I 112 " --> pdb=" O PHE I 108 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS I 121 " --> pdb=" O LYS I 117 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 130 removed outlier: 3.885A pdb=" N PHE I 130 " --> pdb=" O GLY I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 154 removed outlier: 3.607A pdb=" N LYS I 145 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN I 154 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 181 removed outlier: 3.536A pdb=" N TRP I 175 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA I 176 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA I 177 " --> pdb=" O LEU I 173 " (cutoff:3.500A) Processing helix 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: 4.049A pdb=" N TYR I 284 " --> pdb=" O ILE I 280 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE I 294 " --> pdb=" O ARG I 290 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE I 295 " --> pdb=" O PHE I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 321 removed outlier: 3.679A pdb=" N ALA I 321 " --> pdb=" O ILE I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 322 through 324 No H-bonds generated for 'chain 'I' and resid 322 through 324' Processing helix chain 'I' and resid 335 through 344 removed outlier: 3.571A pdb=" N ALA I 339 " --> pdb=" O GLU I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 358 Processing helix chain 'I' and resid 376 through 384 removed outlier: 3.781A pdb=" N GLU I 382 " --> pdb=" O ASN I 378 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS I 383 " --> pdb=" O SER I 379 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 406 removed outlier: 3.611A pdb=" N VAL I 400 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU I 401 " --> pdb=" O ASP I 397 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU I 406 " --> pdb=" O ALA I 402 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 23 removed outlier: 3.663A pdb=" N SER J 17 " --> pdb=" O ASP J 13 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER J 21 " --> pdb=" O SER J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 41 removed outlier: 3.674A pdb=" N SER J 37 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY J 39 " --> pdb=" O ALA J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 56 removed outlier: 3.571A pdb=" N VAL J 48 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 66 removed outlier: 3.767A pdb=" N ILE J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 78 Processing helix chain 'J' and resid 81 through 99 removed outlier: 3.690A pdb=" N LEU J 85 " --> pdb=" O ASN J 81 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE J 86 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 122 removed outlier: 3.822A pdb=" N LYS J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU J 112 " --> pdb=" O PHE J 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 132 removed outlier: 3.559A pdb=" N GLN J 129 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE J 130 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG J 131 " --> pdb=" O GLU J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 140 removed outlier: 3.725A pdb=" N LYS J 138 " --> pdb=" O GLN J 135 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP J 139 " --> pdb=" O GLY J 136 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA J 140 " --> pdb=" O LYS J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 154 removed outlier: 3.782A pdb=" N LYS J 145 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 181 removed outlier: 3.685A pdb=" N TRP J 175 " --> pdb=" O LEU J 171 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA J 176 " --> pdb=" O ALA J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 201 removed outlier: 3.752A 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: 3.745A pdb=" N TYR J 249 " --> pdb=" O ALA J 245 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP J 250 " --> pdb=" O SER J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 Processing helix chain 'J' and resid 274 through 278 removed outlier: 3.968A pdb=" N SER J 277 " --> pdb=" O ASN J 274 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS J 278 " --> pdb=" O LYS J 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 274 through 278' Processing helix chain 'J' and resid 281 through 295 removed outlier: 4.347A pdb=" N GLY J 285 " --> pdb=" O GLY J 281 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU J 286 " --> pdb=" O PHE J 282 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE J 295 " --> pdb=" O PHE J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 321 removed outlier: 3.558A pdb=" N GLY J 320 " --> pdb=" O ARG J 316 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA J 321 " --> pdb=" O ILE J 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 324 No H-bonds generated for 'chain 'J' and resid 322 through 324' Processing helix chain 'J' and resid 335 through 345 removed outlier: 3.823A pdb=" N ALA J 339 " --> pdb=" O GLU J 335 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR J 341 " --> pdb=" O LYS J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 360 Processing helix chain 'J' and resid 371 through 375 Processing helix chain 'J' and resid 376 through 384 removed outlier: 3.529A pdb=" N HIS J 383 " --> pdb=" O SER J 379 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 394 through 408 removed outlier: 3.537A pdb=" N ALA J 402 " --> pdb=" O GLU J 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 23 removed outlier: 3.507A pdb=" N SER K 21 " --> pdb=" O SER K 17 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS K 23 " --> pdb=" O VAL K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 41 removed outlier: 3.632A pdb=" N SER K 37 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY K 39 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS K 40 " --> pdb=" O SER K 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY K 41 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 56 removed outlier: 3.512A pdb=" N VAL K 48 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP K 49 " --> pdb=" O MET K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 66 removed outlier: 3.509A pdb=" N LEU K 63 " --> pdb=" O LEU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 78 Processing helix chain 'K' and resid 81 through 100 removed outlier: 3.558A pdb=" N LEU K 85 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER K 94 " --> pdb=" O THR K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 109 removed outlier: 3.583A pdb=" N GLU K 107 " --> pdb=" O ASP K 103 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 121 removed outlier: 3.815A pdb=" N SER K 114 " --> pdb=" O LYS K 110 " (cutoff:3.500A) removed outlier: 3.573A 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 126 through 132 removed outlier: 4.332A pdb=" N ARG K 131 " --> pdb=" O GLU K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 140 removed outlier: 3.786A pdb=" N LYS K 137 " --> pdb=" O ASN K 134 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS K 138 " --> pdb=" O GLN K 135 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP K 139 " --> pdb=" O GLY K 136 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA K 140 " --> pdb=" O LYS K 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 134 through 140' Processing helix chain 'K' and resid 141 through 153 removed outlier: 3.903A pdb=" N LYS K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU K 146 " --> pdb=" O LYS K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 179 removed outlier: 3.583A pdb=" N ASP K 179 " --> pdb=" O TRP K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 203 removed outlier: 3.503A pdb=" N ASP K 202 " --> pdb=" O GLN K 199 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU K 203 " --> pdb=" O ASN K 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 199 through 203' Processing helix chain 'K' and resid 244 through 252 Processing helix chain 'K' and resid 252 through 258 removed outlier: 3.546A pdb=" N ILE K 257 " --> pdb=" O ILE K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 295 removed outlier: 4.321A pdb=" N VAL K 283 " --> pdb=" O THR K 279 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR K 284 " --> pdb=" O ILE K 280 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG K 290 " --> pdb=" O GLU K 286 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE K 291 " --> pdb=" O MET K 287 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY K 292 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU K 293 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE K 295 " --> pdb=" O PHE K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 321 Processing helix chain 'K' and resid 322 through 324 No H-bonds generated for 'chain 'K' and resid 322 through 324' Processing helix chain 'K' and resid 335 through 345 removed outlier: 3.524A pdb=" N ALA K 339 " --> pdb=" O GLU K 335 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER K 344 " --> pdb=" O ILE K 340 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS K 345 " --> pdb=" O THR K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 361 removed outlier: 3.531A pdb=" N THR K 357 " --> pdb=" O LYS K 353 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 375 removed outlier: 3.899A pdb=" N ALA K 375 " --> pdb=" O GLY K 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 372 through 375' Processing helix chain 'K' and resid 376 through 381 Processing helix chain 'K' and resid 382 through 384 No H-bonds generated for 'chain 'K' and resid 382 through 384' Processing helix chain 'K' and resid 395 through 406 Processing helix chain 'L' and resid 11 through 22 Processing helix chain 'L' and resid 44 through 56 removed outlier: 3.819A pdb=" N VAL L 48 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TRP L 49 " --> pdb=" O MET L 45 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS L 50 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 66 removed outlier: 3.510A pdb=" N LEU L 60 " --> pdb=" O TYR L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 77 removed outlier: 3.852A pdb=" N ASP L 76 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN L 77 " --> pdb=" O ILE L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 99 removed outlier: 3.621A pdb=" N ASP L 87 " --> pdb=" O GLU L 83 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 122 removed outlier: 3.768A pdb=" N GLU L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.575A pdb=" N GLN L 129 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU L 132 " --> pdb=" O GLN L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 140 removed outlier: 3.628A pdb=" N LYS L 137 " --> pdb=" O ASN L 134 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS L 138 " --> pdb=" O GLN L 135 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP L 139 " --> pdb=" O GLY L 136 " (cutoff:3.500A) removed outlier: 6.661A 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 154 removed outlier: 3.596A pdb=" N LYS L 145 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER L 153 " --> pdb=" O SER L 149 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN L 154 " --> pdb=" O LYS L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 181 removed outlier: 3.572A pdb=" N TRP L 175 " --> pdb=" O LEU L 171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA L 176 " --> pdb=" O ALA L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 201 removed outlier: 3.842A pdb=" N PHE L 201 " --> pdb=" O PRO L 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 198 through 201' Processing helix chain 'L' and resid 244 through 250 Processing helix chain 'L' and resid 252 through 259 Processing helix chain 'L' and resid 283 through 295 removed outlier: 3.612A pdb=" N PHE L 288 " --> pdb=" O TYR L 284 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG L 289 " --> pdb=" O GLY L 285 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 290 " --> pdb=" O GLU L 286 " (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 335 through 345 removed outlier: 3.744A pdb=" N ALA L 339 " --> pdb=" O GLU L 335 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS L 345 " --> pdb=" O THR L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 349 through 360 removed outlier: 3.545A pdb=" N LEU L 358 " --> pdb=" O ALA L 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 375 removed outlier: 3.582A pdb=" N ALA L 375 " --> pdb=" O GLY L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 383 Processing helix chain 'L' and resid 393 through 407 removed outlier: 3.877A pdb=" N ASP L 397 " --> pdb=" O ASP L 393 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 137 Processing helix chain 'M' and resid 140 through 145 Proline residue: M 145 - end of helix Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 182 through 196 removed outlier: 3.583A pdb=" N LYS M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER M 195 " --> pdb=" O THR M 191 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU M 196 " --> pdb=" O ARG M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 271 removed outlier: 3.853A pdb=" N LEU M 266 " --> pdb=" O GLY M 262 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE M 267 " --> pdb=" O PHE M 263 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG M 271 " --> pdb=" O ILE M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 287 Processing helix chain 'M' and resid 288 through 291 removed outlier: 3.640A pdb=" N THR M 291 " --> pdb=" O ILE M 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 288 through 291' Processing helix chain 'M' and resid 321 through 331 removed outlier: 3.506A pdb=" N TRP M 325 " --> pdb=" O LYS M 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 344 No H-bonds generated for 'chain 'M' and resid 342 through 344' Processing helix chain 'M' and resid 345 through 356 removed outlier: 3.591A pdb=" N LEU M 349 " --> pdb=" O SER M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 372 removed outlier: 3.693A pdb=" N PHE M 371 " --> pdb=" O ASP M 367 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 385 removed outlier: 4.001A pdb=" N VAL M 378 " --> pdb=" O VAL M 374 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA M 385 " --> pdb=" O ILE M 381 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 392 Processing helix chain 'M' and resid 407 through 422 removed outlier: 3.527A pdb=" N LYS M 411 " --> pdb=" O THR M 407 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA M 412 " --> pdb=" O HIS M 408 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET M 413 " --> pdb=" O TRP M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 450 Processing helix chain 'M' and resid 452 through 465 removed outlier: 4.070A pdb=" N ALA M 458 " --> pdb=" O LEU M 454 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG M 463 " --> pdb=" O GLU M 459 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY M 465 " --> pdb=" O LEU M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 466 through 469 removed outlier: 3.995A pdb=" N SER M 469 " --> pdb=" O GLN M 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 466 through 469' Processing helix chain 'M' and resid 478 through 483 removed outlier: 4.243A pdb=" N TYR M 482 " --> pdb=" O GLU M 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 517 through 521 removed outlier: 3.664A pdb=" N LEU M 521 " --> pdb=" O PRO M 518 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 539 through 550 removed outlier: 3.855A pdb=" N GLN M 544 " --> pdb=" O GLU M 540 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA M 545 " --> pdb=" O ARG M 541 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU M 546 " --> pdb=" O ASP M 542 " (cutoff:3.500A) Processing helix chain 'M' and resid 557 through 564 removed outlier: 3.619A pdb=" N GLN M 560 " --> pdb=" O ILE M 557 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER M 562 " --> pdb=" O LYS M 559 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU M 564 " --> pdb=" O ILE M 561 " (cutoff:3.500A) Processing helix chain 'M' and resid 597 through 603 removed outlier: 4.099A pdb=" N GLU M 601 " --> pdb=" O VAL M 597 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 33 removed outlier: 3.836A pdb=" N GLN N 32 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 137 removed outlier: 3.687A 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 196 removed outlier: 3.601A pdb=" N PHE N 186 " --> pdb=" O GLY N 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 217 removed outlier: 3.748A pdb=" N THR N 217 " --> pdb=" O GLN N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 268 removed outlier: 3.676A pdb=" N GLY N 265 " --> pdb=" O LEU N 261 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE N 267 " --> pdb=" O PHE N 263 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS N 268 " --> pdb=" O ALA N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 287 Processing helix chain 'N' and resid 288 through 291 Processing helix chain 'N' and resid 322 through 331 Processing helix chain 'N' and resid 342 through 346 Processing helix chain 'N' and resid 347 through 355 Processing helix chain 'N' and resid 367 through 372 removed outlier: 3.850A pdb=" N PHE N 371 " --> pdb=" O ASP N 367 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER N 372 " --> pdb=" O ALA N 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 367 through 372' Processing helix chain 'N' and resid 374 through 386 removed outlier: 3.699A pdb=" N VAL N 378 " --> pdb=" O VAL N 374 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU N 386 " --> pdb=" O GLN N 382 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 422 removed outlier: 3.968A pdb=" N LYS N 411 " --> pdb=" O THR N 407 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA N 412 " --> pdb=" O HIS N 408 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU N 416 " --> pdb=" O ALA N 412 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL N 417 " --> pdb=" O MET N 413 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY N 422 " --> pdb=" O ASP N 418 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 465 removed outlier: 3.580A pdb=" N ILE N 460 " --> pdb=" O MET N 456 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY N 465 " --> pdb=" O LEU N 461 " (cutoff:3.500A) Processing helix chain 'N' and resid 498 through 503 Processing helix chain 'N' and resid 517 through 521 Processing helix chain 'N' and resid 524 through 527 Processing helix chain 'N' and resid 539 through 550 removed outlier: 3.541A pdb=" N ALA N 545 " --> pdb=" O ARG N 541 " (cutoff:3.500A) Processing helix chain 'N' and resid 557 through 564 removed outlier: 3.681A pdb=" N GLN N 560 " --> pdb=" O ILE N 557 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER N 562 " --> pdb=" O LYS N 559 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU N 564 " --> pdb=" O ILE N 561 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 137 removed outlier: 3.575A pdb=" N ILE O 135 " --> pdb=" O ASP O 131 " (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 170 removed outlier: 3.506A pdb=" N SER O 170 " --> pdb=" O ASP O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 198 removed outlier: 3.523A pdb=" N PHE O 186 " --> pdb=" O GLY O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 217 removed outlier: 3.813A pdb=" N THR O 217 " --> pdb=" O GLN O 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 261 through 271 Processing helix chain 'O' and resid 277 through 287 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: 3.637A 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: 4.040A pdb=" N LEU O 349 " --> pdb=" O SER O 345 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA O 351 " --> pdb=" O ALA O 347 " (cutoff:3.500A) Processing helix chain 'O' and resid 367 through 385 removed outlier: 3.759A 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 389 through 393 removed outlier: 4.192A pdb=" N ILE O 393 " --> pdb=" O ARG O 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 389 through 393' Processing helix chain 'O' and resid 407 through 422 removed outlier: 3.906A pdb=" N LYS O 411 " --> pdb=" O THR O 407 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA O 412 " --> pdb=" O HIS O 408 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP O 418 " --> pdb=" O SER O 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 465 removed outlier: 3.649A pdb=" N GLY O 465 " --> pdb=" O LEU O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 479 through 482 Processing helix chain 'O' and resid 490 through 494 removed outlier: 3.617A pdb=" N GLN O 493 " --> pdb=" O ILE O 490 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE O 494 " --> pdb=" O ASP O 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 490 through 494' Processing helix chain 'O' and resid 496 through 507 removed outlier: 3.588A pdb=" N LEU O 500 " --> pdb=" O ALA O 496 " (cutoff:3.500A) Processing helix chain 'O' and resid 517 through 521 Processing helix chain 'O' and resid 539 through 548 removed outlier: 3.545A pdb=" N LEU O 543 " --> pdb=" O ASN O 539 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU O 546 " --> pdb=" O ASP O 542 " (cutoff:3.500A) Processing helix chain 'O' and resid 559 through 564 removed outlier: 4.215A pdb=" N SER O 562 " --> pdb=" O LYS O 559 " (cutoff:3.500A) Processing helix chain 'O' and resid 597 through 603 removed outlier: 3.678A pdb=" N GLU O 601 " --> pdb=" O VAL O 597 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 34 removed outlier: 4.335A pdb=" N GLN P 32 " --> pdb=" O GLU P 29 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY P 33 " --> pdb=" O GLY P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 137 Processing helix chain 'P' and resid 140 through 144 removed outlier: 3.717A pdb=" N GLU P 143 " --> pdb=" O ASP P 140 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU P 144 " --> pdb=" O LYS P 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 140 through 144' Processing helix chain 'P' and resid 165 through 169 Processing helix chain 'P' and resid 182 through 198 removed outlier: 3.543A pdb=" N PHE P 186 " --> pdb=" O GLY P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 217 Processing helix chain 'P' and resid 261 through 271 removed outlier: 3.753A pdb=" N LEU P 266 " --> pdb=" O GLY P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 276 through 287 removed outlier: 4.045A pdb=" N ALA P 280 " --> pdb=" O THR P 276 " (cutoff:3.500A) Processing helix chain 'P' and resid 318 through 322 removed outlier: 3.698A pdb=" N LYS P 321 " --> pdb=" O ASN P 318 " (cutoff:3.500A) Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.565A pdb=" N THR P 348 " --> pdb=" O LYS P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 375 through 386 removed outlier: 3.615A pdb=" N ILE P 381 " --> pdb=" O LEU P 377 " (cutoff:3.500A) Processing helix chain 'P' and resid 387 through 394 removed outlier: 3.670A pdb=" N LYS P 391 " --> pdb=" O ASP P 387 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER P 392 " --> pdb=" O ILE P 388 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE P 393 " --> pdb=" O ARG P 389 " (cutoff:3.500A) Processing helix chain 'P' and resid 407 through 418 Processing helix chain 'P' and resid 446 through 465 removed outlier: 3.966A pdb=" N ARG P 463 " --> pdb=" O GLU P 459 " (cutoff:3.500A) Processing helix chain 'P' and resid 497 through 504 Processing helix chain 'P' and resid 505 through 507 No H-bonds generated for 'chain 'P' and resid 505 through 507' Processing helix chain 'P' and resid 517 through 521 Processing helix chain 'P' and resid 525 through 527 No H-bonds generated for 'chain 'P' and resid 525 through 527' Processing helix chain 'P' and resid 539 through 548 removed outlier: 3.651A pdb=" N LEU P 543 " --> pdb=" O ASN P 539 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA P 545 " --> pdb=" O ARG P 541 " (cutoff:3.500A) Processing helix chain 'P' and resid 557 through 564 removed outlier: 3.669A pdb=" N ILE P 561 " --> pdb=" O LEU P 558 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER P 562 " --> pdb=" O LYS P 559 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY P 563 " --> pdb=" O GLN P 560 " (cutoff:3.500A) Processing helix chain 'P' and resid 598 through 603 removed outlier: 4.036A pdb=" N ALA P 603 " --> pdb=" O GLU P 600 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 138 removed outlier: 3.683A pdb=" N LEU Q 133 " --> pdb=" O THR Q 129 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN Q 134 " --> pdb=" O SER Q 130 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE Q 135 " --> pdb=" O ASP Q 131 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 147 removed outlier: 3.641A 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 182 through 198 Processing helix chain 'Q' and resid 213 through 217 Processing helix chain 'Q' and resid 261 through 270 removed outlier: 3.810A pdb=" N LEU Q 270 " --> pdb=" O LEU Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 286 Processing helix chain 'Q' and resid 321 through 332 Processing helix chain 'Q' and resid 344 through 355 removed outlier: 4.286A pdb=" N THR Q 348 " --> pdb=" O LYS Q 344 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 373 removed outlier: 3.810A pdb=" N SER Q 372 " --> pdb=" O ALA Q 368 " (cutoff:3.500A) Processing helix chain 'Q' and resid 374 through 386 removed outlier: 4.535A pdb=" N GLU Q 386 " --> pdb=" O GLN Q 382 " (cutoff:3.500A) Processing helix chain 'Q' and resid 387 through 393 removed outlier: 4.161A pdb=" N ILE Q 393 " --> pdb=" O ARG Q 389 " (cutoff:3.500A) Processing helix chain 'Q' and resid 409 through 421 removed outlier: 3.527A pdb=" N GLU Q 416 " --> pdb=" O ALA Q 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 445 through 465 removed outlier: 3.514A pdb=" N LEU Q 449 " --> pdb=" O HIS Q 445 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA Q 452 " --> pdb=" O MET Q 448 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG Q 463 " --> pdb=" O GLU Q 459 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG Q 464 " --> pdb=" O ILE Q 460 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY Q 465 " --> pdb=" O LEU Q 461 " (cutoff:3.500A) Processing helix chain 'Q' and resid 478 through 482 Processing helix chain 'Q' and resid 522 through 527 removed outlier: 3.856A pdb=" N LEU Q 526 " --> pdb=" O SER Q 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 539 through 550 removed outlier: 3.532A pdb=" N LEU Q 543 " --> pdb=" O ASN Q 539 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA Q 545 " --> pdb=" O ARG Q 541 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU Q 546 " --> pdb=" O ASP Q 542 " (cutoff:3.500A) Processing helix chain 'Q' and resid 557 through 564 removed outlier: 4.163A pdb=" N SER Q 562 " --> pdb=" O LYS Q 559 " (cutoff:3.500A) Processing helix chain 'Q' and resid 597 through 602 removed outlier: 4.235A pdb=" N GLU Q 601 " --> pdb=" O VAL Q 597 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.541A pdb=" N ASN A 27 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N PHE A 303 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY A 29 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ASN A 305 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 31 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 164 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 221 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 207 Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.507A pdb=" N THR B 300 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL B 330 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 302 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N TYR B 332 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 304 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 28 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N PHE B 165 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 30 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 164 " --> pdb=" O TYR B 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 188 through 189 Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 207 Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AA9, first strand: chain 'C' and resid 8 through 9 removed outlier: 3.725A pdb=" N ASN C 8 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C 28 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N PHE C 165 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL C 30 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 164 " --> pdb=" O TYR C 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB2, first strand: chain 'C' and resid 232 through 234 Processing sheet with id=AB3, first strand: chain 'D' and resid 8 through 10 removed outlier: 3.733A pdb=" N ASN D 8 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 5 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE D 3 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL D 28 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE D 165 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL D 30 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE D 164 " --> pdb=" O TYR D 224 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN D 183 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU D 223 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE D 185 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LYS D 225 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 188 through 189 Processing sheet with id=AB5, first strand: chain 'D' and resid 203 through 207 Processing sheet with id=AB6, first strand: chain 'D' and resid 232 through 234 Processing sheet with id=AB7, first strand: chain 'E' and resid 8 through 9 removed outlier: 3.711A pdb=" N ASN E 8 " --> pdb=" O GLN E 5 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL E 28 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N PHE E 165 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL E 30 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE E 164 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 188 through 189 Processing sheet with id=AB9, first strand: chain 'E' and resid 232 through 234 Processing sheet with id=AC1, first strand: chain 'F' and resid 8 through 9 removed outlier: 8.544A pdb=" N THR F 367 " --> pdb=" O PHE F 327 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL F 329 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL F 369 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 331 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN F 27 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE F 303 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY F 29 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN F 305 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU F 31 " --> pdb=" O ASN F 305 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL F 28 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE F 165 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL F 30 " --> pdb=" O PHE F 165 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE F 164 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLN F 183 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU F 223 " --> pdb=" O GLN F 183 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE F 185 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LYS F 225 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 188 through 189 Processing sheet with id=AC3, first strand: chain 'F' and resid 203 through 207 Processing sheet with id=AC4, first strand: chain 'F' and resid 232 through 234 Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 4 Processing sheet with id=AC6, first strand: chain 'G' and resid 183 through 185 removed outlier: 6.783A pdb=" N ILE G 164 " --> pdb=" O TYR G 224 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL G 30 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N GLY G 29 " --> pdb=" O PHE G 303 " (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 234 Processing sheet with id=AC9, first strand: chain 'H' and resid 8 through 9 removed outlier: 3.575A pdb=" N ASN H 8 " --> pdb=" O GLN H 5 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL H 28 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N PHE H 165 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL H 30 " --> pdb=" O PHE H 165 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE H 164 " --> pdb=" O TYR H 224 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN H 183 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU H 223 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE H 185 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 7.880A 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 Processing sheet with id=AD2, first strand: chain 'H' and resid 203 through 207 Processing sheet with id=AD3, first strand: chain 'H' and resid 233 through 234 Processing sheet with id=AD4, first strand: chain 'I' and resid 8 through 9 removed outlier: 3.820A pdb=" N ASN I 8 " --> pdb=" O GLN I 5 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN I 27 " --> pdb=" O ALA I 301 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N PHE I 303 " --> pdb=" O ASN I 27 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY I 29 " --> pdb=" O PHE I 303 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN I 305 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU I 31 " --> pdb=" O ASN I 305 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA I 163 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE I 164 " --> pdb=" O TYR I 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 188 through 189 Processing sheet with id=AD6, first strand: chain 'I' and resid 232 through 234 Processing sheet with id=AD7, first strand: chain 'J' and resid 3 through 5 removed outlier: 6.978A pdb=" N VAL J 28 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N PHE J 165 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL J 30 " --> pdb=" O PHE J 165 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE J 164 " --> pdb=" O TYR J 224 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 188 through 189 Processing sheet with id=AD9, first strand: chain 'J' and resid 203 through 204 removed outlier: 3.709A pdb=" N ARG K 206 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 232 through 234 Processing sheet with id=AE2, first strand: chain 'K' and resid 8 through 9 removed outlier: 8.778A pdb=" N THR K 367 " --> pdb=" O PHE K 327 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL K 329 " --> pdb=" O THR K 367 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL K 369 " --> pdb=" O VAL K 329 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE K 331 " --> pdb=" O VAL K 369 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL K 28 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N PHE K 165 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL K 30 " --> pdb=" O PHE K 165 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE K 164 " --> pdb=" O TYR K 224 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN K 183 " --> pdb=" O ALA K 221 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU K 223 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE K 185 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LYS K 225 " --> pdb=" O PHE K 185 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 188 through 189 Processing sheet with id=AE4, first strand: chain 'K' and resid 232 through 234 Processing sheet with id=AE5, first strand: chain 'L' and resid 3 through 5 removed outlier: 3.556A pdb=" N THR L 367 " --> pdb=" O VAL L 329 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN L 27 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N PHE L 303 " --> pdb=" O ASN L 27 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY L 29 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASN L 305 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU L 31 " --> pdb=" O ASN L 305 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL L 28 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N PHE L 165 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL L 30 " --> pdb=" O PHE L 165 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE L 164 " --> pdb=" O TYR L 224 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN L 183 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU L 223 " --> pdb=" O GLN L 183 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE L 185 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LYS L 225 " --> pdb=" O PHE L 185 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 188 through 189 Processing sheet with id=AE7, first strand: chain 'L' and resid 232 through 234 Processing sheet with id=AE8, first strand: chain 'M' and resid 109 through 112 removed outlier: 6.391A pdb=" N ARG M 92 " --> pdb=" O PHE M 70 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE M 70 " --> pdb=" O ARG M 92 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE M 94 " --> pdb=" O MET M 68 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET M 68 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA M 96 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR M 66 " --> pdb=" O ALA M 96 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA M 98 " --> pdb=" O ARG M 64 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG M 64 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY M 100 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP M 55 " --> pdb=" O SER M 124 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER M 124 " --> pdb=" O ASP M 55 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY M 13 " --> pdb=" O ALA M 125 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG M 24 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU M 18 " --> pdb=" O ARG M 22 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ARG M 22 " --> pdb=" O LEU M 18 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU M 27 " --> pdb=" O ARG M 92 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG M 92 " --> pdb=" O LEU M 27 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 35 through 37 Processing sheet with id=AF1, first strand: chain 'M' and resid 160 through 164 removed outlier: 4.235A pdb=" N GLY M 151 " --> pdb=" O ILE M 161 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA M 163 " --> pdb=" O GLU M 149 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU M 149 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA M 174 " --> pdb=" O PHE M 533 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG M 202 " --> pdb=" O VAL M 473 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU M 475 " --> pdb=" O ARG M 202 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL M 204 " --> pdb=" O LEU M 475 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLU M 477 " --> pdb=" O VAL M 204 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE M 206 " --> pdb=" O GLU M 477 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS M 254 " --> pdb=" O ILE M 226 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 256 through 257 removed outlier: 5.788A pdb=" N ILE M 256 " --> pdb=" O ASN M 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'M' and resid 299 through 301 removed outlier: 3.613A pdb=" N PHE M 308 " --> pdb=" O LEU M 300 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 13 through 17 removed outlier: 6.455A pdb=" N ARG N 24 " --> pdb=" O VAL N 16 " (cutoff:3.500A) 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: 6.382A pdb=" N LEU N 60 " --> pdb=" O PHE N 101 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE N 101 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL N 62 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE N 95 " --> pdb=" O THR N 66 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET N 68 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 6.927A 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 109 through 112 current: chain 'O' and resid 22 through 27 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 22 through 27 current: chain 'O' and resid 60 through 70 removed outlier: 6.325A pdb=" N LEU O 60 " --> pdb=" O PHE O 101 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE O 101 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL O 62 " --> pdb=" O ILE O 99 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE O 95 " --> pdb=" O THR O 66 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N MET O 68 " --> pdb=" O GLN O 93 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLN O 93 " --> pdb=" O MET O 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 109 through 112 current: chain 'P' and resid 22 through 27 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 22 through 27 current: chain 'P' and resid 59 through 70 removed outlier: 3.698A pdb=" N GLY P 100 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG P 64 " --> pdb=" O ALA P 98 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA P 98 " --> pdb=" O ARG P 64 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR P 66 " --> pdb=" O ALA P 96 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALA P 96 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET P 68 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE P 94 " --> pdb=" O MET P 68 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE P 70 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG P 92 " --> pdb=" O PHE P 70 " (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: 3.785A pdb=" N GLY Q 100 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG Q 64 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA Q 98 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR Q 66 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA Q 96 " --> pdb=" O THR Q 66 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET Q 68 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE Q 94 " --> pdb=" O MET Q 68 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE Q 70 " --> pdb=" O ARG Q 92 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG Q 92 " --> pdb=" O PHE Q 70 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 35 through 38 removed outlier: 3.519A pdb=" N GLY N 41 " --> pdb=" O HIS N 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 160 through 164 removed outlier: 7.069A pdb=" N ILE N 161 " --> pdb=" O LEU N 150 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N HIS N 172 " --> pdb=" O ASN N 531 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N PHE N 533 " --> pdb=" O HIS N 172 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA N 174 " --> pdb=" O PHE N 533 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL N 204 " --> pdb=" O LEU N 475 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS N 223 " --> pdb=" O ILE N 435 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASN N 437 " --> pdb=" O LYS N 223 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR N 225 " --> pdb=" O ASN N 437 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 256 through 257 removed outlier: 6.490A pdb=" N ILE N 256 " --> pdb=" O ASN N 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'N' and resid 292 through 293 removed outlier: 4.677A pdb=" N ILE N 298 " --> pdb=" O LEU N 310 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE N 308 " --> pdb=" O LEU N 300 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 356 through 358 Processing sheet with id=AG1, first strand: chain 'O' and resid 35 through 38 Processing sheet with id=AG2, first strand: chain 'O' and resid 160 through 164 removed outlier: 6.950A pdb=" N ILE O 161 " --> pdb=" O LEU O 150 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA O 174 " --> pdb=" O PHE O 533 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL O 204 " --> pdb=" O LEU O 475 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLU O 477 " --> pdb=" O VAL O 204 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE O 206 " --> pdb=" O GLU O 477 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS O 223 " --> pdb=" O ILE O 435 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASN O 437 " --> pdb=" O LYS O 223 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR O 225 " --> pdb=" O ASN O 437 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LYS O 254 " --> pdb=" O HIS O 224 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE O 226 " --> pdb=" O LYS O 254 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 256 through 257 removed outlier: 6.670A pdb=" N ILE O 256 " --> pdb=" O ASN O 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'O' and resid 292 through 293 Processing sheet with id=AG5, first strand: chain 'P' and resid 37 through 38 Processing sheet with id=AG6, first strand: chain 'P' and resid 160 through 164 removed outlier: 7.057A pdb=" N ILE P 161 " --> pdb=" O LEU P 150 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N HIS P 172 " --> pdb=" O SER P 530 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP P 532 " --> pdb=" O HIS P 172 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA P 174 " --> pdb=" O TRP P 532 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU P 173 " --> pdb=" O VAL P 513 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR P 515 " --> pdb=" O LEU P 173 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL P 175 " --> pdb=" O THR P 515 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR P 472 " --> pdb=" O SER P 510 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE P 512 " --> pdb=" O THR P 472 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU P 474 " --> pdb=" O ILE P 512 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER P 514 " --> pdb=" O LEU P 474 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS P 434 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL P 436 " --> pdb=" O ILE P 205 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS P 223 " --> pdb=" O ILE P 435 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ASN P 437 " --> pdb=" O LYS P 223 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR P 225 " --> pdb=" O ASN P 437 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N LYS P 254 " --> pdb=" O HIS P 224 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE P 226 " --> pdb=" O LYS P 254 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 292 through 293 removed outlier: 3.694A pdb=" N HIS P 292 " --> pdb=" O TYR P 299 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR P 299 " --> pdb=" O HIS P 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'Q' and resid 160 through 161 removed outlier: 3.560A pdb=" N GLY Q 151 " --> pdb=" O ILE Q 161 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL Q 580 " --> pdb=" O ALA Q 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL Q 570 " --> pdb=" O SER Q 534 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER Q 534 " --> pdb=" O VAL Q 570 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE Q 572 " --> pdb=" O TRP Q 532 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 173 through 176 removed outlier: 3.532A pdb=" N VAL Q 513 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU Q 474 " --> pdb=" O SER Q 510 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER Q 514 " --> pdb=" O LEU Q 476 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL Q 204 " --> pdb=" O LEU Q 475 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR Q 225 " --> pdb=" O ASN Q 437 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE Q 226 " --> pdb=" O LYS Q 254 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 256 through 257 removed outlier: 7.033A pdb=" N ILE Q 256 " --> pdb=" O ASN Q 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'Q' and resid 292 through 293 2130 hydrogen bonds defined for protein. 6039 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: 26.21 Time building geometry restraints manager: 13.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19703 1.34 - 1.46: 10798 1.46 - 1.58: 31814 1.58 - 1.70: 63 1.70 - 1.82: 206 Bond restraints: 62584 Sorted by residual: bond pdb=" C ALA P 446 " pdb=" N PRO P 447 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.38e-02 5.25e+03 4.91e+00 bond pdb=" CB VAL J 243 " pdb=" CG1 VAL J 243 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.40e+00 bond pdb=" CA GLY P 20 " pdb=" C GLY P 20 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.97e+00 bond pdb=" CB VAL A 243 " pdb=" CG1 VAL A 243 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" CG ARG J 194 " pdb=" CD ARG J 194 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.43e+00 ... (remaining 62579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 83550 2.41 - 4.81: 961 4.81 - 7.22: 128 7.22 - 9.63: 19 9.63 - 12.03: 9 Bond angle restraints: 84667 Sorted by residual: angle pdb=" C LEU L 323 " pdb=" N ASN L 324 " pdb=" CA ASN L 324 " ideal model delta sigma weight residual 121.61 129.81 -8.20 1.39e+00 5.18e-01 3.48e+01 angle pdb=" N ILE P 288 " pdb=" CA ILE P 288 " pdb=" C ILE P 288 " ideal model delta sigma weight residual 113.53 108.36 5.17 9.80e-01 1.04e+00 2.78e+01 angle pdb=" C HIS C 383 " pdb=" N LEU C 384 " pdb=" CA LEU C 384 " ideal model delta sigma weight residual 120.94 130.75 -9.81 1.90e+00 2.77e-01 2.67e+01 angle pdb=" C SER L 379 " pdb=" N PHE L 380 " pdb=" CA PHE L 380 " ideal model delta sigma weight residual 121.66 112.84 8.82 1.76e+00 3.23e-01 2.51e+01 angle pdb=" C ARG N 192 " pdb=" N LYS N 193 " pdb=" CA LYS N 193 " ideal model delta sigma weight residual 122.38 115.13 7.25 1.81e+00 3.05e-01 1.60e+01 ... (remaining 84662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 36492 33.88 - 67.76: 830 67.76 - 101.64: 105 101.64 - 135.51: 2 135.51 - 169.39: 5 Dihedral angle restraints: 37434 sinusoidal: 15422 harmonic: 22012 Sorted by residual: dihedral pdb=" C5' ADP P 701 " pdb=" O5' ADP P 701 " pdb=" PA ADP P 701 " pdb=" O2A ADP P 701 " ideal model delta sinusoidal sigma weight residual -60.00 107.76 -167.76 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" CA HIS D 218 " pdb=" C HIS D 218 " pdb=" N TYR D 219 " pdb=" CA TYR D 219 " ideal model delta harmonic sigma weight residual 180.00 149.72 30.28 0 5.00e+00 4.00e-02 3.67e+01 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 -150.02 -29.98 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 37431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 6348 0.044 - 0.087: 2248 0.087 - 0.131: 544 0.131 - 0.175: 59 0.175 - 0.218: 3 Chirality restraints: 9202 Sorted by residual: chirality pdb=" CB VAL O 16 " pdb=" CA VAL O 16 " pdb=" CG1 VAL O 16 " pdb=" CG2 VAL O 16 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE P 89 " pdb=" CA ILE P 89 " pdb=" CG1 ILE P 89 " pdb=" CG2 ILE P 89 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA TYR H 252 " pdb=" N TYR H 252 " pdb=" C TYR H 252 " pdb=" CB TYR H 252 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 9199 not shown) Planarity restraints: 10852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR H 270 " -0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO H 271 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO H 271 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 271 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 333 " -0.053 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO E 334 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 334 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 334 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE P 219 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO P 220 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO P 220 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO P 220 " 0.031 5.00e-02 4.00e+02 ... (remaining 10849 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 194 2.54 - 3.13: 42565 3.13 - 3.72: 82130 3.72 - 4.31: 116407 4.31 - 4.90: 206571 Nonbonded interactions: 447867 Sorted by model distance: nonbonded pdb=" OG SER P 184 " pdb="MG MG P 702 " model vdw 1.948 2.170 nonbonded pdb=" O3B ADP O 701 " pdb="MG MG O 702 " model vdw 1.979 2.170 nonbonded pdb=" O3B ADP N 701 " pdb="MG MG N 702 " model vdw 2.004 2.170 nonbonded pdb=" O ASN M 134 " pdb=" OG SER M 138 " model vdw 2.033 3.040 nonbonded pdb=" OD2 ASP Q 153 " pdb=" OG1 THR Q 156 " model vdw 2.041 3.040 ... (remaining 447862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'B' and (resid 2 through 387 or resid 395 through 406 or resid 501)) selection = (chain 'C' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'D' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'E' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'F' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'G' and (resid 2 through 208 or resid 218 through 406 or resid 501)) selection = (chain 'H' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'I' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'J' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'K' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'L' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) } ncs_group { reference = (chain 'M' and (resid 4 through 36 or resid 42 through 229 or resid 238 through \ 328 or resid 336 through 355 or resid 375 through 602 or resid 701 through 702)) \ selection = (chain 'N' and (resid 4 through 36 or resid 42 through 229 or resid 238 through \ 328 or resid 336 through 355 or resid 375 through 484 or resid 498 through 602 o \ r resid 701 through 702)) selection = (chain 'O' and (resid 4 through 36 or resid 42 through 71 or resid 89 through 22 \ 9 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 602 or resid 701 through 702)) selection = (chain 'P' and (resid 4 through 36 or resid 42 through 229 or resid 238 through \ 355 or resid 375 through 484 or resid 498 through 602 or resid 701 through 702)) \ selection = (chain 'Q' and (resid 4 through 328 or resid 336 through 355 or resid 375 throug \ h 484 or resid 498 through 602 or resid 701 through 702)) } 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.960 Check model and map are aligned: 0.340 Set scattering table: 0.450 Process input model: 110.140 Find NCS groups from input model: 3.660 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: 0.020 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 62584 Z= 0.300 Angle : 0.701 12.034 84667 Z= 0.369 Chirality : 0.046 0.218 9202 Planarity : 0.005 0.083 10852 Dihedral : 15.078 169.393 23356 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.09), residues: 7515 helix: -0.29 (0.09), residues: 3013 sheet: -0.21 (0.17), residues: 926 loop : -1.79 (0.09), residues: 3576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 431 HIS 0.012 0.002 HIS B 313 PHE 0.037 0.002 PHE L 380 TYR 0.030 0.002 TYR A 386 ARG 0.008 0.001 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 900 time to evaluate : 5.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.9093 (t) cc_final: 0.8789 (m) REVERT: A 73 ILE cc_start: 0.8061 (tt) cc_final: 0.7825 (tp) REVERT: A 266 GLN cc_start: 0.7849 (mt0) cc_final: 0.7629 (mt0) REVERT: A 312 TYR cc_start: 0.8823 (t80) cc_final: 0.8600 (t80) REVERT: B 12 GLU cc_start: 0.7749 (tt0) cc_final: 0.7383 (tp30) REVERT: B 74 ASP cc_start: 0.7582 (m-30) cc_final: 0.6990 (m-30) REVERT: B 107 GLU cc_start: 0.8255 (tp30) cc_final: 0.7764 (tp30) REVERT: B 110 LYS cc_start: 0.7864 (mttp) cc_final: 0.7543 (mtmt) REVERT: B 342 LYS cc_start: 0.8168 (mttm) cc_final: 0.7687 (tttp) REVERT: C 106 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6939 (tp30) REVERT: C 352 GLU cc_start: 0.7436 (mp0) cc_final: 0.7001 (mp0) REVERT: E 102 GLU cc_start: 0.7163 (pm20) cc_final: 0.6945 (tm-30) REVERT: F 76 ASP cc_start: 0.6606 (m-30) cc_final: 0.6349 (m-30) REVERT: F 117 LYS cc_start: 0.8122 (tttt) cc_final: 0.7712 (ttmm) REVERT: F 337 LYS cc_start: 0.7282 (pttt) cc_final: 0.6737 (mmpt) REVERT: G 9 LYS cc_start: 0.6122 (ttmt) cc_final: 0.5577 (pptt) REVERT: G 101 CYS cc_start: 0.7136 (t) cc_final: 0.6933 (t) REVERT: G 143 TYR cc_start: 0.6860 (m-80) cc_final: 0.6141 (m-80) REVERT: G 260 ASP cc_start: 0.5946 (p0) cc_final: 0.5493 (t0) REVERT: G 345 LYS cc_start: 0.4864 (mptt) cc_final: 0.4262 (tmtm) REVERT: G 361 MET cc_start: 0.5665 (mmm) cc_final: 0.5259 (pmt) REVERT: H 110 LYS cc_start: 0.7617 (mtmm) cc_final: 0.7012 (ttpt) REVERT: H 316 ARG cc_start: 0.7728 (mmm160) cc_final: 0.7191 (mmm160) REVERT: I 259 LYS cc_start: 0.7093 (mmmt) cc_final: 0.6855 (ttmt) REVERT: J 74 ASP cc_start: 0.7752 (m-30) cc_final: 0.7509 (m-30) REVERT: J 337 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7291 (mptp) REVERT: K 74 ASP cc_start: 0.7873 (m-30) cc_final: 0.7668 (m-30) REVERT: K 79 LEU cc_start: 0.9045 (mt) cc_final: 0.8756 (mt) REVERT: K 106 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7086 (OUTLIER) REVERT: K 287 MET cc_start: 0.9072 (mmt) cc_final: 0.8765 (mmp) REVERT: L 235 ASN cc_start: 0.6203 (m-40) cc_final: 0.5784 (p0) REVERT: L 342 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7565 (tttm) REVERT: M 18 LEU cc_start: 0.8338 (mt) cc_final: 0.7911 (mm) REVERT: M 153 ASP cc_start: 0.7943 (t0) cc_final: 0.7706 (t0) REVERT: M 413 MET cc_start: 0.5946 (ttt) cc_final: 0.5394 (ppp) REVERT: M 498 GLU cc_start: 0.3601 (pt0) cc_final: 0.2949 (mp0) REVERT: M 550 MET cc_start: 0.7442 (ptt) cc_final: 0.7239 (ptm) REVERT: M 592 LYS cc_start: 0.7332 (tttt) cc_final: 0.6830 (ttpt) REVERT: N 67 ASP cc_start: 0.8989 (m-30) cc_final: 0.8759 (m-30) REVERT: N 131 ASP cc_start: 0.8595 (m-30) cc_final: 0.8358 (m-30) REVERT: N 242 LYS cc_start: 0.7160 (tttp) cc_final: 0.6899 (tptt) REVERT: N 327 ASP cc_start: 0.6656 (t0) cc_final: 0.6168 (m-30) REVERT: N 508 LYS cc_start: 0.8242 (mttp) cc_final: 0.7895 (mtpm) REVERT: N 592 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7405 (tppt) REVERT: O 382 GLN cc_start: 0.6000 (mt0) cc_final: 0.5209 (mm110) REVERT: O 383 GLN cc_start: 0.5210 (tm-30) cc_final: 0.4957 (pt0) REVERT: O 550 MET cc_start: 0.8996 (ptm) cc_final: 0.8761 (ptp) REVERT: O 559 LYS cc_start: 0.8871 (mttt) cc_final: 0.8554 (mtpm) REVERT: P 55 ASP cc_start: 0.7796 (t0) cc_final: 0.7555 (p0) REVERT: P 413 MET cc_start: 0.3248 (ttp) cc_final: 0.2561 (mpt) REVERT: P 478 GLU cc_start: 0.7808 (mp0) cc_final: 0.7280 (mm-30) REVERT: P 540 GLU cc_start: 0.7178 (tp30) cc_final: 0.6671 (tp30) REVERT: Q 413 MET cc_start: 0.5253 (ttm) cc_final: 0.4856 (ttt) REVERT: Q 536 ARG cc_start: 0.5284 (ttt180) cc_final: 0.4849 (tmm-80) outliers start: 0 outliers final: 3 residues processed: 900 average time/residue: 1.5952 time to fit residues: 1796.1930 Evaluate side-chains 437 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 435 time to evaluate : 6.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain N residue 107 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 637 optimal weight: 6.9990 chunk 572 optimal weight: 10.0000 chunk 317 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 386 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 591 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 359 optimal weight: 8.9990 chunk 440 optimal weight: 1.9990 chunk 685 optimal weight: 0.1980 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN B 220 HIS C 405 ASN F 55 ASN G 227 HIS ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 274 ASN M 172 HIS M 289 ASN M 297 ASN M 382 GLN M 544 GLN N 224 HIS N 289 ASN N 382 GLN N 383 GLN O 544 GLN P 429 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 62584 Z= 0.378 Angle : 0.729 12.061 84667 Z= 0.374 Chirality : 0.049 0.231 9202 Planarity : 0.005 0.079 10852 Dihedral : 10.290 171.864 8929 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.00 % Allowed : 9.26 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.09), residues: 7515 helix: -0.13 (0.09), residues: 3014 sheet: -0.05 (0.17), residues: 891 loop : -1.86 (0.09), residues: 3610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 116 HIS 0.015 0.002 HIS B 313 PHE 0.029 0.002 PHE J 205 TYR 0.026 0.002 TYR C 116 ARG 0.014 0.001 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 459 time to evaluate : 5.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8131 (tt) cc_final: 0.7905 (tp) REVERT: A 266 GLN cc_start: 0.7922 (mt0) cc_final: 0.7709 (mt0) REVERT: A 312 TYR cc_start: 0.8752 (t80) cc_final: 0.8526 (t80) REVERT: B 12 GLU cc_start: 0.7744 (tt0) cc_final: 0.7262 (tp30) REVERT: B 110 LYS cc_start: 0.7878 (mttp) cc_final: 0.7533 (mtmt) REVERT: B 342 LYS cc_start: 0.8200 (mttm) cc_final: 0.7701 (tttp) REVERT: C 106 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7037 (tp30) REVERT: C 352 GLU cc_start: 0.7638 (mp0) cc_final: 0.7045 (mp0) REVERT: E 386 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7594 (t80) REVERT: F 97 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7460 (tttt) REVERT: F 117 LYS cc_start: 0.8196 (tttt) cc_final: 0.7731 (ttmm) REVERT: G 9 LYS cc_start: 0.6160 (ttmt) cc_final: 0.5594 (pptt) REVERT: G 137 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.6344 (pmtt) REVERT: G 143 TYR cc_start: 0.6662 (m-80) cc_final: 0.6167 (m-80) REVERT: G 313 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.7326 (m90) REVERT: G 361 MET cc_start: 0.5708 (mmm) cc_final: 0.5320 (pmt) REVERT: H 110 LYS cc_start: 0.7209 (mtmm) cc_final: 0.6945 (ttpt) REVERT: H 316 ARG cc_start: 0.7633 (mmm160) cc_final: 0.7111 (mmm160) REVERT: I 30 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8590 (t) REVERT: I 259 LYS cc_start: 0.7064 (mmmt) cc_final: 0.6734 (tttt) REVERT: I 361 MET cc_start: 0.7966 (mtp) cc_final: 0.7721 (mtp) REVERT: I 363 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: I 374 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7975 (mtmt) REVERT: J 74 ASP cc_start: 0.7611 (m-30) cc_final: 0.7367 (m-30) REVERT: J 207 ASN cc_start: 0.7452 (OUTLIER) cc_final: 0.7224 (t0) REVERT: J 264 ARG cc_start: 0.6214 (mpp-170) cc_final: 0.5898 (mpt180) REVERT: J 337 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7358 (mptp) REVERT: J 352 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: K 79 LEU cc_start: 0.9061 (mt) cc_final: 0.8785 (mt) REVERT: K 106 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7217 (tp30) REVERT: K 287 MET cc_start: 0.9074 (mmt) cc_final: 0.8761 (mmp) REVERT: K 352 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: L 128 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7297 (tp30) REVERT: L 235 ASN cc_start: 0.6390 (m-40) cc_final: 0.5915 (p0) REVERT: L 342 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7590 (tttm) REVERT: M 34 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6370 (ptm160) REVERT: M 153 ASP cc_start: 0.7956 (t0) cc_final: 0.7726 (t0) REVERT: M 410 ASP cc_start: 0.6027 (m-30) cc_final: 0.5575 (p0) REVERT: M 413 MET cc_start: 0.5618 (ttt) cc_final: 0.5128 (ppp) REVERT: M 478 GLU cc_start: 0.8156 (mp0) cc_final: 0.7646 (mp0) REVERT: M 498 GLU cc_start: 0.4056 (pt0) cc_final: 0.2989 (mp0) REVERT: M 548 TYR cc_start: 0.7360 (t80) cc_final: 0.7064 (t80) REVERT: M 550 MET cc_start: 0.6989 (ptt) cc_final: 0.6742 (ptm) REVERT: M 592 LYS cc_start: 0.7478 (tttt) cc_final: 0.6890 (ttpt) REVERT: N 67 ASP cc_start: 0.9027 (m-30) cc_final: 0.8793 (m-30) REVERT: N 131 ASP cc_start: 0.8652 (m-30) cc_final: 0.8384 (m-30) REVERT: N 229 GLU cc_start: 0.7275 (pp20) cc_final: 0.6947 (pm20) REVERT: N 242 LYS cc_start: 0.7126 (tttp) cc_final: 0.6888 (tptt) REVERT: N 478 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: N 506 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7821 (mtmt) REVERT: N 508 LYS cc_start: 0.8222 (mttp) cc_final: 0.7832 (mtpm) REVERT: N 592 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7373 (tppt) REVERT: O 107 ASN cc_start: 0.7187 (OUTLIER) cc_final: 0.6837 (t0) REVERT: O 266 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6292 (mm) REVERT: O 382 GLN cc_start: 0.6018 (mt0) cc_final: 0.5162 (mm-40) REVERT: O 383 GLN cc_start: 0.4923 (tm-30) cc_final: 0.4651 (pt0) REVERT: O 427 GLN cc_start: 0.7069 (mm-40) cc_final: 0.6606 (mt0) REVERT: P 413 MET cc_start: 0.4185 (ttp) cc_final: 0.2811 (mpt) REVERT: P 478 GLU cc_start: 0.7684 (mp0) cc_final: 0.7339 (mm-30) REVERT: P 551 GLU cc_start: 0.3701 (OUTLIER) cc_final: 0.3031 (mm-30) REVERT: Q 156 THR cc_start: 0.6752 (OUTLIER) cc_final: 0.6541 (t) REVERT: Q 413 MET cc_start: 0.5206 (ttm) cc_final: 0.3769 (ptt) REVERT: Q 448 MET cc_start: 0.2926 (tpt) cc_final: 0.1685 (pmm) REVERT: Q 463 ARG cc_start: 0.3540 (tpm170) cc_final: 0.3253 (tpm170) REVERT: Q 536 ARG cc_start: 0.5629 (ttt180) cc_final: 0.5154 (tmm-80) outliers start: 130 outliers final: 54 residues processed: 550 average time/residue: 1.4187 time to fit residues: 1004.8386 Evaluate side-chains 457 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 386 time to evaluate : 5.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 313 HIS Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 341 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain I residue 374 LYS Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 352 GLU Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 478 GLU Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 539 ASN Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 251 TYR Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 510 SER Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 162 PHE Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 570 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 381 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 570 optimal weight: 0.7980 chunk 466 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 686 optimal weight: 7.9990 chunk 742 optimal weight: 0.5980 chunk 611 optimal weight: 5.9990 chunk 681 optimal weight: 30.0000 chunk 234 optimal weight: 2.9990 chunk 551 optimal weight: 0.1980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN G 78 ASN H 313 HIS M 289 ASN M 556 GLN N 383 GLN O 241 GLN O 480 HIS P 429 ASN P 432 ASN Q 224 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 62584 Z= 0.142 Angle : 0.536 13.150 84667 Z= 0.274 Chirality : 0.041 0.184 9202 Planarity : 0.004 0.058 10852 Dihedral : 9.483 166.384 8927 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.76 % Allowed : 11.48 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: -0.88 (0.09), residues: 7515 helix: 0.41 (0.10), residues: 3030 sheet: 0.16 (0.17), residues: 904 loop : -1.69 (0.09), residues: 3581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 116 HIS 0.008 0.001 HIS G 267 PHE 0.026 0.001 PHE M 371 TYR 0.017 0.001 TYR H 284 ARG 0.017 0.000 ARG Q 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 457 time to evaluate : 5.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8023 (tt) cc_final: 0.7805 (tp) REVERT: A 264 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6764 (mmm160) REVERT: A 312 TYR cc_start: 0.8572 (t80) cc_final: 0.8337 (t80) REVERT: B 12 GLU cc_start: 0.7730 (tt0) cc_final: 0.7333 (tp30) REVERT: B 74 ASP cc_start: 0.7535 (m-30) cc_final: 0.6816 (m-30) REVERT: B 110 LYS cc_start: 0.7587 (mttp) cc_final: 0.7312 (mtmt) REVERT: B 342 LYS cc_start: 0.8089 (mttm) cc_final: 0.7614 (tttp) REVERT: C 8 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7434 (m-40) REVERT: C 54 GLN cc_start: 0.8006 (tt0) cc_final: 0.7730 (tt0) REVERT: C 88 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: C 106 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7067 (tp30) REVERT: D 100 ARG cc_start: 0.7696 (mtp85) cc_final: 0.7066 (mtt-85) REVERT: E 288 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.8052 (t80) REVERT: E 386 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7509 (t80) REVERT: F 117 LYS cc_start: 0.8269 (tttt) cc_final: 0.7815 (ttmm) REVERT: F 156 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6907 (mp10) REVERT: F 337 LYS cc_start: 0.6823 (pttt) cc_final: 0.6224 (mmpt) REVERT: G 9 LYS cc_start: 0.6159 (ttmt) cc_final: 0.5625 (pptt) REVERT: G 143 TYR cc_start: 0.6628 (m-80) cc_final: 0.6112 (m-80) REVERT: G 313 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7332 (m90) REVERT: G 361 MET cc_start: 0.5317 (mmm) cc_final: 0.5102 (pmt) REVERT: H 316 ARG cc_start: 0.7608 (mmm160) cc_final: 0.6960 (mmm160) REVERT: I 259 LYS cc_start: 0.6767 (mmmt) cc_final: 0.6503 (tttt) REVERT: I 361 MET cc_start: 0.7896 (mtp) cc_final: 0.7689 (mtp) REVERT: I 363 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: J 264 ARG cc_start: 0.6062 (mpp-170) cc_final: 0.5795 (mpt180) REVERT: J 293 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7915 (mt-10) REVERT: J 337 LYS cc_start: 0.8005 (ttpp) cc_final: 0.7371 (mptp) REVERT: K 106 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7192 (tp30) REVERT: K 287 MET cc_start: 0.9012 (mmt) cc_final: 0.8598 (mmp) REVERT: L 128 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7367 (tp30) REVERT: L 132 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: L 235 ASN cc_start: 0.6262 (m-40) cc_final: 0.5825 (p0) REVERT: L 296 SER cc_start: 0.8415 (m) cc_final: 0.8172 (p) REVERT: L 342 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7502 (mtpt) REVERT: L 380 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7797 (t80) REVERT: M 34 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6209 (ptm160) REVERT: M 413 MET cc_start: 0.5580 (ttt) cc_final: 0.5170 (ppp) REVERT: M 438 MET cc_start: 0.8008 (mtp) cc_final: 0.7735 (mtp) REVERT: M 478 GLU cc_start: 0.8025 (mp0) cc_final: 0.7537 (mp0) REVERT: M 498 GLU cc_start: 0.4173 (pt0) cc_final: 0.3002 (mp0) REVERT: M 548 TYR cc_start: 0.7341 (t80) cc_final: 0.7113 (t80) REVERT: M 550 MET cc_start: 0.6681 (ptt) cc_final: 0.6409 (ptm) REVERT: M 592 LYS cc_start: 0.7388 (tttt) cc_final: 0.6864 (tttt) REVERT: M 600 GLU cc_start: 0.7022 (mp0) cc_final: 0.6737 (mm-30) REVERT: N 67 ASP cc_start: 0.8921 (m-30) cc_final: 0.8680 (m-30) REVERT: N 131 ASP cc_start: 0.8567 (m-30) cc_final: 0.8304 (m-30) REVERT: N 229 GLU cc_start: 0.7194 (pp20) cc_final: 0.6990 (pm20) REVERT: N 466 GLN cc_start: 0.7093 (mp10) cc_final: 0.6617 (mp10) REVERT: N 506 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7852 (mtmt) REVERT: N 508 LYS cc_start: 0.8137 (mttp) cc_final: 0.7804 (mtpm) REVERT: N 592 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7398 (tppt) REVERT: O 105 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7009 (tp30) REVERT: O 340 TRP cc_start: 0.6752 (m100) cc_final: 0.6390 (m100) REVERT: O 382 GLN cc_start: 0.5967 (mt0) cc_final: 0.5165 (mm110) REVERT: O 427 GLN cc_start: 0.6975 (mm-40) cc_final: 0.6466 (mt0) REVERT: P 413 MET cc_start: 0.3583 (ttp) cc_final: 0.2421 (mpm) REVERT: P 478 GLU cc_start: 0.7748 (mp0) cc_final: 0.7342 (mm-30) REVERT: P 499 ARG cc_start: 0.6221 (ttm170) cc_final: 0.5807 (ttt180) REVERT: P 551 GLU cc_start: 0.3508 (OUTLIER) cc_final: 0.2954 (mm-30) REVERT: Q 1 MET cc_start: 0.6388 (mmt) cc_final: 0.4262 (mmt) REVERT: Q 35 LEU cc_start: 0.1985 (OUTLIER) cc_final: 0.1337 (tt) REVERT: Q 413 MET cc_start: 0.5108 (ttm) cc_final: 0.3663 (ptm) REVERT: Q 438 MET cc_start: -0.0062 (pmm) cc_final: -0.0409 (mpt) REVERT: Q 456 MET cc_start: 0.0886 (mmt) cc_final: -0.0447 (pp-130) REVERT: Q 463 ARG cc_start: 0.2578 (OUTLIER) cc_final: 0.2370 (tpm170) REVERT: Q 528 MET cc_start: 0.6262 (mpp) cc_final: 0.5936 (mtt) REVERT: Q 536 ARG cc_start: 0.5447 (ttt180) cc_final: 0.5163 (tmm-80) outliers start: 114 outliers final: 39 residues processed: 537 average time/residue: 1.3904 time to fit residues: 975.3299 Evaluate side-chains 446 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 392 time to evaluate : 5.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 313 HIS Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 461 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 463 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 678 optimal weight: 0.9980 chunk 516 optimal weight: 0.4980 chunk 356 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 327 optimal weight: 9.9990 chunk 461 optimal weight: 9.9990 chunk 689 optimal weight: 9.9990 chunk 729 optimal weight: 1.9990 chunk 360 optimal weight: 9.9990 chunk 653 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN F 218 HIS F 324 ASN H 313 HIS J 54 GLN N 221 ASN Q 437 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 62584 Z= 0.136 Angle : 0.515 12.707 84667 Z= 0.261 Chirality : 0.041 0.179 9202 Planarity : 0.003 0.048 10852 Dihedral : 9.109 168.788 8927 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.02 % Allowed : 12.65 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.10), residues: 7515 helix: 0.66 (0.10), residues: 3040 sheet: 0.28 (0.17), residues: 928 loop : -1.57 (0.10), residues: 3547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 116 HIS 0.006 0.001 HIS G 267 PHE 0.025 0.001 PHE Q 263 TYR 0.023 0.001 TYR O 258 ARG 0.010 0.000 ARG Q 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 435 time to evaluate : 5.318 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 73 ILE cc_start: 0.7991 (tt) cc_final: 0.7773 (tp) REVERT: A 264 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6765 (mmm160) REVERT: B 12 GLU cc_start: 0.7690 (tt0) cc_final: 0.7274 (tp30) REVERT: B 68 LEU cc_start: 0.8937 (mp) cc_final: 0.8736 (mt) REVERT: B 74 ASP cc_start: 0.7526 (m-30) cc_final: 0.6830 (m-30) REVERT: B 77 ASN cc_start: 0.6093 (m-40) cc_final: 0.5540 (t0) REVERT: B 107 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7218 (tp30) REVERT: B 110 LYS cc_start: 0.7632 (mttp) cc_final: 0.7405 (mtmt) REVERT: B 342 LYS cc_start: 0.8063 (mttm) cc_final: 0.7590 (tttp) REVERT: C 54 GLN cc_start: 0.8026 (tt0) cc_final: 0.7723 (tt0) REVERT: C 88 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: C 106 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6970 (tp30) REVERT: D 83 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6098 (mm-30) REVERT: D 100 ARG cc_start: 0.7671 (mtp85) cc_final: 0.7057 (mtt-85) REVERT: E 288 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7908 (t80) REVERT: E 338 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: E 386 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7465 (t80) REVERT: F 117 LYS cc_start: 0.8259 (tttt) cc_final: 0.7803 (ttmm) REVERT: F 156 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6971 (mp-120) REVERT: F 337 LYS cc_start: 0.6834 (pttt) cc_final: 0.6249 (mmpt) REVERT: G 9 LYS cc_start: 0.6129 (ttmt) cc_final: 0.5603 (pptt) REVERT: G 143 TYR cc_start: 0.6666 (m-80) cc_final: 0.6167 (m-80) REVERT: H 316 ARG cc_start: 0.7597 (mmm160) cc_final: 0.6940 (mmm160) REVERT: J 54 GLN cc_start: 0.7980 (tt0) cc_final: 0.7738 (tm-30) REVERT: J 264 ARG cc_start: 0.6054 (mpp-170) cc_final: 0.5803 (mpt180) REVERT: J 293 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7896 (mt-10) REVERT: J 337 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7373 (mptp) REVERT: J 342 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7762 (tttp) REVERT: K 106 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7228 (tp30) REVERT: K 287 MET cc_start: 0.9014 (mmt) cc_final: 0.8637 (mmp) REVERT: K 352 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: L 128 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7423 (tp30) REVERT: L 132 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: L 235 ASN cc_start: 0.6239 (m-40) cc_final: 0.5803 (p0) REVERT: L 342 LYS cc_start: 0.7844 (ttmt) cc_final: 0.7514 (mtpt) REVERT: L 380 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7771 (t80) REVERT: L 382 GLU cc_start: 0.8316 (tp30) cc_final: 0.8107 (mm-30) REVERT: M 34 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.5977 (ptm160) REVERT: M 277 GLN cc_start: 0.3302 (mt0) cc_final: 0.3091 (mt0) REVERT: M 410 ASP cc_start: 0.6209 (m-30) cc_final: 0.5722 (p0) REVERT: M 413 MET cc_start: 0.5881 (ttt) cc_final: 0.5439 (ppp) REVERT: M 478 GLU cc_start: 0.8020 (mp0) cc_final: 0.7599 (mp0) REVERT: M 498 GLU cc_start: 0.4068 (pt0) cc_final: 0.2932 (mp0) REVERT: M 550 MET cc_start: 0.6424 (ptt) cc_final: 0.6116 (ptm) REVERT: M 555 GLU cc_start: 0.7054 (tp30) cc_final: 0.6727 (tm-30) REVERT: M 556 GLN cc_start: 0.8243 (pm20) cc_final: 0.7222 (pp30) REVERT: M 592 LYS cc_start: 0.7369 (tttt) cc_final: 0.6913 (tttt) REVERT: M 600 GLU cc_start: 0.7081 (mp0) cc_final: 0.6879 (mm-30) REVERT: N 67 ASP cc_start: 0.8960 (m-30) cc_final: 0.8706 (m-30) REVERT: N 131 ASP cc_start: 0.8553 (m-30) cc_final: 0.8288 (m-30) REVERT: N 325 TRP cc_start: 0.6129 (m100) cc_final: 0.5818 (m100) REVERT: N 466 GLN cc_start: 0.7134 (mp10) cc_final: 0.6665 (mp10) REVERT: N 506 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7889 (mtmt) REVERT: N 508 LYS cc_start: 0.8134 (mttp) cc_final: 0.7802 (mtpm) REVERT: N 592 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7400 (tppt) REVERT: O 105 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6969 (tp30) REVERT: O 340 TRP cc_start: 0.6725 (m100) cc_final: 0.6452 (m100) REVERT: O 382 GLN cc_start: 0.5796 (mt0) cc_final: 0.5073 (mm110) REVERT: O 427 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6436 (mt0) REVERT: O 559 LYS cc_start: 0.8564 (mttt) cc_final: 0.8245 (mtpm) REVERT: P 241 GLN cc_start: 0.5894 (OUTLIER) cc_final: 0.5610 (mm-40) REVERT: P 413 MET cc_start: 0.3410 (ttp) cc_final: 0.2428 (mpm) REVERT: P 478 GLU cc_start: 0.7713 (mp0) cc_final: 0.7393 (mm-30) REVERT: P 499 ARG cc_start: 0.6262 (ttm170) cc_final: 0.5945 (ttt180) REVERT: P 551 GLU cc_start: 0.3382 (OUTLIER) cc_final: 0.2719 (mm-30) REVERT: Q 35 LEU cc_start: 0.2108 (OUTLIER) cc_final: 0.1475 (tt) REVERT: Q 413 MET cc_start: 0.5141 (ttm) cc_final: 0.3806 (ptm) REVERT: Q 438 MET cc_start: -0.0036 (OUTLIER) cc_final: -0.0576 (mpt) REVERT: Q 448 MET cc_start: 0.2760 (tpt) cc_final: 0.1835 (pmt) REVERT: Q 456 MET cc_start: 0.1111 (mmt) cc_final: -0.0327 (pp-130) REVERT: Q 463 ARG cc_start: 0.2865 (OUTLIER) cc_final: 0.2625 (tpm170) REVERT: Q 519 SER cc_start: 0.6113 (t) cc_final: 0.5727 (p) REVERT: Q 528 MET cc_start: 0.6404 (mpp) cc_final: 0.6093 (mtt) outliers start: 131 outliers final: 59 residues processed: 530 average time/residue: 1.4705 time to fit residues: 1008.1258 Evaluate side-chains 464 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 387 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 116 TYR Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 558 LEU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 592 LYS Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 159 VAL Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 463 ARG Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 607 optimal weight: 7.9990 chunk 414 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 543 optimal weight: 3.9990 chunk 301 optimal weight: 10.0000 chunk 622 optimal weight: 20.0000 chunk 504 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 372 optimal weight: 4.9990 chunk 655 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 159 GLN G 360 ASN H 313 HIS I 227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 62584 Z= 0.314 Angle : 0.659 14.845 84667 Z= 0.335 Chirality : 0.046 0.203 9202 Planarity : 0.004 0.053 10852 Dihedral : 9.609 172.125 8925 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.30 % Allowed : 13.50 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: -0.88 (0.09), residues: 7515 helix: 0.41 (0.10), residues: 3042 sheet: 0.16 (0.17), residues: 913 loop : -1.70 (0.09), residues: 3560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 116 HIS 0.011 0.001 HIS D 227 PHE 0.020 0.002 PHE J 205 TYR 0.019 0.002 TYR B 143 ARG 0.009 0.001 ARG Q 541 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 402 time to evaluate : 5.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8079 (tt) cc_final: 0.7855 (tp) REVERT: A 259 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7999 (ttpt) REVERT: B 12 GLU cc_start: 0.7720 (tt0) cc_final: 0.7319 (tp30) REVERT: B 68 LEU cc_start: 0.8979 (mp) cc_final: 0.8742 (mt) REVERT: B 74 ASP cc_start: 0.7614 (m-30) cc_final: 0.6914 (m-30) REVERT: B 77 ASN cc_start: 0.6486 (m-40) cc_final: 0.5625 (t0) REVERT: B 87 ASP cc_start: 0.8139 (m-30) cc_final: 0.7886 (m-30) REVERT: B 110 LYS cc_start: 0.7737 (mttp) cc_final: 0.7497 (mtmt) REVERT: B 342 LYS cc_start: 0.8166 (mttm) cc_final: 0.7682 (tttp) REVERT: C 54 GLN cc_start: 0.8087 (tt0) cc_final: 0.7752 (tt0) REVERT: C 106 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6899 (tp30) REVERT: D 83 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6357 (mm-30) REVERT: E 230 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8995 (mt) REVERT: E 266 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: E 288 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7992 (t80) REVERT: E 386 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7567 (t80) REVERT: F 337 LYS cc_start: 0.6833 (pttt) cc_final: 0.6226 (mmpt) REVERT: G 9 LYS cc_start: 0.6074 (ttmt) cc_final: 0.5534 (pptt) REVERT: G 143 TYR cc_start: 0.6963 (m-80) cc_final: 0.6349 (m-80) REVERT: H 316 ARG cc_start: 0.7606 (mmm160) cc_final: 0.7057 (mmm160) REVERT: I 152 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8674 (mm) REVERT: I 289 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7739 (mtp180) REVERT: I 374 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7093 (mmtt) REVERT: J 264 ARG cc_start: 0.6063 (mpp-170) cc_final: 0.5767 (mpt180) REVERT: J 293 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7997 (mt-10) REVERT: J 337 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7359 (mptp) REVERT: J 352 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: K 83 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: K 106 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7145 (tp30) REVERT: K 287 MET cc_start: 0.9015 (mmt) cc_final: 0.8717 (mmp) REVERT: K 352 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: L 69 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8488 (mp) REVERT: L 100 ARG cc_start: 0.7978 (tpp80) cc_final: 0.7485 (mtt180) REVERT: L 128 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: L 132 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: L 235 ASN cc_start: 0.6522 (m-40) cc_final: 0.6012 (p0) REVERT: L 342 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7603 (mtpt) REVERT: L 380 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7887 (t80) REVERT: M 34 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6234 (ptm160) REVERT: M 277 GLN cc_start: 0.3532 (mt0) cc_final: 0.3315 (mt0) REVERT: M 410 ASP cc_start: 0.6072 (m-30) cc_final: 0.5712 (p0) REVERT: M 413 MET cc_start: 0.5796 (ttt) cc_final: 0.5203 (ppp) REVERT: M 438 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7957 (mtp) REVERT: M 478 GLU cc_start: 0.8095 (mp0) cc_final: 0.7595 (mp0) REVERT: M 498 GLU cc_start: 0.3822 (pt0) cc_final: 0.2992 (mm-30) REVERT: M 550 MET cc_start: 0.6815 (ptt) cc_final: 0.6565 (ptm) REVERT: M 555 GLU cc_start: 0.6971 (tp30) cc_final: 0.6691 (tm-30) REVERT: M 592 LYS cc_start: 0.7662 (tttt) cc_final: 0.7141 (tttt) REVERT: N 67 ASP cc_start: 0.9016 (m-30) cc_final: 0.8757 (m-30) REVERT: N 131 ASP cc_start: 0.8626 (m-30) cc_final: 0.8350 (m-30) REVERT: N 466 GLN cc_start: 0.7203 (mp10) cc_final: 0.6716 (mp10) REVERT: N 508 LYS cc_start: 0.8346 (mttp) cc_final: 0.7913 (mtpm) REVERT: N 592 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7428 (tppt) REVERT: O 105 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: O 382 GLN cc_start: 0.5560 (mt0) cc_final: 0.4978 (mm-40) REVERT: O 427 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6679 (mt0) REVERT: O 467 GLU cc_start: 0.6900 (mp0) cc_final: 0.6578 (mp0) REVERT: P 241 GLN cc_start: 0.6231 (OUTLIER) cc_final: 0.5886 (mm-40) REVERT: P 413 MET cc_start: 0.3836 (ttp) cc_final: 0.2624 (mpm) REVERT: P 448 MET cc_start: 0.7417 (pp-130) cc_final: 0.7174 (ppp) REVERT: P 478 GLU cc_start: 0.7683 (mp0) cc_final: 0.7368 (mm-30) REVERT: P 499 ARG cc_start: 0.6646 (ttm170) cc_final: 0.6315 (ttt180) REVERT: P 551 GLU cc_start: 0.3641 (OUTLIER) cc_final: 0.3107 (mm-30) REVERT: Q 35 LEU cc_start: 0.2161 (OUTLIER) cc_final: 0.1242 (tp) REVERT: Q 156 THR cc_start: 0.7644 (p) cc_final: 0.7343 (t) REVERT: Q 413 MET cc_start: 0.5135 (ttm) cc_final: 0.3864 (ptm) REVERT: Q 438 MET cc_start: 0.0039 (OUTLIER) cc_final: -0.1002 (mpt) REVERT: Q 463 ARG cc_start: 0.3019 (OUTLIER) cc_final: 0.2718 (tpm170) REVERT: Q 519 SER cc_start: 0.6606 (t) cc_final: 0.6369 (p) REVERT: Q 528 MET cc_start: 0.6556 (mpp) cc_final: 0.6353 (mtt) outliers start: 149 outliers final: 66 residues processed: 514 average time/residue: 1.3761 time to fit residues: 916.2565 Evaluate side-chains 460 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 370 time to evaluate : 5.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 374 LYS Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 352 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 341 THR Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 461 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 558 LEU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 198 TYR Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 463 ARG Chi-restraints excluded: chain Q residue 515 THR Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 245 optimal weight: 10.0000 chunk 657 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 428 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 730 optimal weight: 9.9990 chunk 606 optimal weight: 8.9990 chunk 338 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 241 optimal weight: 30.0000 chunk 383 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN D 378 ASN H 313 HIS I 227 HIS M 187 ASN Q 560 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 62584 Z= 0.144 Angle : 0.524 13.422 84667 Z= 0.268 Chirality : 0.041 0.183 9202 Planarity : 0.003 0.048 10852 Dihedral : 9.153 170.229 8925 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.91 % Allowed : 14.70 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: -0.59 (0.10), residues: 7515 helix: 0.72 (0.10), residues: 3024 sheet: 0.27 (0.17), residues: 900 loop : -1.59 (0.10), residues: 3591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 116 HIS 0.007 0.001 HIS P 445 PHE 0.028 0.001 PHE Q 263 TYR 0.039 0.001 TYR Q 198 ARG 0.007 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 408 time to evaluate : 5.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8029 (tt) cc_final: 0.7807 (tp) REVERT: B 12 GLU cc_start: 0.7575 (tt0) cc_final: 0.7173 (tp30) REVERT: B 68 LEU cc_start: 0.8964 (mp) cc_final: 0.8755 (mt) REVERT: B 74 ASP cc_start: 0.7538 (m-30) cc_final: 0.6863 (m-30) REVERT: B 77 ASN cc_start: 0.6192 (m-40) cc_final: 0.5643 (t0) REVERT: B 87 ASP cc_start: 0.8090 (m-30) cc_final: 0.7873 (m-30) REVERT: B 107 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: B 110 LYS cc_start: 0.7623 (mttp) cc_final: 0.7403 (mtmt) REVERT: B 342 LYS cc_start: 0.8081 (mttm) cc_final: 0.7619 (tttp) REVERT: C 54 GLN cc_start: 0.8020 (tt0) cc_final: 0.7645 (tt0) REVERT: D 83 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6203 (mm-30) REVERT: D 100 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7053 (mtt-85) REVERT: E 219 TYR cc_start: 0.7175 (m-10) cc_final: 0.6843 (m-10) REVERT: E 288 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7934 (t80) REVERT: E 363 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: E 386 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7557 (t80) REVERT: F 117 LYS cc_start: 0.8260 (tttt) cc_final: 0.7807 (ttmm) REVERT: F 156 GLN cc_start: 0.7119 (mm-40) cc_final: 0.6812 (mp10) REVERT: F 337 LYS cc_start: 0.6808 (pttt) cc_final: 0.6214 (mmpt) REVERT: G 143 TYR cc_start: 0.6885 (m-80) cc_final: 0.6293 (m-80) REVERT: H 316 ARG cc_start: 0.7615 (mmm160) cc_final: 0.6963 (mmm160) REVERT: I 106 GLU cc_start: 0.7861 (tp30) cc_final: 0.7485 (pt0) REVERT: I 289 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7642 (mtp180) REVERT: J 264 ARG cc_start: 0.6092 (mpp-170) cc_final: 0.5766 (mpt180) REVERT: J 293 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7720 (mt-10) REVERT: J 337 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7377 (mptp) REVERT: K 106 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7175 (tp30) REVERT: K 287 MET cc_start: 0.8995 (mmt) cc_final: 0.8622 (mmp) REVERT: K 352 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: L 128 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: L 132 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7640 (mt-10) REVERT: L 235 ASN cc_start: 0.6359 (m-40) cc_final: 0.5932 (p0) REVERT: L 342 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7583 (mtpt) REVERT: L 380 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7827 (t80) REVERT: M 34 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.5965 (ptm160) REVERT: M 410 ASP cc_start: 0.5768 (m-30) cc_final: 0.5475 (p0) REVERT: M 413 MET cc_start: 0.5733 (ttt) cc_final: 0.5164 (ppp) REVERT: M 438 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7797 (mtp) REVERT: M 478 GLU cc_start: 0.8059 (mp0) cc_final: 0.7561 (mp0) REVERT: M 498 GLU cc_start: 0.3968 (pt0) cc_final: 0.2972 (mp0) REVERT: M 550 MET cc_start: 0.6542 (ptt) cc_final: 0.6268 (ptm) REVERT: M 556 GLN cc_start: 0.8236 (pm20) cc_final: 0.7125 (pp30) REVERT: M 592 LYS cc_start: 0.7712 (tttt) cc_final: 0.7250 (tttt) REVERT: M 600 GLU cc_start: 0.7098 (mp0) cc_final: 0.6775 (mm-30) REVERT: N 67 ASP cc_start: 0.8945 (m-30) cc_final: 0.8699 (m-30) REVERT: N 131 ASP cc_start: 0.8562 (m-30) cc_final: 0.8295 (m-30) REVERT: N 229 GLU cc_start: 0.7208 (pp20) cc_final: 0.6841 (pm20) REVERT: N 466 GLN cc_start: 0.7241 (mp10) cc_final: 0.6747 (mp10) REVERT: N 508 LYS cc_start: 0.8175 (mttp) cc_final: 0.7772 (mtpm) REVERT: O 105 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7024 (tp30) REVERT: O 340 TRP cc_start: 0.6781 (m100) cc_final: 0.6463 (m100) REVERT: O 382 GLN cc_start: 0.5566 (mt0) cc_final: 0.4922 (mm-40) REVERT: O 427 GLN cc_start: 0.7006 (mm-40) cc_final: 0.6554 (mt0) REVERT: P 9 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8103 (mm) REVERT: P 131 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: P 241 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5883 (mm-40) REVERT: P 413 MET cc_start: 0.3796 (ttp) cc_final: 0.2513 (mpm) REVERT: P 478 GLU cc_start: 0.7618 (mp0) cc_final: 0.7308 (mm-30) REVERT: P 499 ARG cc_start: 0.6683 (ttm170) cc_final: 0.6312 (ttm170) REVERT: P 551 GLU cc_start: 0.3559 (OUTLIER) cc_final: 0.2969 (mm-30) REVERT: Q 35 LEU cc_start: 0.2294 (OUTLIER) cc_final: 0.1582 (tt) REVERT: Q 156 THR cc_start: 0.7803 (p) cc_final: 0.7509 (t) REVERT: Q 413 MET cc_start: 0.4924 (ttm) cc_final: 0.4075 (ptm) REVERT: Q 438 MET cc_start: -0.0242 (OUTLIER) cc_final: -0.0701 (mpt) REVERT: Q 463 ARG cc_start: 0.3001 (OUTLIER) cc_final: 0.2759 (tpm170) outliers start: 124 outliers final: 64 residues processed: 500 average time/residue: 1.3666 time to fit residues: 891.6304 Evaluate side-chains 469 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 385 time to evaluate : 5.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 363 PHE Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain K residue 374 LYS Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 538 THR Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 438 MET Chi-restraints excluded: chain P residue 461 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 463 ARG Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 704 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 416 optimal weight: 6.9990 chunk 533 optimal weight: 0.3980 chunk 413 optimal weight: 0.6980 chunk 614 optimal weight: 6.9990 chunk 407 optimal weight: 0.7980 chunk 727 optimal weight: 30.0000 chunk 455 optimal weight: 6.9990 chunk 443 optimal weight: 3.9990 chunk 335 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN G 360 ASN H 313 HIS I 227 HIS J 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 62584 Z= 0.149 Angle : 0.523 13.640 84667 Z= 0.265 Chirality : 0.041 0.191 9202 Planarity : 0.003 0.045 10852 Dihedral : 8.996 171.800 8925 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.00 % Allowed : 15.38 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.10), residues: 7515 helix: 0.83 (0.10), residues: 3036 sheet: 0.34 (0.17), residues: 920 loop : -1.53 (0.10), residues: 3559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 325 HIS 0.005 0.001 HIS G 267 PHE 0.023 0.001 PHE Q 263 TYR 0.019 0.001 TYR H 284 ARG 0.010 0.000 ARG Q 547 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 414 time to evaluate : 5.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8000 (tt) cc_final: 0.7775 (tp) REVERT: B 12 GLU cc_start: 0.7548 (tt0) cc_final: 0.7137 (tp30) REVERT: B 68 LEU cc_start: 0.8935 (mp) cc_final: 0.8728 (mt) REVERT: B 74 ASP cc_start: 0.7524 (m-30) cc_final: 0.6841 (m-30) REVERT: B 77 ASN cc_start: 0.6192 (m-40) cc_final: 0.5658 (t0) REVERT: B 87 ASP cc_start: 0.8095 (m-30) cc_final: 0.7866 (m-30) REVERT: B 110 LYS cc_start: 0.7614 (mttp) cc_final: 0.7413 (mtmt) REVERT: B 342 LYS cc_start: 0.8061 (mttm) cc_final: 0.7604 (tttp) REVERT: C 88 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: D 83 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6195 (mm-30) REVERT: D 100 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7063 (mtt-85) REVERT: E 288 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7930 (t80) REVERT: E 363 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7216 (m-10) REVERT: E 386 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7603 (t80) REVERT: F 117 LYS cc_start: 0.8262 (tttt) cc_final: 0.7802 (ttmm) REVERT: F 156 GLN cc_start: 0.7165 (mm-40) cc_final: 0.6805 (mp10) REVERT: F 337 LYS cc_start: 0.7080 (pttt) cc_final: 0.6483 (mmpt) REVERT: G 143 TYR cc_start: 0.6881 (m-80) cc_final: 0.6419 (m-80) REVERT: H 316 ARG cc_start: 0.7614 (mmm160) cc_final: 0.6970 (mmm160) REVERT: I 289 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7656 (mtp180) REVERT: I 374 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7004 (mmtt) REVERT: J 264 ARG cc_start: 0.6048 (mpp-170) cc_final: 0.5715 (mpt180) REVERT: J 293 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7694 (mt-10) REVERT: J 337 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7445 (mptp) REVERT: J 352 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: K 83 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: K 106 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7172 (tp30) REVERT: K 287 MET cc_start: 0.8994 (mmt) cc_final: 0.8654 (mmp) REVERT: K 352 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: L 69 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8352 (mp) REVERT: L 128 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: L 132 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: L 235 ASN cc_start: 0.6360 (m-40) cc_final: 0.5928 (p0) REVERT: L 342 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7598 (mtpt) REVERT: L 380 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7791 (t80) REVERT: M 34 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.5863 (ptm160) REVERT: M 413 MET cc_start: 0.5766 (ttt) cc_final: 0.5211 (ppp) REVERT: M 438 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7908 (mtp) REVERT: M 478 GLU cc_start: 0.8022 (mp0) cc_final: 0.7559 (mp0) REVERT: M 498 GLU cc_start: 0.4027 (pt0) cc_final: 0.2978 (mp0) REVERT: M 550 MET cc_start: 0.6444 (ptt) cc_final: 0.6153 (ptm) REVERT: M 592 LYS cc_start: 0.7703 (tttt) cc_final: 0.7278 (tttt) REVERT: M 600 GLU cc_start: 0.7083 (mp0) cc_final: 0.6790 (mm-30) REVERT: N 67 ASP cc_start: 0.8951 (m-30) cc_final: 0.8705 (m-30) REVERT: N 131 ASP cc_start: 0.8557 (m-30) cc_final: 0.8293 (m-30) REVERT: N 229 GLU cc_start: 0.7239 (pp20) cc_final: 0.6965 (pm20) REVERT: N 332 ARG cc_start: 0.6716 (ttm110) cc_final: 0.6443 (ttm110) REVERT: N 466 GLN cc_start: 0.7256 (mp10) cc_final: 0.6785 (mp10) REVERT: N 508 LYS cc_start: 0.8205 (mttp) cc_final: 0.7761 (mtpm) REVERT: O 105 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7024 (tp30) REVERT: O 340 TRP cc_start: 0.6790 (m100) cc_final: 0.6448 (m100) REVERT: O 382 GLN cc_start: 0.5551 (mt0) cc_final: 0.4915 (mm-40) REVERT: O 427 GLN cc_start: 0.7020 (mm-40) cc_final: 0.6547 (mt0) REVERT: P 9 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8053 (mm) REVERT: P 131 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: P 241 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.6026 (tm-30) REVERT: P 413 MET cc_start: 0.3741 (ttp) cc_final: 0.2498 (mpm) REVERT: P 478 GLU cc_start: 0.7526 (mp0) cc_final: 0.7256 (mm-30) REVERT: P 551 GLU cc_start: 0.3452 (OUTLIER) cc_final: 0.2810 (mm-30) REVERT: Q 35 LEU cc_start: 0.2256 (OUTLIER) cc_final: 0.1546 (tp) REVERT: Q 156 THR cc_start: 0.8134 (p) cc_final: 0.7805 (t) REVERT: Q 413 MET cc_start: 0.4757 (ttm) cc_final: 0.4096 (ptm) REVERT: Q 438 MET cc_start: -0.0019 (OUTLIER) cc_final: -0.0543 (mpt) REVERT: Q 456 MET cc_start: 0.2405 (mpm) cc_final: 0.0697 (ttm) REVERT: Q 472 THR cc_start: 0.6890 (m) cc_final: 0.6408 (p) REVERT: Q 536 ARG cc_start: 0.6508 (tpt-90) cc_final: 0.6296 (tpt-90) outliers start: 130 outliers final: 69 residues processed: 509 average time/residue: 1.3487 time to fit residues: 894.1774 Evaluate side-chains 478 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 386 time to evaluate : 5.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 363 PHE Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 374 LYS Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 352 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 341 THR Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain K residue 374 LYS Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 374 VAL Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 538 THR Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 461 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 438 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 450 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 434 optimal weight: 6.9990 chunk 219 optimal weight: 0.0980 chunk 142 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 462 optimal weight: 0.9980 chunk 495 optimal weight: 7.9990 chunk 359 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 571 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 324 ASN G 78 ASN H 78 ASN H 313 HIS I 227 HIS J 55 ASN O 466 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 62584 Z= 0.244 Angle : 0.600 14.391 84667 Z= 0.305 Chirality : 0.043 0.195 9202 Planarity : 0.004 0.047 10852 Dihedral : 9.277 170.434 8925 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.99 % Allowed : 15.59 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: 7515 helix: 0.69 (0.10), residues: 3025 sheet: 0.27 (0.17), residues: 903 loop : -1.63 (0.10), residues: 3587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 325 HIS 0.008 0.001 HIS D 227 PHE 0.037 0.002 PHE G 380 TYR 0.017 0.001 TYR B 143 ARG 0.011 0.000 ARG Q 566 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 388 time to evaluate : 5.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8048 (tt) cc_final: 0.7818 (tp) REVERT: B 12 GLU cc_start: 0.7658 (tt0) cc_final: 0.7229 (tp30) REVERT: B 68 LEU cc_start: 0.8965 (mp) cc_final: 0.8736 (mt) REVERT: B 74 ASP cc_start: 0.7547 (m-30) cc_final: 0.6874 (m-30) REVERT: B 77 ASN cc_start: 0.6296 (m-40) cc_final: 0.5743 (t0) REVERT: B 87 ASP cc_start: 0.8194 (m-30) cc_final: 0.7960 (m-30) REVERT: B 88 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: B 110 LYS cc_start: 0.7760 (mttp) cc_final: 0.7536 (mtmt) REVERT: B 342 LYS cc_start: 0.8125 (mttm) cc_final: 0.7655 (tttp) REVERT: D 83 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6361 (mm-30) REVERT: E 288 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8007 (t80) REVERT: E 386 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7489 (t80) REVERT: F 117 LYS cc_start: 0.8269 (tttt) cc_final: 0.7825 (ttmm) REVERT: F 156 GLN cc_start: 0.7288 (mm-40) cc_final: 0.6964 (mp10) REVERT: F 337 LYS cc_start: 0.7107 (pttt) cc_final: 0.6485 (mmpt) REVERT: G 9 LYS cc_start: 0.5998 (ttpp) cc_final: 0.5148 (pptt) REVERT: G 143 TYR cc_start: 0.6922 (m-80) cc_final: 0.6469 (m-80) REVERT: H 316 ARG cc_start: 0.7632 (mmm160) cc_final: 0.6991 (mmm160) REVERT: I 106 GLU cc_start: 0.7971 (tp30) cc_final: 0.7609 (pt0) REVERT: I 289 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7768 (mtp180) REVERT: I 374 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7076 (mmtt) REVERT: J 264 ARG cc_start: 0.6096 (mpp-170) cc_final: 0.5713 (mpt180) REVERT: J 293 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7855 (mt-10) REVERT: J 337 LYS cc_start: 0.7990 (ttpp) cc_final: 0.7407 (mptp) REVERT: J 352 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: K 83 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: K 106 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7142 (tp30) REVERT: K 287 MET cc_start: 0.8996 (mmt) cc_final: 0.8695 (mmp) REVERT: K 352 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: L 69 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8424 (mp) REVERT: L 128 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: L 132 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: L 235 ASN cc_start: 0.6563 (m-40) cc_final: 0.6065 (p0) REVERT: L 342 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7599 (mtpt) REVERT: L 380 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7813 (t80) REVERT: M 5 LYS cc_start: 0.5467 (tptt) cc_final: 0.4800 (mttt) REVERT: M 34 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6018 (ptm160) REVERT: M 202 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.6101 (ttp-170) REVERT: M 413 MET cc_start: 0.5538 (ttt) cc_final: 0.5093 (ppp) REVERT: M 438 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7939 (mtp) REVERT: M 478 GLU cc_start: 0.8093 (mp0) cc_final: 0.7623 (mp0) REVERT: M 498 GLU cc_start: 0.3835 (pt0) cc_final: 0.2840 (OUTLIER) REVERT: M 550 MET cc_start: 0.6756 (ptt) cc_final: 0.6504 (ptm) REVERT: M 592 LYS cc_start: 0.7789 (tttt) cc_final: 0.7256 (ttpt) REVERT: M 600 GLU cc_start: 0.7140 (mp0) cc_final: 0.6848 (mm-30) REVERT: N 67 ASP cc_start: 0.8981 (m-30) cc_final: 0.8741 (m-30) REVERT: N 131 ASP cc_start: 0.8623 (m-30) cc_final: 0.8354 (m-30) REVERT: N 229 GLU cc_start: 0.7364 (pp20) cc_final: 0.7133 (pm20) REVERT: N 332 ARG cc_start: 0.6656 (ttm110) cc_final: 0.6374 (ttm110) REVERT: N 466 GLN cc_start: 0.7264 (mp10) cc_final: 0.6792 (mp10) REVERT: N 506 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7876 (mtmt) REVERT: O 105 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7081 (tp30) REVERT: O 382 GLN cc_start: 0.5486 (mt0) cc_final: 0.4867 (mm-40) REVERT: O 427 GLN cc_start: 0.7144 (mm-40) cc_final: 0.6725 (mt0) REVERT: P 9 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8117 (mm) REVERT: P 131 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: P 241 GLN cc_start: 0.6484 (OUTLIER) cc_final: 0.6141 (tm-30) REVERT: P 413 MET cc_start: 0.3901 (ttp) cc_final: 0.2766 (mpm) REVERT: P 478 GLU cc_start: 0.7509 (mp0) cc_final: 0.7245 (mm-30) REVERT: P 551 GLU cc_start: 0.3923 (OUTLIER) cc_final: 0.3221 (mm-30) REVERT: Q 35 LEU cc_start: 0.2325 (OUTLIER) cc_final: 0.1503 (tp) REVERT: Q 413 MET cc_start: 0.4859 (ttm) cc_final: 0.4256 (ptm) REVERT: Q 438 MET cc_start: -0.0083 (OUTLIER) cc_final: -0.0668 (mpt) REVERT: Q 456 MET cc_start: 0.2378 (mpm) cc_final: 0.0840 (ttm) REVERT: Q 463 ARG cc_start: 0.2868 (tpm170) cc_final: 0.0820 (mmp-170) REVERT: Q 566 ARG cc_start: 0.6696 (ttt180) cc_final: 0.6473 (ttm110) outliers start: 129 outliers final: 74 residues processed: 485 average time/residue: 1.3588 time to fit residues: 855.3945 Evaluate side-chains 468 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 372 time to evaluate : 5.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 374 LYS Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 352 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 341 THR Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 374 VAL Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 538 THR Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 461 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 661 optimal weight: 2.9990 chunk 697 optimal weight: 9.9990 chunk 636 optimal weight: 3.9990 chunk 678 optimal weight: 0.0670 chunk 696 optimal weight: 0.9990 chunk 408 optimal weight: 0.0000 chunk 295 optimal weight: 0.7980 chunk 532 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 612 optimal weight: 9.9990 chunk 641 optimal weight: 9.9990 overall best weight: 0.9726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 360 ASN H 313 HIS I 227 HIS ** J 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 62584 Z= 0.131 Angle : 0.515 13.629 84667 Z= 0.262 Chirality : 0.041 0.175 9202 Planarity : 0.003 0.054 10852 Dihedral : 8.925 174.374 8925 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.65 % Allowed : 16.18 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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 (0.10), residues: 7515 helix: 0.90 (0.10), residues: 3035 sheet: 0.41 (0.17), residues: 901 loop : -1.51 (0.10), residues: 3579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 325 HIS 0.005 0.001 HIS G 267 PHE 0.040 0.001 PHE Q 462 TYR 0.025 0.001 TYR O 258 ARG 0.009 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 392 time to evaluate : 5.249 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 73 ILE cc_start: 0.7986 (tt) cc_final: 0.7758 (tp) REVERT: B 12 GLU cc_start: 0.7510 (tt0) cc_final: 0.7118 (tp30) REVERT: B 68 LEU cc_start: 0.8938 (mp) cc_final: 0.8712 (mt) REVERT: B 74 ASP cc_start: 0.7495 (m-30) cc_final: 0.6823 (m-30) REVERT: B 77 ASN cc_start: 0.6190 (m-40) cc_final: 0.5664 (t0) REVERT: B 87 ASP cc_start: 0.8131 (m-30) cc_final: 0.7896 (m-30) REVERT: B 88 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: B 342 LYS cc_start: 0.8054 (mttm) cc_final: 0.7602 (tttp) REVERT: D 83 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6168 (mm-30) REVERT: D 100 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7047 (mtt-85) REVERT: E 288 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7940 (t80) REVERT: E 386 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7542 (t80) REVERT: F 117 LYS cc_start: 0.8254 (tttt) cc_final: 0.7797 (ttmm) REVERT: F 156 GLN cc_start: 0.7167 (mm-40) cc_final: 0.6854 (mp10) REVERT: F 337 LYS cc_start: 0.7069 (pttt) cc_final: 0.6446 (mmpt) REVERT: G 143 TYR cc_start: 0.6864 (m-80) cc_final: 0.6425 (m-80) REVERT: H 316 ARG cc_start: 0.7638 (mmm160) cc_final: 0.7007 (mmm160) REVERT: I 106 GLU cc_start: 0.7922 (tp30) cc_final: 0.7585 (pt0) REVERT: I 289 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7638 (mtp180) REVERT: I 374 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7014 (mmtt) REVERT: J 264 ARG cc_start: 0.6046 (mpp-170) cc_final: 0.5724 (mpt180) REVERT: J 293 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7775 (mt-10) REVERT: J 337 LYS cc_start: 0.7997 (ttpp) cc_final: 0.7446 (mptp) REVERT: J 342 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7791 (tttp) REVERT: J 352 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: K 83 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: K 106 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7243 (tp30) REVERT: K 139 ASP cc_start: 0.8125 (m-30) cc_final: 0.7805 (t0) REVERT: K 287 MET cc_start: 0.8998 (mmt) cc_final: 0.8624 (mmp) REVERT: K 352 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: L 69 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8331 (mp) REVERT: L 128 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: L 132 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: L 235 ASN cc_start: 0.6375 (m-40) cc_final: 0.5942 (p0) REVERT: L 342 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7578 (mtpt) REVERT: L 380 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7757 (t80) REVERT: M 5 LYS cc_start: 0.5470 (tptt) cc_final: 0.4816 (mttt) REVERT: M 34 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.5793 (ptm160) REVERT: M 202 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.6100 (tpp-160) REVERT: M 413 MET cc_start: 0.5104 (ttt) cc_final: 0.4731 (tmm) REVERT: M 438 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7831 (mtp) REVERT: M 478 GLU cc_start: 0.8055 (mp0) cc_final: 0.7595 (mp0) REVERT: M 498 GLU cc_start: 0.3899 (pt0) cc_final: 0.2841 (OUTLIER) REVERT: M 550 MET cc_start: 0.6588 (ptt) cc_final: 0.6331 (ptm) REVERT: M 556 GLN cc_start: 0.7975 (pm20) cc_final: 0.6849 (pp30) REVERT: M 600 GLU cc_start: 0.7130 (mp0) cc_final: 0.6860 (mm-30) REVERT: N 67 ASP cc_start: 0.8914 (m-30) cc_final: 0.8677 (m-30) REVERT: N 131 ASP cc_start: 0.8548 (m-30) cc_final: 0.8297 (m-30) REVERT: N 332 ARG cc_start: 0.6668 (ttm110) cc_final: 0.6397 (ttm110) REVERT: N 466 GLN cc_start: 0.7218 (mp10) cc_final: 0.6747 (mp10) REVERT: N 506 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7816 (mtmt) REVERT: O 105 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: O 258 TYR cc_start: 0.6775 (p90) cc_final: 0.6531 (p90) REVERT: O 340 TRP cc_start: 0.6801 (m100) cc_final: 0.6500 (m100) REVERT: O 382 GLN cc_start: 0.5490 (mt0) cc_final: 0.4855 (mm-40) REVERT: O 427 GLN cc_start: 0.7016 (mm-40) cc_final: 0.6588 (mt0) REVERT: P 9 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8031 (mm) REVERT: P 131 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7209 (m-30) REVERT: P 241 GLN cc_start: 0.6410 (OUTLIER) cc_final: 0.5628 (tm-30) REVERT: P 413 MET cc_start: 0.4000 (ttp) cc_final: 0.2777 (mpm) REVERT: Q 35 LEU cc_start: 0.2210 (OUTLIER) cc_final: 0.1495 (tp) REVERT: Q 144 LEU cc_start: 0.6337 (mt) cc_final: 0.5957 (mm) REVERT: Q 413 MET cc_start: 0.5090 (ttm) cc_final: 0.4605 (ptm) REVERT: Q 456 MET cc_start: 0.2753 (mpm) cc_final: 0.1090 (ttm) REVERT: Q 463 ARG cc_start: 0.2797 (tpm170) cc_final: 0.0988 (mmp-170) REVERT: Q 472 THR cc_start: 0.7105 (m) cc_final: 0.6607 (p) REVERT: Q 516 GLN cc_start: 0.6564 (pt0) cc_final: 0.6023 (pm20) outliers start: 107 outliers final: 67 residues processed: 475 average time/residue: 1.3573 time to fit residues: 837.5429 Evaluate side-chains 460 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 373 time to evaluate : 5.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 374 LYS Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 352 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 374 VAL Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain O residue 538 THR Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 461 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 675 optimal weight: 20.0000 chunk 445 optimal weight: 8.9990 chunk 717 optimal weight: 6.9990 chunk 437 optimal weight: 0.0050 chunk 340 optimal weight: 0.8980 chunk 498 optimal weight: 3.9990 chunk 752 optimal weight: 5.9990 chunk 692 optimal weight: 10.0000 chunk 598 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 462 optimal weight: 0.8980 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 394 ASN H 313 HIS I 227 HIS P 539 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 62584 Z= 0.198 Angle : 0.570 14.234 84667 Z= 0.289 Chirality : 0.042 0.188 9202 Planarity : 0.004 0.051 10852 Dihedral : 9.085 173.538 8925 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.49 % Allowed : 16.44 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.10), residues: 7515 helix: 0.86 (0.10), residues: 3019 sheet: 0.40 (0.17), residues: 916 loop : -1.57 (0.10), residues: 3580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 325 HIS 0.006 0.001 HIS B 313 PHE 0.045 0.001 PHE Q 462 TYR 0.026 0.001 TYR O 258 ARG 0.009 0.000 ARG Q 547 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 388 time to evaluate : 5.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8025 (tt) cc_final: 0.7794 (tp) REVERT: B 12 GLU cc_start: 0.7576 (tt0) cc_final: 0.7154 (tp30) REVERT: B 68 LEU cc_start: 0.8944 (mp) cc_final: 0.8713 (mt) REVERT: B 74 ASP cc_start: 0.7509 (m-30) cc_final: 0.6837 (m-30) REVERT: B 77 ASN cc_start: 0.6284 (m-40) cc_final: 0.5749 (t0) REVERT: B 87 ASP cc_start: 0.8098 (m-30) cc_final: 0.7866 (m-30) REVERT: B 88 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: B 342 LYS cc_start: 0.8096 (mttm) cc_final: 0.7633 (tttp) REVERT: D 83 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6266 (mm-30) REVERT: D 100 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7104 (mtt-85) REVERT: E 288 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7926 (t80) REVERT: E 386 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7471 (t80) REVERT: F 117 LYS cc_start: 0.8265 (tttt) cc_final: 0.7816 (ttmm) REVERT: F 156 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6989 (mp10) REVERT: F 337 LYS cc_start: 0.7087 (pttt) cc_final: 0.6465 (mmpt) REVERT: G 9 LYS cc_start: 0.5949 (ttpp) cc_final: 0.5090 (pptt) REVERT: G 143 TYR cc_start: 0.6868 (m-80) cc_final: 0.6437 (m-80) REVERT: H 316 ARG cc_start: 0.7658 (mmm160) cc_final: 0.7029 (mmm160) REVERT: I 289 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7616 (mtp180) REVERT: I 374 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.6987 (mmtt) REVERT: J 293 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7790 (mt-10) REVERT: J 337 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7367 (mptp) REVERT: J 342 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7823 (tttp) REVERT: J 352 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: K 83 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: K 106 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7145 (tp30) REVERT: K 139 ASP cc_start: 0.8133 (m-30) cc_final: 0.7807 (t0) REVERT: K 287 MET cc_start: 0.9003 (mmt) cc_final: 0.8688 (mmp) REVERT: K 352 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: L 69 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8415 (mp) REVERT: L 128 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7367 (tp30) REVERT: L 132 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: L 235 ASN cc_start: 0.6466 (m-40) cc_final: 0.5935 (p0) REVERT: L 342 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7607 (mtpt) REVERT: L 380 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7767 (t80) REVERT: M 5 LYS cc_start: 0.5580 (tptt) cc_final: 0.4940 (mptt) REVERT: M 34 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.5881 (ptm160) REVERT: M 202 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.6082 (ttp-170) REVERT: M 413 MET cc_start: 0.5044 (ttt) cc_final: 0.4763 (tmm) REVERT: M 438 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7911 (mtp) REVERT: M 478 GLU cc_start: 0.8079 (mp0) cc_final: 0.7601 (mp0) REVERT: M 498 GLU cc_start: 0.3777 (pt0) cc_final: 0.2914 (mm-30) REVERT: M 550 MET cc_start: 0.6731 (ptt) cc_final: 0.6495 (ptm) REVERT: M 592 LYS cc_start: 0.7793 (tttt) cc_final: 0.7269 (ttpt) REVERT: M 600 GLU cc_start: 0.7198 (mp0) cc_final: 0.6944 (mm-30) REVERT: N 67 ASP cc_start: 0.8977 (m-30) cc_final: 0.8730 (m-30) REVERT: N 131 ASP cc_start: 0.8570 (m-30) cc_final: 0.8296 (m-30) REVERT: N 229 GLU cc_start: 0.7252 (pp20) cc_final: 0.7031 (pm20) REVERT: N 332 ARG cc_start: 0.6694 (ttm110) cc_final: 0.6427 (ttm110) REVERT: N 466 GLN cc_start: 0.7229 (mp10) cc_final: 0.6757 (mp10) REVERT: N 506 LYS cc_start: 0.8157 (mtpp) cc_final: 0.7849 (mtmt) REVERT: O 382 GLN cc_start: 0.5466 (mt0) cc_final: 0.4863 (mm-40) REVERT: O 427 GLN cc_start: 0.7136 (mm-40) cc_final: 0.6728 (mt0) REVERT: P 9 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8063 (mm) REVERT: P 413 MET cc_start: 0.3992 (ttp) cc_final: 0.2749 (mpm) REVERT: P 468 ARG cc_start: 0.4429 (mtm-85) cc_final: 0.4028 (mmt-90) REVERT: Q 35 LEU cc_start: 0.2282 (OUTLIER) cc_final: 0.1512 (tp) REVERT: Q 413 MET cc_start: 0.5109 (ttm) cc_final: 0.4129 (ttm) REVERT: Q 448 MET cc_start: 0.3241 (mmm) cc_final: 0.1928 (pmt) REVERT: Q 456 MET cc_start: 0.2733 (mpm) cc_final: 0.1216 (ttm) REVERT: Q 463 ARG cc_start: 0.2772 (tpm170) cc_final: 0.0965 (mmp-170) REVERT: Q 472 THR cc_start: 0.7075 (m) cc_final: 0.6528 (p) REVERT: Q 516 GLN cc_start: 0.7007 (pt0) cc_final: 0.6520 (pm20) outliers start: 97 outliers final: 64 residues processed: 465 average time/residue: 1.4467 time to fit residues: 878.1330 Evaluate side-chains 461 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 379 time to evaluate : 5.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 374 LYS Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 352 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 349 LEU Chi-restraints excluded: chain O residue 374 VAL Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 449 LEU Chi-restraints excluded: chain O residue 538 THR Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 461 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 367 optimal weight: 5.9990 chunk 475 optimal weight: 0.8980 chunk 638 optimal weight: 8.9990 chunk 183 optimal weight: 0.5980 chunk 552 optimal weight: 0.0870 chunk 88 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 599 optimal weight: 0.0270 chunk 251 optimal weight: 1.9990 chunk 616 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 274 ASN G 360 ASN H 313 HIS K 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.178039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120282 restraints weight = 77706.698| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.92 r_work: 0.3197 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 62584 Z= 0.125 Angle : 0.503 13.523 84667 Z= 0.254 Chirality : 0.040 0.167 9202 Planarity : 0.003 0.049 10852 Dihedral : 8.718 177.891 8925 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.17 % Allowed : 16.93 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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 (0.10), residues: 7515 helix: 1.03 (0.10), residues: 3039 sheet: 0.46 (0.17), residues: 908 loop : -1.44 (0.10), residues: 3568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 325 HIS 0.005 0.000 HIS G 267 PHE 0.043 0.001 PHE Q 462 TYR 0.019 0.001 TYR H 284 ARG 0.009 0.000 ARG A 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17592.56 seconds wall clock time: 303 minutes 4.10 seconds (18184.10 seconds total)