Starting phenix.real_space_refine on Thu Sep 26 19:02:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/09_2024/6ks8_0760.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/09_2024/6ks8_0760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/09_2024/6ks8_0760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/09_2024/6ks8_0760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/09_2024/6ks8_0760.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/09_2024/6ks8_0760.cif" } resolution = 4.69 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= 0.021 sd= 0.143 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: 4 Type Number sf(0) Gaussians S 316 5.16 5 C 38884 2.51 5 N 10714 2.21 5 O 12029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 61943 Number of models: 1 Model: "" Number of chains: 16 Chain: "a" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3908 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 10, 'TRANS': 508} Chain breaks: 1 Chain: "A" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3859 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 10, 'TRANS': 501} Chain breaks: 2 Chain: "b" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3811 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 10, 'TRANS': 491} Chain: "B" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3708 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 10, 'TRANS': 478} Chain breaks: 1 Chain: "d" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3816 Classifications: {'peptide': 499} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 485} Chain breaks: 1 Chain: "D" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3655 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 467} Chain breaks: 2 Chain: "e" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3982 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 15, 'TRANS': 502} Chain: "E" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3848 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 15, 'TRANS': 486} Chain breaks: 1 Chain: "g" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3775 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 18, 'TRANS': 474} Chain breaks: 2 Chain: "G" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3709 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 2 Chain: "h" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3882 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 12, 'TRANS': 494} Chain: "H" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3882 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 12, 'TRANS': 494} Chain: "q" Number of atoms: 3974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3974 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 18, 'TRANS': 504} Chain: "Q" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3978 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 18, 'TRANS': 505} Chain: "z" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4086 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 15, 'TRANS': 515} Chain: "Z" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4070 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Time building chain proxies: 30.15, per 1000 atoms: 0.49 Number of scatterers: 61943 At special positions: 0 Unit cell: (192.428, 192.428, 204.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 316 16.00 O 12029 8.00 N 10714 7.00 C 38884 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: 11.78 Conformation dependent library (CDL) restraints added in 6.6 seconds 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15120 Finding SS restraints... Secondary structure from input PDB file: 333 helices and 92 sheets defined 55.3% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'a' and resid 22 through 41 removed outlier: 4.157A pdb=" N ARG a 26 " --> pdb=" O GLY a 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN a 27 " --> pdb=" O ASP a 23 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL a 30 " --> pdb=" O ARG a 26 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL a 36 " --> pdb=" O ALA a 32 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL a 39 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL a 40 " --> pdb=" O VAL a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 73 removed outlier: 3.539A pdb=" N ILE a 69 " --> pdb=" O ASP a 65 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 94 removed outlier: 3.668A pdb=" N VAL a 84 " --> pdb=" O GLY a 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU a 93 " --> pdb=" O GLN a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 115 removed outlier: 3.519A pdb=" N VAL a 102 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE a 103 " --> pdb=" O THR a 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU a 107 " --> pdb=" O ILE a 103 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU a 115 " --> pdb=" O ARG a 111 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 142 removed outlier: 3.651A pdb=" N ARG a 138 " --> pdb=" O ARG a 134 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN a 141 " --> pdb=" O ILE a 137 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU a 142 " --> pdb=" O ARG a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 removed outlier: 3.872A pdb=" N ALA a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER a 163 " --> pdb=" O ILE a 159 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 167 No H-bonds generated for 'chain 'a' and resid 165 through 167' Processing helix chain 'a' and resid 168 through 188 removed outlier: 4.191A pdb=" N ASP a 172 " --> pdb=" O ILE a 168 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASP a 174 " --> pdb=" O GLY a 170 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE a 175 " --> pdb=" O ALA a 171 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET a 179 " --> pdb=" O PHE a 175 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA a 186 " --> pdb=" O ASP a 182 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS a 188 " --> pdb=" O LEU a 184 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 Processing helix chain 'a' and resid 277 through 290 removed outlier: 3.917A pdb=" N VAL a 281 " --> pdb=" O GLU a 277 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG a 284 " --> pdb=" O ILE a 280 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL a 285 " --> pdb=" O VAL a 281 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS a 287 " --> pdb=" O GLU a 283 " (cutoff:3.500A) Processing helix chain 'a' and resid 304 through 313 removed outlier: 3.778A pdb=" N GLU a 309 " --> pdb=" O LEU a 305 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE a 310 " --> pdb=" O CYS a 306 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA a 313 " --> pdb=" O GLU a 309 " (cutoff:3.500A) Processing helix chain 'a' and resid 322 through 334 removed outlier: 3.588A pdb=" N ARG a 327 " --> pdb=" O LYS a 323 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG a 328 " --> pdb=" O GLU a 324 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG a 331 " --> pdb=" O ARG a 327 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 415 removed outlier: 3.750A pdb=" N GLU a 397 " --> pdb=" O TYR a 393 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP a 404 " --> pdb=" O ARG a 400 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL a 408 " --> pdb=" O ASP a 404 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER a 415 " --> pdb=" O ARG a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 437 removed outlier: 3.658A pdb=" N ASN a 435 " --> pdb=" O ILE a 431 " (cutoff:3.500A) Processing helix chain 'a' and resid 438 through 440 No H-bonds generated for 'chain 'a' and resid 438 through 440' Processing helix chain 'a' and resid 443 through 455 removed outlier: 3.898A pdb=" N ALA a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU a 455 " --> pdb=" O PHE a 451 " (cutoff:3.500A) Processing helix chain 'a' and resid 456 through 465 removed outlier: 3.545A pdb=" N LEU a 462 " --> pdb=" O ILE a 458 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA a 463 " --> pdb=" O PRO a 459 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL a 464 " --> pdb=" O LYS a 460 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) Processing helix chain 'a' and resid 469 through 485 removed outlier: 3.543A pdb=" N LEU a 473 " --> pdb=" O ASP a 469 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL a 474 " --> pdb=" O SER a 470 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA a 475 " --> pdb=" O SER a 471 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR a 480 " --> pdb=" O LYS a 476 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA a 483 " --> pdb=" O SER a 479 " (cutoff:3.500A) Processing helix chain 'a' and resid 512 through 516 Processing helix chain 'a' and resid 521 through 540 removed outlier: 3.514A pdb=" N GLU a 533 " --> pdb=" O LYS a 529 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA a 537 " --> pdb=" O GLU a 533 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE a 538 " --> pdb=" O ALA a 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 38 removed outlier: 3.994A pdb=" N ARG A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.690A pdb=" N ILE A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 92 removed outlier: 4.214A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 88 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.554A pdb=" N VAL A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.504A pdb=" N ILE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.808A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 removed outlier: 4.294A pdb=" N ASP A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 277 through 291 removed outlier: 4.352A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.630A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 334 removed outlier: 4.032A pdb=" N ARG A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 3.700A pdb=" N VAL A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.630A pdb=" N ASN A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 443 through 454 removed outlier: 3.914A pdb=" N ALA A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.624A pdb=" N ARG A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.745A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 34 removed outlier: 3.522A pdb=" N LEU b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 37 No H-bonds generated for 'chain 'b' and resid 35 through 37' Processing helix chain 'b' and resid 59 through 67 Processing helix chain 'b' and resid 73 through 88 removed outlier: 4.180A pdb=" N LEU b 77 " --> pdb=" O ALA b 73 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL b 83 " --> pdb=" O ASN b 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 111 removed outlier: 3.505A pdb=" N GLU b 107 " --> pdb=" O LEU b 103 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS b 108 " --> pdb=" O ARG b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 138 removed outlier: 3.553A pdb=" N ALA b 129 " --> pdb=" O ARG b 125 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA b 130 " --> pdb=" O LEU b 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 161 removed outlier: 3.581A pdb=" N PHE b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 168 Processing helix chain 'b' and resid 169 through 183 removed outlier: 4.685A pdb=" N GLU b 175 " --> pdb=" O ASP b 171 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU b 176 " --> pdb=" O HIS b 172 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG b 183 " --> pdb=" O ASN b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 191 No H-bonds generated for 'chain 'b' and resid 189 through 191' Processing helix chain 'b' and resid 202 through 206 Processing helix chain 'b' and resid 254 through 278 removed outlier: 3.501A pdb=" N ALA b 259 " --> pdb=" O THR b 255 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN b 260 " --> pdb=" O ALA b 256 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU b 261 " --> pdb=" O LYS b 257 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA b 264 " --> pdb=" O GLN b 260 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU b 265 " --> pdb=" O LEU b 261 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG b 266 " --> pdb=" O GLU b 262 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN b 271 " --> pdb=" O GLU b 267 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 301 removed outlier: 3.856A pdb=" N THR b 299 " --> pdb=" O GLU b 295 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP b 300 " --> pdb=" O GLN b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 310 through 319 removed outlier: 3.605A pdb=" N LEU b 319 " --> pdb=" O GLU b 315 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 394 removed outlier: 3.558A pdb=" N GLU b 379 " --> pdb=" O GLN b 375 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG b 382 " --> pdb=" O ASP b 378 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL b 390 " --> pdb=" O ASP b 386 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN b 393 " --> pdb=" O SER b 389 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 419 removed outlier: 3.535A pdb=" N MET b 409 " --> pdb=" O GLY b 405 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS b 413 " --> pdb=" O MET b 409 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA b 414 " --> pdb=" O VAL b 410 " (cutoff:3.500A) Processing helix chain 'b' and resid 423 through 438 removed outlier: 4.481A pdb=" N LEU b 428 " --> pdb=" O GLY b 424 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA b 429 " --> pdb=" O LYS b 425 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE b 433 " --> pdb=" O ALA b 429 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG b 435 " --> pdb=" O GLU b 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG b 438 " --> pdb=" O ALA b 434 " (cutoff:3.500A) Processing helix chain 'b' and resid 438 through 449 Processing helix chain 'b' and resid 451 through 465 removed outlier: 3.560A pdb=" N LEU b 459 " --> pdb=" O LEU b 455 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER b 462 " --> pdb=" O LYS b 458 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN b 465 " --> pdb=" O SER b 461 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 486 Processing helix chain 'b' and resid 491 through 510 removed outlier: 3.529A pdb=" N ALA b 496 " --> pdb=" O LYS b 492 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU b 508 " --> pdb=" O ALA b 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 removed outlier: 3.578A pdb=" N LEU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 71 through 88 removed outlier: 3.519A pdb=" N VAL B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 105 removed outlier: 3.658A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 138 removed outlier: 3.675A pdb=" N ALA B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.695A pdb=" N GLU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.628A pdb=" N GLN B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 183 removed outlier: 4.644A pdb=" N GLU B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 176 " --> pdb=" O HIS B 172 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 183 " --> pdb=" O ASN B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.906A pdb=" N LEU B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.545A pdb=" N PHE B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.578A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 397 removed outlier: 3.714A pdb=" N GLU B 379 " --> pdb=" O GLN B 375 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 418 removed outlier: 3.593A pdb=" N MET B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 425 through 438 removed outlier: 4.182A pdb=" N ALA B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 451 through 465 removed outlier: 3.522A pdb=" N VAL B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 491 through 511 removed outlier: 3.529A pdb=" N VAL B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'd' and resid 18 through 36 removed outlier: 3.588A pdb=" N VAL d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA d 34 " --> pdb=" O SER d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 68 Processing helix chain 'd' and resid 72 through 89 removed outlier: 3.611A pdb=" N MET d 77 " --> pdb=" O PRO d 73 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU d 78 " --> pdb=" O VAL d 74 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU d 80 " --> pdb=" O ARG d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 107 removed outlier: 3.862A pdb=" N VAL d 97 " --> pdb=" O THR d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 113 removed outlier: 3.818A pdb=" N ASN d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS d 113 " --> pdb=" O ARG d 109 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 139 removed outlier: 3.843A pdb=" N GLN d 125 " --> pdb=" O ALA d 121 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER d 126 " --> pdb=" O ASP d 122 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP d 133 " --> pdb=" O LYS d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 157 removed outlier: 4.035A pdb=" N LEU d 150 " --> pdb=" O ASP d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 166 through 182 removed outlier: 3.878A pdb=" N LEU d 170 " --> pdb=" O TYR d 166 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA d 171 " --> pdb=" O SER d 167 " (cutoff:3.500A) Proline residue: d 172 - end of helix removed outlier: 3.587A pdb=" N ILE d 181 " --> pdb=" O SER d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 194 removed outlier: 3.742A pdb=" N ASP d 193 " --> pdb=" O ASP d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 256 through 280 removed outlier: 3.583A pdb=" N ILE d 274 " --> pdb=" O TYR d 270 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS d 275 " --> pdb=" O LEU d 271 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS d 277 " --> pdb=" O ASN d 273 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE d 278 " --> pdb=" O ILE d 274 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 308 removed outlier: 3.827A pdb=" N LYS d 307 " --> pdb=" O HIS d 303 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU d 308 " --> pdb=" O PHE d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 320 through 328 removed outlier: 3.942A pdb=" N LYS d 326 " --> pdb=" O GLU d 322 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU d 328 " --> pdb=" O LEU d 324 " (cutoff:3.500A) Processing helix chain 'd' and resid 340 through 344 removed outlier: 3.596A pdb=" N ARG d 343 " --> pdb=" O THR d 340 " (cutoff:3.500A) Processing helix chain 'd' and resid 383 through 407 removed outlier: 3.800A pdb=" N ILE d 387 " --> pdb=" O ASN d 383 " (cutoff:3.500A) Processing helix chain 'd' and resid 415 through 429 removed outlier: 3.695A pdb=" N ILE d 419 " --> pdb=" O GLY d 415 " (cutoff:3.500A) Processing helix chain 'd' and resid 430 through 433 removed outlier: 5.984A pdb=" N GLU d 433 " --> pdb=" O ARG d 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 430 through 433' Processing helix chain 'd' and resid 434 through 440 removed outlier: 4.081A pdb=" N PHE d 438 " --> pdb=" O GLY d 434 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP d 440 " --> pdb=" O GLN d 436 " (cutoff:3.500A) Processing helix chain 'd' and resid 441 through 446 removed outlier: 3.955A pdb=" N SER d 445 " --> pdb=" O GLN d 441 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA d 446 " --> pdb=" O GLU d 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 441 through 446' Processing helix chain 'd' and resid 448 through 458 Processing helix chain 'd' and resid 461 through 476 removed outlier: 3.511A pdb=" N VAL d 466 " --> pdb=" O SER d 462 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS d 472 " --> pdb=" O GLU d 468 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU d 474 " --> pdb=" O ARG d 470 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN d 475 " --> pdb=" O SER d 471 " (cutoff:3.500A) Processing helix chain 'd' and resid 501 through 520 removed outlier: 3.763A pdb=" N ILE d 508 " --> pdb=" O SER d 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 36 removed outlier: 3.584A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 72 through 89 removed outlier: 3.548A pdb=" N MET D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 113 removed outlier: 3.874A pdb=" N VAL D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 139 removed outlier: 3.559A pdb=" N GLN D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP D 133 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 157 removed outlier: 3.919A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.678A pdb=" N SER D 168 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 179 removed outlier: 4.156A pdb=" N LEU D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 267 through 282 removed outlier: 3.524A pdb=" N ILE D 274 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 removed outlier: 3.778A pdb=" N LYS D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 removed outlier: 3.969A pdb=" N GLU D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 327 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 407 removed outlier: 3.659A pdb=" N ILE D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 389 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 430 removed outlier: 3.569A pdb=" N SER D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS D 427 " --> pdb=" O ARG D 423 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG D 430 " --> pdb=" O SER D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 removed outlier: 3.704A pdb=" N ILE D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 461 through 473 Processing helix chain 'D' and resid 501 through 520 removed outlier: 3.609A pdb=" N ILE D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 513 " --> pdb=" O THR D 509 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 63 removed outlier: 3.643A pdb=" N HIS e 50 " --> pdb=" O ALA e 46 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE e 61 " --> pdb=" O VAL e 57 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR e 63 " --> pdb=" O SER e 59 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 94 removed outlier: 3.537A pdb=" N ILE e 90 " --> pdb=" O ASP e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 115 removed outlier: 3.615A pdb=" N LEU e 103 " --> pdb=" O GLU e 99 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU e 104 " --> pdb=" O ILE e 100 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER e 108 " --> pdb=" O LEU e 104 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER e 110 " --> pdb=" O GLN e 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 139 removed outlier: 4.199A pdb=" N VAL e 123 " --> pdb=" O THR e 119 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL e 124 " --> pdb=" O THR e 120 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU e 129 " --> pdb=" O LEU e 125 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU e 136 " --> pdb=" O GLN e 132 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN e 138 " --> pdb=" O LEU e 134 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS e 139 " --> pdb=" O GLU e 135 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 163 removed outlier: 3.661A pdb=" N GLU e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 173 through 188 removed outlier: 3.785A pdb=" N ARG e 177 " --> pdb=" O ASP e 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG e 182 " --> pdb=" O ASP e 178 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA e 184 " --> pdb=" O LEU e 180 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS e 185 " --> pdb=" O LEU e 181 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR e 186 " --> pdb=" O ARG e 182 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU e 188 " --> pdb=" O ALA e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 195 Processing helix chain 'e' and resid 196 through 211 removed outlier: 4.782A pdb=" N GLU e 202 " --> pdb=" O ASP e 198 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET e 203 " --> pdb=" O ARG e 199 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA e 204 " --> pdb=" O PHE e 200 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL e 205 " --> pdb=" O ALA e 201 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL e 208 " --> pdb=" O ALA e 204 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE e 209 " --> pdb=" O VAL e 205 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN e 210 " --> pdb=" O GLU e 206 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL e 211 " --> pdb=" O ALA e 207 " (cutoff:3.500A) Processing helix chain 'e' and resid 233 through 237 removed outlier: 3.625A pdb=" N ASP e 236 " --> pdb=" O SER e 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 291 through 317 removed outlier: 3.529A pdb=" N TYR e 295 " --> pdb=" O SER e 291 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE e 306 " --> pdb=" O GLU e 302 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS e 307 " --> pdb=" O GLN e 303 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU e 308 " --> pdb=" O ASP e 304 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE e 310 " --> pdb=" O PHE e 306 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL e 313 " --> pdb=" O MET e 309 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS e 314 " --> pdb=" O ILE e 310 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA e 316 " --> pdb=" O ASP e 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 328 through 338 removed outlier: 3.646A pdb=" N GLN e 337 " --> pdb=" O HIS e 333 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN e 338 " --> pdb=" O LEU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 347 through 358 removed outlier: 3.516A pdb=" N LEU e 351 " --> pdb=" O GLY e 347 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU e 352 " --> pdb=" O GLY e 348 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS e 353 " --> pdb=" O GLN e 349 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE e 354 " --> pdb=" O GLU e 350 " (cutoff:3.500A) Processing helix chain 'e' and resid 412 through 436 removed outlier: 3.573A pdb=" N ASN e 432 " --> pdb=" O CYS e 428 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 462 removed outlier: 3.881A pdb=" N VAL e 448 " --> pdb=" O GLY e 444 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA e 453 " --> pdb=" O THR e 449 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL e 454 " --> pdb=" O MET e 450 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER e 455 " --> pdb=" O SER e 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU e 456 " --> pdb=" O LEU e 452 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU e 457 " --> pdb=" O ALA e 453 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP e 459 " --> pdb=" O SER e 455 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN e 461 " --> pdb=" O GLU e 457 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG e 462 " --> pdb=" O ALA e 458 " (cutoff:3.500A) Processing helix chain 'e' and resid 465 through 477 Processing helix chain 'e' and resid 477 through 487 removed outlier: 3.655A pdb=" N ASN e 486 " --> pdb=" O THR e 482 " (cutoff:3.500A) Processing helix chain 'e' and resid 490 through 502 removed outlier: 3.668A pdb=" N GLN e 502 " --> pdb=" O LEU e 498 " (cutoff:3.500A) Processing helix chain 'e' and resid 512 through 516 removed outlier: 3.538A pdb=" N LEU e 515 " --> pdb=" O VAL e 512 " (cutoff:3.500A) Processing helix chain 'e' and resid 521 through 526 removed outlier: 3.635A pdb=" N PHE e 526 " --> pdb=" O LYS e 523 " (cutoff:3.500A) Processing helix chain 'e' and resid 531 through 550 Processing helix chain 'E' and resid 44 through 59 removed outlier: 3.712A pdb=" N ILE E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 98 through 115 removed outlier: 3.946A pdb=" N LEU E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER E 110 " --> pdb=" O GLN E 106 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 139 removed outlier: 4.103A pdb=" N VAL E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 130 " --> pdb=" O ALA E 126 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 135 " --> pdb=" O ASP E 131 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 164 removed outlier: 3.574A pdb=" N ASP E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 152 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 182 removed outlier: 3.537A pdb=" N ARG E 177 " --> pdb=" O ASP E 173 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 188 removed outlier: 4.502A pdb=" N SER E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 183 through 188' Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 196 through 211 removed outlier: 4.623A pdb=" N GLU E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET E 203 " --> pdb=" O ARG E 199 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN E 210 " --> pdb=" O GLU E 206 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 211 " --> pdb=" O ALA E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 302 through 317 removed outlier: 3.554A pdb=" N LYS E 307 " --> pdb=" O GLN E 303 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 4.237A pdb=" N LEU E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 330 through 335' Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.960A pdb=" N GLU E 352 " --> pdb=" O GLY E 348 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS E 353 " --> pdb=" O GLN E 349 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 369 removed outlier: 3.506A pdb=" N LEU E 369 " --> pdb=" O PHE E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 436 Processing helix chain 'E' and resid 445 through 459 removed outlier: 4.485A pdb=" N ASP E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 477 removed outlier: 3.740A pdb=" N ALA E 468 " --> pdb=" O ILE E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 487 Processing helix chain 'E' and resid 490 through 501 removed outlier: 4.029A pdb=" N SER E 496 " --> pdb=" O ILE E 492 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 501 " --> pdb=" O THR E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 550 Processing helix chain 'g' and resid 19 through 33 removed outlier: 3.564A pdb=" N VAL g 31 " --> pdb=" O ALA g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 39 removed outlier: 4.099A pdb=" N THR g 37 " --> pdb=" O VAL g 34 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU g 39 " --> pdb=" O ARG g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 67 removed outlier: 3.531A pdb=" N LEU g 65 " --> pdb=" O GLY g 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG g 66 " --> pdb=" O HIS g 62 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU g 67 " --> pdb=" O ALA g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 89 removed outlier: 3.975A pdb=" N LYS g 76 " --> pdb=" O HIS g 72 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET g 78 " --> pdb=" O ALA g 74 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU g 87 " --> pdb=" O ARG g 83 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU g 88 " --> pdb=" O THR g 84 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 107 removed outlier: 3.702A pdb=" N VAL g 96 " --> pdb=" O GLY g 92 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE g 97 " --> pdb=" O THR g 93 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 112 Processing helix chain 'g' and resid 117 through 140 removed outlier: 3.568A pdb=" N LYS g 127 " --> pdb=" O GLN g 123 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR g 130 " --> pdb=" O LYS g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 147 through 156 removed outlier: 3.574A pdb=" N LYS g 152 " --> pdb=" O ASP g 148 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU g 154 " --> pdb=" O ALA g 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 157 through 159 No H-bonds generated for 'chain 'g' and resid 157 through 159' Processing helix chain 'g' and resid 162 through 166 removed outlier: 4.166A pdb=" N HIS g 166 " --> pdb=" O TYR g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 183 removed outlier: 3.742A pdb=" N GLU g 173 " --> pdb=" O GLU g 169 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL g 179 " --> pdb=" O ALA g 175 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR g 181 " --> pdb=" O ASP g 177 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL g 182 " --> pdb=" O ALA g 178 " (cutoff:3.500A) Processing helix chain 'g' and resid 272 through 288 removed outlier: 3.533A pdb=" N GLN g 286 " --> pdb=" O LEU g 282 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE g 287 " --> pdb=" O MET g 283 " (cutoff:3.500A) Processing helix chain 'g' and resid 289 through 291 No H-bonds generated for 'chain 'g' and resid 289 through 291' Processing helix chain 'g' and resid 302 through 309 removed outlier: 3.769A pdb=" N HIS g 307 " --> pdb=" O ASP g 303 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR g 308 " --> pdb=" O LEU g 304 " (cutoff:3.500A) Processing helix chain 'g' and resid 321 through 333 removed outlier: 3.536A pdb=" N ASN g 325 " --> pdb=" O LYS g 321 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN g 326 " --> pdb=" O LYS g 322 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG g 327 " --> pdb=" O SER g 323 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG g 330 " --> pdb=" O ASN g 326 " (cutoff:3.500A) Processing helix chain 'g' and resid 339 through 343 removed outlier: 3.788A pdb=" N LEU g 343 " --> pdb=" O VAL g 340 " (cutoff:3.500A) Processing helix chain 'g' and resid 445 through 468 removed outlier: 3.699A pdb=" N ARG g 454 " --> pdb=" O ASN g 450 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL g 462 " --> pdb=" O ASP g 458 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET g 467 " --> pdb=" O ALA g 463 " (cutoff:3.500A) Processing helix chain 'g' and resid 477 through 490 removed outlier: 3.637A pdb=" N SER g 484 " --> pdb=" O GLU g 480 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA g 488 " --> pdb=" O SER g 484 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU g 489 " --> pdb=" O VAL g 485 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS g 490 " --> pdb=" O LYS g 486 " (cutoff:3.500A) Processing helix chain 'g' and resid 491 through 494 Processing helix chain 'g' and resid 498 through 510 removed outlier: 3.585A pdb=" N TYR g 502 " --> pdb=" O GLN g 498 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA g 504 " --> pdb=" O TRP g 500 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL g 505 " --> pdb=" O PRO g 501 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA g 506 " --> pdb=" O TYR g 502 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU g 510 " --> pdb=" O ALA g 506 " (cutoff:3.500A) Processing helix chain 'g' and resid 510 through 521 removed outlier: 3.585A pdb=" N LEU g 516 " --> pdb=" O ILE g 512 " (cutoff:3.500A) Processing helix chain 'g' and resid 523 through 538 removed outlier: 3.710A pdb=" N ALA g 536 " --> pdb=" O ARG g 532 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN g 537 " --> pdb=" O ALA g 533 " (cutoff:3.500A) Processing helix chain 'g' and resid 563 through 583 removed outlier: 3.837A pdb=" N VAL g 583 " --> pdb=" O LEU g 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 35 removed outlier: 3.770A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 38 No H-bonds generated for 'chain 'G' and resid 36 through 38' Processing helix chain 'G' and resid 60 through 67 removed outlier: 3.569A pdb=" N ARG G 66 " --> pdb=" O HIS G 62 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 89 removed outlier: 4.062A pdb=" N LYS G 76 " --> pdb=" O HIS G 72 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 3.703A pdb=" N VAL G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 117 through 140 Processing helix chain 'G' and resid 149 through 160 removed outlier: 3.988A pdb=" N LYS G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER G 158 " --> pdb=" O LEU G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 166 removed outlier: 4.041A pdb=" N HIS G 166 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 removed outlier: 3.780A pdb=" N GLU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 178 " --> pdb=" O LEU G 174 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR G 181 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG G 183 " --> pdb=" O VAL G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 217 Processing helix chain 'G' and resid 278 through 288 removed outlier: 3.814A pdb=" N ILE G 287 " --> pdb=" O MET G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 291 No H-bonds generated for 'chain 'G' and resid 289 through 291' Processing helix chain 'G' and resid 302 through 311 removed outlier: 3.683A pdb=" N HIS G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR G 308 " --> pdb=" O LEU G 304 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS G 311 " --> pdb=" O HIS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.536A pdb=" N ASN G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN G 326 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG G 327 " --> pdb=" O SER G 323 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 331 " --> pdb=" O ARG G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 343 removed outlier: 3.611A pdb=" N LEU G 343 " --> pdb=" O VAL G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 468 removed outlier: 3.749A pdb=" N ARG G 454 " --> pdb=" O ASN G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 493 removed outlier: 3.626A pdb=" N LYS G 486 " --> pdb=" O ALA G 482 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS G 492 " --> pdb=" O ALA G 488 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN G 493 " --> pdb=" O GLU G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 510 removed outlier: 3.717A pdb=" N ALA G 504 " --> pdb=" O TRP G 500 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL G 505 " --> pdb=" O PRO G 501 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA G 506 " --> pdb=" O TYR G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 521 Processing helix chain 'G' and resid 523 through 537 removed outlier: 3.546A pdb=" N SER G 529 " --> pdb=" O ILE G 525 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS G 535 " --> pdb=" O LEU G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 563 through 582 removed outlier: 3.532A pdb=" N GLU G 575 " --> pdb=" O LYS G 571 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 580 " --> pdb=" O SER G 576 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 41 removed outlier: 3.803A pdb=" N VAL h 36 " --> pdb=" O ALA h 32 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU h 40 " --> pdb=" O VAL h 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 72 Processing helix chain 'h' and resid 77 through 94 removed outlier: 3.627A pdb=" N LYS h 81 " --> pdb=" O HIS h 77 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR h 82 " --> pdb=" O PRO h 78 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 112 removed outlier: 3.775A pdb=" N THR h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU h 108 " --> pdb=" O LEU h 104 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N MET h 109 " --> pdb=" O ALA h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 118 removed outlier: 3.727A pdb=" N GLU h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU h 118 " --> pdb=" O PRO h 114 " (cutoff:3.500A) Processing helix chain 'h' and resid 121 through 144 removed outlier: 3.676A pdb=" N ILE h 125 " --> pdb=" O SER h 121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG h 130 " --> pdb=" O MET h 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA h 132 " --> pdb=" O GLY h 128 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU h 135 " --> pdb=" O LYS h 131 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU h 138 " --> pdb=" O SER h 134 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU h 142 " --> pdb=" O GLU h 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 153 through 166 removed outlier: 3.767A pdb=" N LEU h 158 " --> pdb=" O GLY h 154 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS h 161 " --> pdb=" O LEU h 157 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG h 163 " --> pdb=" O GLU h 159 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR h 164 " --> pdb=" O ARG h 160 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA h 165 " --> pdb=" O CYS h 161 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET h 166 " --> pdb=" O ALA h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 174 through 188 removed outlier: 3.623A pdb=" N PHE h 178 " --> pdb=" O ASN h 174 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS h 180 " --> pdb=" O ASP h 176 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET h 181 " --> pdb=" O PHE h 177 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP h 184 " --> pdb=" O LYS h 180 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL h 186 " --> pdb=" O CYS h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 195 through 197 No H-bonds generated for 'chain 'h' and resid 195 through 197' Processing helix chain 'h' and resid 208 through 212 removed outlier: 3.673A pdb=" N GLU h 211 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER h 212 " --> pdb=" O MET h 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 208 through 212' Processing helix chain 'h' and resid 265 through 289 removed outlier: 3.995A pdb=" N ALA h 269 " --> pdb=" O GLU h 265 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS h 281 " --> pdb=" O LEU h 277 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL h 285 " --> pdb=" O LYS h 281 " (cutoff:3.500A) Processing helix chain 'h' and resid 300 through 310 removed outlier: 3.644A pdb=" N THR h 304 " --> pdb=" O GLY h 300 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA h 308 " --> pdb=" O THR h 304 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP h 309 " --> pdb=" O GLN h 305 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG h 310 " --> pdb=" O PHE h 306 " (cutoff:3.500A) Processing helix chain 'h' and resid 319 through 331 removed outlier: 3.618A pdb=" N ARG h 325 " --> pdb=" O ASP h 321 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN h 328 " --> pdb=" O ASN h 324 " (cutoff:3.500A) Processing helix chain 'h' and resid 342 through 346 Processing helix chain 'h' and resid 382 through 406 removed outlier: 3.612A pdb=" N ASP h 395 " --> pdb=" O ARG h 391 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA h 396 " --> pdb=" O SER h 392 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU h 404 " --> pdb=" O VAL h 400 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN h 405 " --> pdb=" O LYS h 401 " (cutoff:3.500A) Processing helix chain 'h' and resid 414 through 430 removed outlier: 3.564A pdb=" N SER h 421 " --> pdb=" O GLU h 417 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU h 424 " --> pdb=" O VAL h 420 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP h 426 " --> pdb=" O LYS h 422 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR h 430 " --> pdb=" O ASP h 426 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 446 Processing helix chain 'h' and resid 447 through 458 removed outlier: 3.544A pdb=" N ALA h 457 " --> pdb=" O LEU h 453 " (cutoff:3.500A) Processing helix chain 'h' and resid 460 through 472 removed outlier: 3.611A pdb=" N LEU h 465 " --> pdb=" O ALA h 461 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN h 466 " --> pdb=" O ILE h 462 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG h 469 " --> pdb=" O LEU h 465 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU h 470 " --> pdb=" O ASN h 466 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA h 471 " --> pdb=" O LYS h 467 " (cutoff:3.500A) Processing helix chain 'h' and resid 491 through 495 Processing helix chain 'h' and resid 500 through 519 Processing helix chain 'H' and resid 23 through 41 removed outlier: 3.539A pdb=" N ASN H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.947A pdb=" N ASP H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 94 removed outlier: 3.624A pdb=" N LEU H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 112 removed outlier: 3.912A pdb=" N THR H 102 " --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 removed outlier: 3.871A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU H 118 " --> pdb=" O PRO H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 144 removed outlier: 3.504A pdb=" N TYR H 129 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS H 131 " --> pdb=" O LYS H 127 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU H 142 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 166 removed outlier: 4.416A pdb=" N LEU H 158 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR H 164 " --> pdb=" O ARG H 160 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA H 165 " --> pdb=" O CYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 188 removed outlier: 4.115A pdb=" N LYS H 180 " --> pdb=" O ASP H 176 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET H 181 " --> pdb=" O PHE H 177 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL H 186 " --> pdb=" O CYS H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 208 through 212 removed outlier: 3.582A pdb=" N GLU H 211 " --> pdb=" O ALA H 208 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER H 212 " --> pdb=" O MET H 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 208 through 212' Processing helix chain 'H' and resid 263 through 289 removed outlier: 3.613A pdb=" N TYR H 267 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN H 268 " --> pdb=" O VAL H 264 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL H 271 " --> pdb=" O TYR H 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 278 " --> pdb=" O GLU H 274 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS H 281 " --> pdb=" O LEU H 277 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY H 289 " --> pdb=" O VAL H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 310 removed outlier: 3.824A pdb=" N THR H 304 " --> pdb=" O GLY H 300 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP H 309 " --> pdb=" O GLN H 305 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG H 310 " --> pdb=" O PHE H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 331 removed outlier: 3.784A pdb=" N ARG H 325 " --> pdb=" O ASP H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 346 Processing helix chain 'H' and resid 382 through 406 removed outlier: 3.562A pdb=" N GLU H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP H 395 " --> pdb=" O ARG H 391 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE H 399 " --> pdb=" O ASP H 395 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU H 404 " --> pdb=" O VAL H 400 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN H 405 " --> pdb=" O LYS H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 429 removed outlier: 3.786A pdb=" N SER H 421 " --> pdb=" O GLU H 417 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 424 " --> pdb=" O VAL H 420 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP H 426 " --> pdb=" O LYS H 422 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 446 Processing helix chain 'H' and resid 447 through 457 Processing helix chain 'H' and resid 460 through 473 removed outlier: 3.545A pdb=" N ILE H 464 " --> pdb=" O ASP H 460 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN H 466 " --> pdb=" O ILE H 462 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG H 469 " --> pdb=" O LEU H 465 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 470 " --> pdb=" O ASN H 466 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA H 471 " --> pdb=" O LYS H 467 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER H 473 " --> pdb=" O ARG H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 491 through 495 Processing helix chain 'H' and resid 500 through 519 removed outlier: 3.614A pdb=" N LEU H 507 " --> pdb=" O LYS H 503 " (cutoff:3.500A) Processing helix chain 'q' and resid 28 through 44 removed outlier: 3.602A pdb=" N LEU q 38 " --> pdb=" O ALA q 34 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS q 42 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR q 44 " --> pdb=" O GLN q 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 75 removed outlier: 3.902A pdb=" N MET q 71 " --> pdb=" O ASP q 67 " (cutoff:3.500A) Processing helix chain 'q' and resid 79 through 94 removed outlier: 4.020A pdb=" N LEU q 85 " --> pdb=" O ALA q 81 " (cutoff:3.500A) Processing helix chain 'q' and resid 99 through 114 removed outlier: 3.782A pdb=" N MET q 104 " --> pdb=" O THR q 100 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) Processing helix chain 'q' and resid 114 through 121 Processing helix chain 'q' and resid 123 through 145 removed outlier: 3.511A pdb=" N ILE q 127 " --> pdb=" O SER q 123 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP q 143 " --> pdb=" O LEU q 139 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU q 144 " --> pdb=" O LYS q 140 " (cutoff:3.500A) Processing helix chain 'q' and resid 155 through 168 removed outlier: 3.537A pdb=" N LEU q 160 " --> pdb=" O LYS q 156 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS q 161 " --> pdb=" O ASN q 157 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET q 162 " --> pdb=" O GLU q 158 " (cutoff:3.500A) Proline residue: q 165 - end of helix Processing helix chain 'q' and resid 176 through 190 removed outlier: 4.387A pdb=" N GLU q 180 " --> pdb=" O ASP q 176 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU q 181 " --> pdb=" O ILE q 177 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL q 189 " --> pdb=" O ALA q 185 " (cutoff:3.500A) Processing helix chain 'q' and resid 216 through 220 removed outlier: 3.800A pdb=" N ASN q 219 " --> pdb=" O SER q 216 " (cutoff:3.500A) Processing helix chain 'q' and resid 269 through 293 removed outlier: 3.624A pdb=" N MET q 273 " --> pdb=" O ASN q 269 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU q 274 " --> pdb=" O ALA q 270 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP q 275 " --> pdb=" O GLN q 271 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU q 290 " --> pdb=" O ALA q 286 " (cutoff:3.500A) Processing helix chain 'q' and resid 306 through 316 removed outlier: 3.562A pdb=" N HIS q 311 " --> pdb=" O GLU q 307 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR q 312 " --> pdb=" O LEU q 308 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU q 313 " --> pdb=" O ALA q 309 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG q 315 " --> pdb=" O HIS q 311 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR q 316 " --> pdb=" O TYR q 312 " (cutoff:3.500A) Processing helix chain 'q' and resid 325 through 334 removed outlier: 3.945A pdb=" N LEU q 329 " --> pdb=" O SER q 325 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG q 330 " --> pdb=" O LYS q 326 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG q 331 " --> pdb=" O PHE q 327 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS q 333 " --> pdb=" O LEU q 329 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG q 334 " --> pdb=" O ARG q 330 " (cutoff:3.500A) Processing helix chain 'q' and resid 348 through 352 Processing helix chain 'q' and resid 390 through 409 removed outlier: 3.502A pdb=" N ASP q 396 " --> pdb=" O ASN q 392 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU q 398 " --> pdb=" O LEU q 394 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG q 399 " --> pdb=" O ASP q 395 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL q 408 " --> pdb=" O GLY q 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS q 409 " --> pdb=" O VAL q 405 " (cutoff:3.500A) Processing helix chain 'q' and resid 424 through 441 removed outlier: 3.539A pdb=" N ILE q 428 " --> pdb=" O GLY q 424 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER q 432 " --> pdb=" O ILE q 428 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG q 433 " --> pdb=" O GLU q 429 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS q 436 " --> pdb=" O SER q 432 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR q 437 " --> pdb=" O ARG q 433 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU q 439 " --> pdb=" O THR q 435 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG q 440 " --> pdb=" O LYS q 436 " (cutoff:3.500A) Processing helix chain 'q' and resid 444 through 455 removed outlier: 4.260A pdb=" N ALA q 448 " --> pdb=" O LEU q 444 " (cutoff:3.500A) Processing helix chain 'q' and resid 457 through 467 Processing helix chain 'q' and resid 470 through 483 Proline residue: q 476 - end of helix Processing helix chain 'q' and resid 511 through 516 removed outlier: 3.878A pdb=" N GLU q 515 " --> pdb=" O ASP q 511 " (cutoff:3.500A) Processing helix chain 'q' and resid 521 through 539 removed outlier: 3.541A pdb=" N GLU q 533 " --> pdb=" O ASN q 529 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL q 538 " --> pdb=" O ALA q 534 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU q 539 " --> pdb=" O ALA q 535 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 44 removed outlier: 3.708A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 75 Processing helix chain 'Q' and resid 79 through 96 removed outlier: 3.732A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP Q 95 " --> pdb=" O GLN Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 114 removed outlier: 3.701A pdb=" N MET Q 104 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN Q 112 " --> pdb=" O GLY Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 121 Processing helix chain 'Q' and resid 123 through 143 removed outlier: 3.941A pdb=" N ASP Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 168 removed outlier: 3.962A pdb=" N LYS Q 161 " --> pdb=" O ASN Q 157 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) Proline residue: Q 165 - end of helix Processing helix chain 'Q' and resid 176 through 190 removed outlier: 4.365A pdb=" N GLU Q 180 " --> pdb=" O ASP Q 176 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU Q 181 " --> pdb=" O ILE Q 177 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU Q 184 " --> pdb=" O GLU Q 180 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA Q 185 " --> pdb=" O LEU Q 181 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER Q 187 " --> pdb=" O SER Q 183 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS Q 188 " --> pdb=" O GLU Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 216 through 220 Processing helix chain 'Q' and resid 270 through 294 removed outlier: 4.024A pdb=" N LEU Q 274 " --> pdb=" O ALA Q 270 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP Q 275 " --> pdb=" O GLN Q 271 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS Q 282 " --> pdb=" O LYS Q 278 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU Q 290 " --> pdb=" O ALA Q 286 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE Q 291 " --> pdb=" O MET Q 287 " (cutoff:3.500A) Processing helix chain 'Q' and resid 308 through 316 removed outlier: 3.829A pdb=" N TYR Q 312 " --> pdb=" O LEU Q 308 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN Q 314 " --> pdb=" O LEU Q 310 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG Q 315 " --> pdb=" O HIS Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 333 removed outlier: 3.947A pdb=" N LEU Q 329 " --> pdb=" O SER Q 325 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG Q 330 " --> pdb=" O LYS Q 326 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG Q 331 " --> pdb=" O PHE Q 327 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS Q 333 " --> pdb=" O LEU Q 329 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 352 Processing helix chain 'Q' and resid 390 through 409 removed outlier: 3.642A pdb=" N ASP Q 396 " --> pdb=" O ASN Q 392 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA Q 406 " --> pdb=" O ASP Q 402 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA Q 407 " --> pdb=" O ASP Q 403 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL Q 408 " --> pdb=" O GLY Q 404 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS Q 409 " --> pdb=" O VAL Q 405 " (cutoff:3.500A) Processing helix chain 'Q' and resid 410 through 412 No H-bonds generated for 'chain 'Q' and resid 410 through 412' Processing helix chain 'Q' and resid 424 through 441 removed outlier: 3.779A pdb=" N ILE Q 428 " --> pdb=" O GLY Q 424 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU Q 429 " --> pdb=" O ALA Q 425 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE Q 431 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER Q 432 " --> pdb=" O ILE Q 428 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR Q 437 " --> pdb=" O ARG Q 433 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU Q 439 " --> pdb=" O THR Q 435 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG Q 440 " --> pdb=" O LYS Q 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 445 through 455 removed outlier: 3.528A pdb=" N ALA Q 453 " --> pdb=" O ILE Q 449 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL Q 454 " --> pdb=" O LYS Q 450 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 467 Processing helix chain 'Q' and resid 473 through 483 removed outlier: 3.822A pdb=" N TYR Q 479 " --> pdb=" O LEU Q 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA Q 480 " --> pdb=" O PRO Q 476 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA Q 481 " --> pdb=" O ASN Q 477 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS Q 482 " --> pdb=" O LEU Q 478 " (cutoff:3.500A) Processing helix chain 'Q' and resid 511 through 516 removed outlier: 3.964A pdb=" N GLU Q 515 " --> pdb=" O ASP Q 511 " (cutoff:3.500A) Processing helix chain 'Q' and resid 521 through 541 removed outlier: 3.577A pdb=" N PHE Q 526 " --> pdb=" O ALA Q 522 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN Q 529 " --> pdb=" O LYS Q 525 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL Q 538 " --> pdb=" O ALA Q 534 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 34 removed outlier: 3.529A pdb=" N VAL z 32 " --> pdb=" O GLY z 28 " (cutoff:3.500A) Processing helix chain 'z' and resid 35 through 37 No H-bonds generated for 'chain 'z' and resid 35 through 37' Processing helix chain 'z' and resid 58 through 64 removed outlier: 3.600A pdb=" N LEU z 62 " --> pdb=" O ASP z 58 " (cutoff:3.500A) Processing helix chain 'z' and resid 70 through 87 removed outlier: 3.660A pdb=" N VAL z 74 " --> pdb=" O SER z 70 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU z 75 " --> pdb=" O PRO z 71 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE z 76 " --> pdb=" O THR z 72 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA z 82 " --> pdb=" O ARG z 78 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU z 85 " --> pdb=" O ALA z 81 " (cutoff:3.500A) Processing helix chain 'z' and resid 90 through 110 removed outlier: 3.625A pdb=" N LEU z 102 " --> pdb=" O VAL z 98 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG z 107 " --> pdb=" O ARG z 103 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE z 108 " --> pdb=" O GLN z 104 " (cutoff:3.500A) Processing helix chain 'z' and resid 114 through 137 removed outlier: 3.523A pdb=" N ILE z 118 " --> pdb=" O HIS z 114 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE z 122 " --> pdb=" O ILE z 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS z 131 " --> pdb=" O LYS z 127 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU z 135 " --> pdb=" O LYS z 131 " (cutoff:3.500A) Processing helix chain 'z' and resid 143 through 145 No H-bonds generated for 'chain 'z' and resid 143 through 145' Processing helix chain 'z' and resid 146 through 162 removed outlier: 4.241A pdb=" N GLN z 152 " --> pdb=" O GLU z 148 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER z 156 " --> pdb=" O GLN z 152 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER z 157 " --> pdb=" O VAL z 153 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR z 160 " --> pdb=" O SER z 156 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS z 161 " --> pdb=" O SER z 157 " (cutoff:3.500A) Processing helix chain 'z' and resid 166 through 182 Proline residue: z 172 - end of helix removed outlier: 3.552A pdb=" N VAL z 178 " --> pdb=" O VAL z 174 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU z 179 " --> pdb=" O THR z 175 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL z 181 " --> pdb=" O ALA z 177 " (cutoff:3.500A) Processing helix chain 'z' and resid 190 through 194 removed outlier: 3.531A pdb=" N MET z 193 " --> pdb=" O ASP z 190 " (cutoff:3.500A) Processing helix chain 'z' and resid 203 through 207 removed outlier: 3.617A pdb=" N THR z 207 " --> pdb=" O PRO z 204 " (cutoff:3.500A) Processing helix chain 'z' and resid 255 through 284 removed outlier: 3.773A pdb=" N ASP z 260 " --> pdb=" O ALA z 256 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS z 261 " --> pdb=" O ASP z 257 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU z 266 " --> pdb=" O LEU z 262 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE z 269 " --> pdb=" O SER z 265 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL z 270 " --> pdb=" O GLU z 266 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS z 273 " --> pdb=" O PHE z 269 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS z 276 " --> pdb=" O ALA z 272 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE z 277 " --> pdb=" O LYS z 273 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS z 281 " --> pdb=" O ILE z 277 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN z 282 " --> pdb=" O ILE z 278 " (cutoff:3.500A) Processing helix chain 'z' and resid 302 through 312 removed outlier: 3.710A pdb=" N LEU z 306 " --> pdb=" O ASP z 302 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP z 307 " --> pdb=" O PRO z 303 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL z 308 " --> pdb=" O MET z 304 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS z 311 " --> pdb=" O ASP z 307 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS z 312 " --> pdb=" O VAL z 308 " (cutoff:3.500A) Processing helix chain 'z' and resid 321 through 332 removed outlier: 3.763A pdb=" N GLU z 326 " --> pdb=" O ARG z 322 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG z 327 " --> pdb=" O ARG z 323 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN z 329 " --> pdb=" O MET z 325 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU z 330 " --> pdb=" O GLU z 326 " (cutoff:3.500A) Processing helix chain 'z' and resid 339 through 343 Processing helix chain 'z' and resid 384 through 408 removed outlier: 3.871A pdb=" N LEU z 388 " --> pdb=" O THR z 384 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA z 394 " --> pdb=" O GLN z 390 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG z 400 " --> pdb=" O ARG z 396 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL z 405 " --> pdb=" O ALA z 401 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU z 406 " --> pdb=" O VAL z 402 " (cutoff:3.500A) Processing helix chain 'z' and resid 416 through 434 removed outlier: 4.185A pdb=" N MET z 431 " --> pdb=" O ARG z 427 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN z 432 " --> pdb=" O SER z 428 " (cutoff:3.500A) Processing helix chain 'z' and resid 439 through 451 removed outlier: 4.264A pdb=" N GLY z 443 " --> pdb=" O LYS z 439 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU z 451 " --> pdb=" O PHE z 447 " (cutoff:3.500A) Processing helix chain 'z' and resid 452 through 462 removed outlier: 3.619A pdb=" N VAL z 459 " --> pdb=" O PRO z 455 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER z 462 " --> pdb=" O LEU z 458 " (cutoff:3.500A) Processing helix chain 'z' and resid 465 through 483 removed outlier: 3.670A pdb=" N MET z 472 " --> pdb=" O ASP z 468 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL z 473 " --> pdb=" O VAL z 469 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP z 482 " --> pdb=" O ASP z 478 " (cutoff:3.500A) Processing helix chain 'z' and resid 500 through 505 Processing helix chain 'z' and resid 510 through 529 removed outlier: 3.658A pdb=" N ASN z 515 " --> pdb=" O ARG z 511 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE z 517 " --> pdb=" O LEU z 513 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR z 518 " --> pdb=" O ARG z 514 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU z 528 " --> pdb=" O ALA z 524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 34 removed outlier: 3.807A pdb=" N VAL Z 21 " --> pdb=" O ALA Z 17 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL Z 32 " --> pdb=" O GLY Z 28 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Z 33 " --> pdb=" O LEU Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 37 through 41 removed outlier: 3.536A pdb=" N LYS Z 40 " --> pdb=" O LEU Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 66 removed outlier: 3.758A pdb=" N THR Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 87 removed outlier: 3.819A pdb=" N ALA Z 82 " --> pdb=" O ARG Z 78 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN Z 83 " --> pdb=" O ALA Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.572A pdb=" N VAL Z 95 " --> pdb=" O THR Z 91 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG Z 107 " --> pdb=" O ARG Z 103 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE Z 108 " --> pdb=" O GLN Z 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN Z 110 " --> pdb=" O HIS Z 106 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU Z 111 " --> pdb=" O ARG Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 137 removed outlier: 3.515A pdb=" N PHE Z 122 " --> pdb=" O ILE Z 118 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS Z 131 " --> pdb=" O LYS Z 127 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE Z 132 " --> pdb=" O GLU Z 128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 143 through 145 No H-bonds generated for 'chain 'Z' and resid 143 through 145' Processing helix chain 'Z' and resid 146 through 162 removed outlier: 4.076A pdb=" N GLN Z 152 " --> pdb=" O GLU Z 148 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG Z 155 " --> pdb=" O LEU Z 151 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER Z 156 " --> pdb=" O GLN Z 152 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER Z 157 " --> pdb=" O VAL Z 153 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS Z 161 " --> pdb=" O SER Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 182 Proline residue: Z 172 - end of helix removed outlier: 3.708A pdb=" N VAL Z 178 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU Z 179 " --> pdb=" O THR Z 175 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL Z 181 " --> pdb=" O ALA Z 177 " (cutoff:3.500A) Processing helix chain 'Z' and resid 203 through 207 Processing helix chain 'Z' and resid 255 through 284 removed outlier: 3.524A pdb=" N ARG Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP Z 260 " --> pdb=" O ALA Z 256 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS Z 261 " --> pdb=" O ASP Z 257 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA Z 263 " --> pdb=" O ARG Z 259 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE Z 269 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL Z 270 " --> pdb=" O GLU Z 266 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS Z 273 " --> pdb=" O PHE Z 269 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS Z 276 " --> pdb=" O ALA Z 272 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE Z 277 " --> pdb=" O LYS Z 273 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS Z 281 " --> pdb=" O ILE Z 277 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN Z 282 " --> pdb=" O ILE Z 278 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL Z 284 " --> pdb=" O LEU Z 280 " (cutoff:3.500A) Processing helix chain 'Z' and resid 302 through 312 removed outlier: 3.521A pdb=" N LEU Z 306 " --> pdb=" O ASP Z 302 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL Z 308 " --> pdb=" O MET Z 304 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS Z 311 " --> pdb=" O ASP Z 307 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS Z 312 " --> pdb=" O VAL Z 308 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 333 removed outlier: 3.509A pdb=" N GLU Z 326 " --> pdb=" O ARG Z 322 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN Z 329 " --> pdb=" O MET Z 325 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU Z 330 " --> pdb=" O GLU Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 339 through 343 Processing helix chain 'Z' and resid 384 through 408 removed outlier: 3.557A pdb=" N LEU Z 388 " --> pdb=" O THR Z 384 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP Z 393 " --> pdb=" O ALA Z 389 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA Z 394 " --> pdb=" O GLN Z 390 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL Z 405 " --> pdb=" O ALA Z 401 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU Z 406 " --> pdb=" O VAL Z 402 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 434 removed outlier: 3.819A pdb=" N MET Z 431 " --> pdb=" O ARG Z 427 " (cutoff:3.500A) Processing helix chain 'Z' and resid 439 through 451 removed outlier: 4.281A pdb=" N GLY Z 443 " --> pdb=" O LYS Z 439 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU Z 451 " --> pdb=" O PHE Z 447 " (cutoff:3.500A) Processing helix chain 'Z' and resid 452 through 463 removed outlier: 3.717A pdb=" N VAL Z 459 " --> pdb=" O PRO Z 455 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER Z 462 " --> pdb=" O LEU Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 465 through 484 removed outlier: 3.663A pdb=" N VAL Z 469 " --> pdb=" O ASP Z 465 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU Z 470 " --> pdb=" O PRO Z 466 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP Z 479 " --> pdb=" O ASP Z 475 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN Z 481 " --> pdb=" O LEU Z 477 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP Z 482 " --> pdb=" O ASP Z 478 " (cutoff:3.500A) Processing helix chain 'Z' and resid 500 through 505 Processing helix chain 'Z' and resid 510 through 529 removed outlier: 3.516A pdb=" N THR Z 518 " --> pdb=" O ARG Z 514 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU Z 528 " --> pdb=" O ALA Z 524 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 19 through 21 removed outlier: 3.993A pdb=" N ILE a 541 " --> pdb=" O ASP d 45 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N MET d 47 " --> pdb=" O ILE a 541 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR a 543 " --> pdb=" O MET d 47 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS d 49 " --> pdb=" O THR a 543 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE a 545 " --> pdb=" O LYS d 49 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS d 46 " --> pdb=" O SER d 58 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER d 58 " --> pdb=" O LYS d 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 60 through 63 removed outlier: 3.672A pdb=" N THR a 61 " --> pdb=" O LEU a 53 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR a 63 " --> pdb=" O LYS a 51 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS a 51 " --> pdb=" O THR a 63 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL g 587 " --> pdb=" O MET a 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 204 through 208 removed outlier: 5.691A pdb=" N ASN a 204 " --> pdb=" O ILE a 385 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU a 387 " --> pdb=" O ASN a 204 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU a 206 " --> pdb=" O LEU a 387 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER a 384 " --> pdb=" O VAL a 219 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL a 219 " --> pdb=" O SER a 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'a' and resid 223 through 224 removed outlier: 3.599A pdb=" N LEU a 373 " --> pdb=" O VAL a 362 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL a 362 " --> pdb=" O LEU a 373 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL a 361 " --> pdb=" O ILE a 237 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE a 237 " --> pdb=" O VAL a 361 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 244 through 246 removed outlier: 3.508A pdb=" N VAL a 296 " --> pdb=" O MET a 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'a' and resid 500 through 503 removed outlier: 3.783A pdb=" N VAL a 510 " --> pdb=" O GLY a 501 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS a 508 " --> pdb=" O ASP a 503 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.161A pdb=" N ILE A 541 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N MET D 47 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 543 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N LYS D 49 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 545 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS D 46 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER D 58 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 48 " --> pdb=" O ILE D 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 62 through 63 removed outlier: 4.421A pdb=" N THR A 63 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS A 51 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL G 587 " --> pdb=" O MET A 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 204 through 207 removed outlier: 6.065A pdb=" N ASN A 204 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A 387 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A 206 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 219 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 222 through 224 removed outlier: 4.055A pdb=" N LYS A 375 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU A 360 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR A 377 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS A 358 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.569A pdb=" N THR A 298 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AB5, first strand: chain 'b' and resid 56 through 57 removed outlier: 4.061A pdb=" N THR b 57 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS b 44 " --> pdb=" O THR b 57 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP b 43 " --> pdb=" O ILE d 521 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP d 523 " --> pdb=" O ASP b 43 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU b 45 " --> pdb=" O ASP d 523 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA d 525 " --> pdb=" O LEU b 45 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 193 through 199 removed outlier: 6.299A pdb=" N GLN b 194 " --> pdb=" O ILE b 367 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU b 369 " --> pdb=" O GLN b 194 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE b 196 " --> pdb=" O LEU b 369 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY b 371 " --> pdb=" O ILE b 196 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE b 198 " --> pdb=" O GLY b 371 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL b 368 " --> pdb=" O PHE b 207 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE b 207 " --> pdb=" O VAL b 368 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 226 through 229 removed outlier: 6.832A pdb=" N GLU b 227 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL b 342 " --> pdb=" O GLU b 227 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 231 through 233 removed outlier: 6.913A pdb=" N LEU b 232 " --> pdb=" O ILE b 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 400 through 401 Processing sheet with id=AC1, first strand: chain 'b' and resid 470 through 472 removed outlier: 3.629A pdb=" N ALA b 480 " --> pdb=" O GLY b 471 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 511 through 516 removed outlier: 6.991A pdb=" N ASP e 71 " --> pdb=" O VAL b 511 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN b 513 " --> pdb=" O ASP e 71 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE e 73 " --> pdb=" O ASN b 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.844A pdb=" N THR B 57 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 44 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D 525 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 193 through 199 removed outlier: 6.007A pdb=" N GLN B 194 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU B 369 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 196 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY B 371 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 198 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 368 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 207 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 225 through 229 removed outlier: 6.925A pdb=" N ARG B 225 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU B 344 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLU B 227 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 342 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS B 340 " --> pdb=" O CYS B 359 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N CYS B 359 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 233 through 234 Processing sheet with id=AC7, first strand: chain 'B' and resid 400 through 402 Processing sheet with id=AC8, first strand: chain 'B' and resid 470 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 514 through 516 Processing sheet with id=AD1, first strand: chain 'd' and resid 196 through 200 removed outlier: 5.952A pdb=" N VAL d 197 " --> pdb=" O ILE d 379 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY d 381 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS d 199 " --> pdb=" O GLY d 381 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU d 208 " --> pdb=" O VAL d 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 213 through 214 removed outlier: 3.597A pdb=" N GLU d 351 " --> pdb=" O ARG d 362 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU d 349 " --> pdb=" O THR d 364 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP d 348 " --> pdb=" O LYS d 231 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 236 through 237 removed outlier: 3.868A pdb=" N GLN d 289 " --> pdb=" O ILE d 237 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP d 315 " --> pdb=" O ILE d 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 410 through 411 Processing sheet with id=AD5, first strand: chain 'D' and resid 194 through 200 removed outlier: 6.263A pdb=" N ARG D 195 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE D 379 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 197 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY D 381 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS D 199 " --> pdb=" O GLY D 381 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU D 208 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 229 through 232 removed outlier: 6.725A pdb=" N ASP D 348 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 349 " --> pdb=" O THR D 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 351 " --> pdb=" O ARG D 362 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 285 through 289 removed outlier: 3.916A pdb=" N ASP D 315 " --> pdb=" O ILE D 288 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 410 through 411 removed outlier: 3.720A pdb=" N ILE D 411 " --> pdb=" O GLN D 499 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 166 through 167 removed outlier: 3.582A pdb=" N VAL e 440 " --> pdb=" O ASP e 529 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP e 529 " --> pdb=" O VAL e 440 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 224 through 225 removed outlier: 6.509A pdb=" N LYS e 225 " --> pdb=" O CYS e 406 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR e 405 " --> pdb=" O ILE e 240 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE e 240 " --> pdb=" O THR e 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'e' and resid 229 through 230 removed outlier: 6.357A pdb=" N ARG e 229 " --> pdb=" O GLY e 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'e' and resid 342 through 343 removed outlier: 6.907A pdb=" N VAL e 321 " --> pdb=" O VAL e 343 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA e 270 " --> pdb=" O ILE e 322 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N VAL e 363 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE e 271 " --> pdb=" O VAL e 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'e' and resid 380 through 382 Processing sheet with id=AE5, first strand: chain 'e' and resid 551 through 556 removed outlier: 6.548A pdb=" N ASP h 50 " --> pdb=" O ILE e 551 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN e 553 " --> pdb=" O ASP h 50 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE h 53 " --> pdb=" O THR h 61 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR h 61 " --> pdb=" O ILE h 53 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 166 through 167 removed outlier: 3.855A pdb=" N VAL E 440 " --> pdb=" O ASP E 529 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 224 through 228 removed outlier: 6.813A pdb=" N LYS E 225 " --> pdb=" O CYS E 406 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL E 408 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN E 227 " --> pdb=" O VAL E 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'E' and resid 342 through 343 removed outlier: 5.918A pdb=" N VAL E 321 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL E 320 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 379 through 382 removed outlier: 4.322A pdb=" N ARG E 379 " --> pdb=" O GLU E 396 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 551 through 556 removed outlier: 4.012A pdb=" N ILE E 551 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU H 52 " --> pdb=" O ILE E 551 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN E 553 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL H 54 " --> pdb=" O ASN E 553 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE E 555 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE H 51 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER H 63 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'g' and resid 55 through 56 removed outlier: 3.748A pdb=" N LEU g 48 " --> pdb=" O VAL g 56 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU g 45 " --> pdb=" O CYS z 530 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU z 532 " --> pdb=" O LEU g 45 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET g 47 " --> pdb=" O GLU z 532 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'g' and resid 141 through 142 Processing sheet with id=AF4, first strand: chain 'g' and resid 206 through 208 removed outlier: 6.823A pdb=" N GLU g 207 " --> pdb=" O LEU g 441 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 245 through 246 removed outlier: 3.710A pdb=" N LEU g 246 " --> pdb=" O ILE g 296 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 542 through 544 removed outlier: 3.612A pdb=" N GLY g 543 " --> pdb=" O VAL g 552 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL g 552 " --> pdb=" O GLY g 543 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'G' and resid 55 through 56 removed outlier: 4.127A pdb=" N VAL G 56 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU G 48 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU G 45 " --> pdb=" O CYS Z 530 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU Z 532 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET G 47 " --> pdb=" O GLU Z 532 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU Z 534 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 207 through 209 removed outlier: 3.677A pdb=" N GLU G 207 " --> pdb=" O ILE G 439 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU G 441 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG G 218 " --> pdb=" O MET G 440 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 224 through 225 Processing sheet with id=AG1, first strand: chain 'G' and resid 243 through 245 Processing sheet with id=AG2, first strand: chain 'G' and resid 472 through 473 Processing sheet with id=AG3, first strand: chain 'G' and resid 542 through 544 removed outlier: 3.604A pdb=" N VAL G 552 " --> pdb=" O GLY G 543 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 145 through 146 Processing sheet with id=AG5, first strand: chain 'h' and resid 199 through 205 removed outlier: 5.959A pdb=" N GLY h 200 " --> pdb=" O LEU h 376 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU h 378 " --> pdb=" O GLY h 200 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS h 202 " --> pdb=" O LEU h 378 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLY h 380 " --> pdb=" O LYS h 202 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE h 204 " --> pdb=" O GLY h 380 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'h' and resid 235 through 236 removed outlier: 4.011A pdb=" N PHE h 352 " --> pdb=" O PHE h 236 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU h 353 " --> pdb=" O LEU h 364 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU h 364 " --> pdb=" O GLU h 353 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET h 355 " --> pdb=" O TYR h 362 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 241 through 243 removed outlier: 6.703A pdb=" N LEU h 242 " --> pdb=" O LEU h 294 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'h' and resid 479 through 481 removed outlier: 3.864A pdb=" N GLY h 489 " --> pdb=" O GLY h 480 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'h' and resid 523 through 525 removed outlier: 7.002A pdb=" N ILE h 524 " --> pdb=" O VAL q 56 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS q 53 " --> pdb=" O THR q 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR q 65 " --> pdb=" O LYS q 53 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 145 through 146 removed outlier: 3.680A pdb=" N VAL H 145 " --> pdb=" O ILE H 409 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE H 409 " --> pdb=" O VAL H 145 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 199 through 204 removed outlier: 6.549A pdb=" N GLY H 200 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU H 378 " --> pdb=" O GLY H 200 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS H 202 " --> pdb=" O LEU H 378 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 313 through 315 removed outlier: 6.476A pdb=" N VAL H 293 " --> pdb=" O ALA H 315 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY H 347 " --> pdb=" O ILE H 241 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 351 through 355 removed outlier: 3.963A pdb=" N GLU H 353 " --> pdb=" O LEU H 364 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU H 364 " --> pdb=" O GLU H 353 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 479 through 481 removed outlier: 3.699A pdb=" N GLY H 489 " --> pdb=" O GLY H 480 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 523 through 525 removed outlier: 3.926A pdb=" N LYS Q 53 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR Q 65 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'q' and resid 207 through 213 removed outlier: 6.784A pdb=" N ARG q 208 " --> pdb=" O ILE q 384 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU q 386 " --> pdb=" O ARG q 208 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL q 210 " --> pdb=" O LEU q 386 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY q 388 " --> pdb=" O VAL q 210 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE q 212 " --> pdb=" O GLY q 388 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR q 383 " --> pdb=" O ILE q 223 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE q 223 " --> pdb=" O THR q 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'q' and resid 246 through 250 removed outlier: 6.462A pdb=" N LYS q 246 " --> pdb=" O CYS q 298 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL q 300 " --> pdb=" O LYS q 246 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA q 248 " --> pdb=" O VAL q 300 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'q' and resid 360 through 363 Processing sheet with id=AI1, first strand: chain 'q' and resid 419 through 421 removed outlier: 3.526A pdb=" N LEU q 420 " --> pdb=" O ASP q 519 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP q 519 " --> pdb=" O LEU q 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'q' and resid 544 through 546 removed outlier: 6.152A pdb=" N ILE q 545 " --> pdb=" O VAL z 47 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU z 46 " --> pdb=" O LYS z 54 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS z 54 " --> pdb=" O LEU z 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'Q' and resid 207 through 213 removed outlier: 3.695A pdb=" N GLY Q 388 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR Q 221 " --> pdb=" O ILE Q 385 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 319 through 322 removed outlier: 7.111A pdb=" N GLU Q 297 " --> pdb=" O LEU Q 319 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU Q 321 " --> pdb=" O GLU Q 297 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE Q 299 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS Q 246 " --> pdb=" O CYS Q 298 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL Q 300 " --> pdb=" O LYS Q 246 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA Q 248 " --> pdb=" O VAL Q 300 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 360 through 363 Processing sheet with id=AI6, first strand: chain 'Q' and resid 419 through 421 Processing sheet with id=AI7, first strand: chain 'Q' and resid 545 through 546 removed outlier: 3.516A pdb=" N VAL Z 47 " --> pdb=" O ILE Q 545 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'z' and resid 138 through 139 Processing sheet with id=AI9, first strand: chain 'z' and resid 195 through 199 removed outlier: 6.192A pdb=" N GLU z 195 " --> pdb=" O ILE z 378 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE z 380 " --> pdb=" O GLU z 195 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N MET z 197 " --> pdb=" O ILE z 380 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'z' and resid 214 through 215 removed outlier: 3.868A pdb=" N THR z 365 " --> pdb=" O LEU z 215 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'z' and resid 227 through 228 Processing sheet with id=AJ3, first strand: chain 'z' and resid 232 through 233 removed outlier: 3.912A pdb=" N VAL z 233 " --> pdb=" O GLY z 349 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'z' and resid 294 through 295 Processing sheet with id=AJ5, first strand: chain 'z' and resid 490 through 491 Processing sheet with id=AJ6, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AJ7, first strand: chain 'Z' and resid 195 through 199 removed outlier: 5.681A pdb=" N GLU Z 195 " --> pdb=" O ILE Z 378 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE Z 380 " --> pdb=" O GLU Z 195 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N MET Z 197 " --> pdb=" O ILE Z 380 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'Z' and resid 227 through 228 Processing sheet with id=AJ9, first strand: chain 'Z' and resid 231 through 232 removed outlier: 3.596A pdb=" N VAL Z 294 " --> pdb=" O TYR Z 232 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU Z 315 " --> pdb=" O PHE Z 293 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 235 through 236 removed outlier: 6.405A pdb=" N ILE Z 235 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK1 Processing sheet with id=AK2, first strand: chain 'Z' and resid 490 through 491 2645 hydrogen bonds defined for protein. 7647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.11 Time building geometry restraints manager: 14.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 20966 1.34 - 1.46: 11480 1.46 - 1.58: 29660 1.58 - 1.70: 0 1.70 - 1.81: 512 Bond restraints: 62618 Sorted by residual: bond pdb=" C GLU q 231 " pdb=" N PRO q 232 " ideal model delta sigma weight residual 1.334 1.439 -0.105 2.34e-02 1.83e+03 2.03e+01 bond pdb=" C ALA q 346 " pdb=" N PRO q 347 " ideal model delta sigma weight residual 1.334 1.433 -0.099 2.34e-02 1.83e+03 1.80e+01 bond pdb=" C SER g 469 " pdb=" N PRO g 470 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 7.01e+00 bond pdb=" CA ARG Z 14 " pdb=" C ARG Z 14 " ideal model delta sigma weight residual 1.524 1.543 -0.019 9.50e-03 1.11e+04 4.17e+00 bond pdb=" C ARG Z 14 " pdb=" O ARG Z 14 " ideal model delta sigma weight residual 1.243 1.231 0.012 9.50e-03 1.11e+04 1.73e+00 ... (remaining 62613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 83832 1.62 - 3.23: 456 3.23 - 4.85: 140 4.85 - 6.46: 28 6.46 - 8.08: 3 Bond angle restraints: 84459 Sorted by residual: angle pdb=" C LEU Z 13 " pdb=" CA LEU Z 13 " pdb=" CB LEU Z 13 " ideal model delta sigma weight residual 117.23 109.15 8.08 1.36e+00 5.41e-01 3.53e+01 angle pdb=" N ARG z 14 " pdb=" CA ARG z 14 " pdb=" C ARG z 14 " ideal model delta sigma weight residual 113.18 106.04 7.14 1.21e+00 6.83e-01 3.48e+01 angle pdb=" CA LEU Z 13 " pdb=" C LEU Z 13 " pdb=" N ARG Z 14 " ideal model delta sigma weight residual 119.98 115.83 4.15 8.50e-01 1.38e+00 2.39e+01 angle pdb=" N ARG Z 15 " pdb=" CA ARG Z 15 " pdb=" C ARG Z 15 " ideal model delta sigma weight residual 109.59 117.02 -7.43 1.61e+00 3.86e-01 2.13e+01 angle pdb=" N ILE Z 296 " pdb=" CA ILE Z 296 " pdb=" C ILE Z 296 " ideal model delta sigma weight residual 112.29 108.52 3.77 9.40e-01 1.13e+00 1.61e+01 ... (remaining 84454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 38294 15.98 - 31.96: 329 31.96 - 47.94: 208 47.94 - 63.92: 54 63.92 - 79.89: 3 Dihedral angle restraints: 38888 sinusoidal: 15564 harmonic: 23324 Sorted by residual: dihedral pdb=" CA ARG Z 14 " pdb=" C ARG Z 14 " pdb=" N ARG Z 15 " pdb=" CA ARG Z 15 " ideal model delta harmonic sigma weight residual -180.00 -151.86 -28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ASP Z 16 " pdb=" C ASP Z 16 " pdb=" N ALA Z 17 " pdb=" CA ALA Z 17 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA HIS Q 494 " pdb=" C HIS Q 494 " pdb=" N LEU Q 495 " pdb=" CA LEU Q 495 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 38885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 6869 0.031 - 0.063: 2296 0.063 - 0.094: 465 0.094 - 0.126: 518 0.126 - 0.157: 18 Chirality restraints: 10166 Sorted by residual: chirality pdb=" CB ILE z 296 " pdb=" CA ILE z 296 " pdb=" CG1 ILE z 296 " pdb=" CG2 ILE z 296 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA ILE b 422 " pdb=" N ILE b 422 " pdb=" C ILE b 422 " pdb=" CB ILE b 422 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE B 422 " pdb=" N ILE B 422 " pdb=" C ILE B 422 " pdb=" CB ILE B 422 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 10163 not shown) Planarity restraints: 10848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 372 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO D 373 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 373 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 373 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG d 372 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO d 373 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO d 373 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO d 373 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 225 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C ASN A 225 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN A 225 " -0.008 2.00e-02 2.50e+03 pdb=" N CYS A 226 " -0.007 2.00e-02 2.50e+03 ... (remaining 10845 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 9825 2.76 - 3.30: 57926 3.30 - 3.83: 92127 3.83 - 4.37: 109679 4.37 - 4.90: 189641 Nonbonded interactions: 459198 Sorted by model distance: nonbonded pdb=" O SER e 194 " pdb=" ND1 HIS e 197 " model vdw 2.228 3.120 nonbonded pdb=" OH TYR Z 182 " pdb=" O GLN Z 185 " model vdw 2.229 3.040 nonbonded pdb=" O LEU B 317 " pdb=" OG1 THR B 321 " model vdw 2.241 3.040 nonbonded pdb=" O MET d 432 " pdb=" OG SER E 500 " model vdw 2.242 3.040 nonbonded pdb=" O LEU h 198 " pdb=" OG1 THR h 373 " model vdw 2.246 3.040 ... (remaining 459193 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' selection = (chain 'a' and (resid 18 through 256 or resid 264 through 547)) } ncs_group { reference = chain 'B' selection = (chain 'b' and (resid 19 through 242 or resid 256 through 520)) } ncs_group { reference = (chain 'D' and (resid 17 through 479 or resid 493 through 528)) selection = (chain 'd' and (resid 17 through 245 or resid 266 through 528)) } ncs_group { reference = chain 'E' selection = (chain 'e' and (resid 43 through 284 or resid 301 through 560)) } ncs_group { reference = chain 'G' selection = (chain 'g' and (resid 18 through 253 or resid 277 through 590)) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = (chain 'Q' and resid 27 through 549) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and resid 10 through 538) } 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 group one per residue 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.930 Check model and map are aligned: 0.370 Set scattering table: 0.480 Process input model: 117.630 Find NCS groups from input model: 4.980 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 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 : 0.001 0.105 62618 Z= 0.091 Angle : 0.393 8.081 84459 Z= 0.227 Chirality : 0.039 0.157 10166 Planarity : 0.001 0.032 10848 Dihedral : 7.123 79.894 23768 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.54 % Rotamer: Outliers : 0.01 % Allowed : 0.10 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.07), residues: 8065 helix: -3.55 (0.05), residues: 3734 sheet: -1.03 (0.18), residues: 622 loop : -1.14 (0.09), residues: 3709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 440 HIS 0.003 0.000 HIS z 106 PHE 0.016 0.001 PHE H 224 TYR 0.008 0.001 TYR Z 182 ARG 0.003 0.000 ARG Z 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2489 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2488 time to evaluate : 5.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 25 ILE cc_start: 0.8851 (tp) cc_final: 0.8555 (tp) REVERT: a 44 LEU cc_start: 0.9392 (tp) cc_final: 0.9111 (tp) REVERT: a 49 LEU cc_start: 0.7755 (mt) cc_final: 0.7510 (mm) REVERT: a 81 LYS cc_start: 0.9567 (mttt) cc_final: 0.9357 (mttp) REVERT: a 93 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7762 (mp0) REVERT: a 96 ASP cc_start: 0.6156 (t0) cc_final: 0.5890 (m-30) REVERT: a 118 ASN cc_start: 0.8840 (m-40) cc_final: 0.8395 (m110) REVERT: a 142 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8705 (pp20) REVERT: a 179 MET cc_start: 0.7683 (mtp) cc_final: 0.7064 (ptt) REVERT: a 399 GLU cc_start: 0.6535 (tt0) cc_final: 0.6287 (mt-10) REVERT: a 433 LEU cc_start: 0.9607 (mt) cc_final: 0.9394 (mp) REVERT: a 448 ILE cc_start: 0.9329 (mt) cc_final: 0.8869 (tt) REVERT: a 473 LEU cc_start: 0.9635 (mt) cc_final: 0.9286 (mm) REVERT: a 497 TYR cc_start: 0.7814 (m-80) cc_final: 0.7593 (m-80) REVERT: a 530 SER cc_start: 0.9399 (m) cc_final: 0.9045 (p) REVERT: A 20 ILE cc_start: 0.8300 (mm) cc_final: 0.7995 (mm) REVERT: A 89 GLN cc_start: 0.9419 (mt0) cc_final: 0.9079 (mp10) REVERT: A 111 ARG cc_start: 0.9185 (mmt180) cc_final: 0.8977 (tpp80) REVERT: A 131 VAL cc_start: 0.9455 (t) cc_final: 0.8937 (p) REVERT: A 135 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8650 (mm-30) REVERT: A 157 ILE cc_start: 0.9138 (pt) cc_final: 0.8882 (mt) REVERT: A 175 PHE cc_start: 0.6994 (t80) cc_final: 0.6655 (t80) REVERT: A 204 ASN cc_start: 0.7629 (t0) cc_final: 0.7341 (m110) REVERT: A 233 MET cc_start: 0.1347 (mtm) cc_final: 0.0335 (ptt) REVERT: A 320 ARG cc_start: 0.8750 (mtt180) cc_final: 0.8511 (mtt90) REVERT: A 433 LEU cc_start: 0.9638 (mt) cc_final: 0.9397 (pp) REVERT: A 451 PHE cc_start: 0.8287 (t80) cc_final: 0.7801 (t80) REVERT: A 471 SER cc_start: 0.9568 (m) cc_final: 0.8729 (t) REVERT: A 473 LEU cc_start: 0.9377 (mt) cc_final: 0.9162 (mt) REVERT: A 502 LEU cc_start: 0.8035 (mt) cc_final: 0.7247 (mt) REVERT: A 508 LYS cc_start: 0.8452 (pttt) cc_final: 0.8172 (tptp) REVERT: A 512 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8092 (pm20) REVERT: A 533 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8919 (mm-30) REVERT: b 45 LEU cc_start: 0.8660 (tp) cc_final: 0.8308 (pp) REVERT: b 46 LEU cc_start: 0.9306 (mt) cc_final: 0.8857 (mm) REVERT: b 121 ILE cc_start: 0.8916 (mt) cc_final: 0.8583 (mt) REVERT: b 181 ILE cc_start: 0.8706 (mm) cc_final: 0.8317 (pt) REVERT: b 315 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8675 (pp20) REVERT: b 347 MET cc_start: 0.7139 (mmm) cc_final: 0.6292 (tmm) REVERT: b 493 LEU cc_start: 0.9576 (tp) cc_final: 0.9301 (pp) REVERT: B 75 LYS cc_start: 0.8752 (mttt) cc_final: 0.8078 (tttt) REVERT: B 79 ASN cc_start: 0.9168 (m-40) cc_final: 0.8774 (m-40) REVERT: B 96 THR cc_start: 0.9711 (m) cc_final: 0.9451 (t) REVERT: B 97 VAL cc_start: 0.9500 (t) cc_final: 0.9259 (t) REVERT: B 147 THR cc_start: 0.8979 (p) cc_final: 0.8743 (t) REVERT: B 155 HIS cc_start: 0.9121 (m170) cc_final: 0.8732 (m90) REVERT: B 161 LEU cc_start: 0.9421 (mt) cc_final: 0.9205 (mt) REVERT: B 196 ILE cc_start: 0.8655 (mt) cc_final: 0.8222 (mm) REVERT: B 365 CYS cc_start: 0.4245 (m) cc_final: 0.2844 (m) REVERT: B 396 LYS cc_start: 0.8462 (mmtt) cc_final: 0.7888 (ptpt) REVERT: B 408 GLU cc_start: 0.9146 (mp0) cc_final: 0.8561 (pm20) REVERT: B 409 MET cc_start: 0.9243 (tpp) cc_final: 0.8854 (ttt) REVERT: B 413 LYS cc_start: 0.9428 (tttm) cc_final: 0.9106 (ttmm) REVERT: B 452 SER cc_start: 0.8367 (p) cc_final: 0.7851 (m) REVERT: B 513 ASN cc_start: 0.8255 (t0) cc_final: 0.7972 (m110) REVERT: B 515 ILE cc_start: 0.8118 (mt) cc_final: 0.7804 (mm) REVERT: d 44 MET cc_start: 0.8320 (mtp) cc_final: 0.7169 (mtm) REVERT: d 110 LEU cc_start: 0.9304 (mt) cc_final: 0.9020 (mt) REVERT: d 196 LEU cc_start: 0.7852 (mt) cc_final: 0.7595 (mm) REVERT: d 209 MET cc_start: 0.3189 (mtm) cc_final: 0.2777 (ttm) REVERT: d 315 ASP cc_start: 0.3071 (m-30) cc_final: 0.2406 (t70) REVERT: d 422 SER cc_start: 0.9381 (t) cc_final: 0.9117 (p) REVERT: d 426 SER cc_start: 0.8904 (t) cc_final: 0.8006 (p) REVERT: d 513 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9098 (mm-30) REVERT: D 24 ASN cc_start: 0.8208 (m-40) cc_final: 0.7809 (m110) REVERT: D 112 ASN cc_start: 0.8978 (m-40) cc_final: 0.8761 (m110) REVERT: D 132 VAL cc_start: 0.9134 (t) cc_final: 0.8842 (p) REVERT: D 137 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8370 (tm-30) REVERT: D 138 MET cc_start: 0.7531 (ptp) cc_final: 0.6186 (mmt) REVERT: D 502 LEU cc_start: 0.9230 (tp) cc_final: 0.8978 (tp) REVERT: D 509 THR cc_start: 0.9165 (m) cc_final: 0.8747 (t) REVERT: e 61 ILE cc_start: 0.9183 (pt) cc_final: 0.8902 (tt) REVERT: e 114 GLU cc_start: 0.9114 (tp30) cc_final: 0.8887 (pt0) REVERT: e 131 ASP cc_start: 0.9065 (t70) cc_final: 0.8824 (m-30) REVERT: e 132 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8671 (mm-40) REVERT: e 182 ARG cc_start: 0.9240 (mtt180) cc_final: 0.8927 (tpt90) REVERT: e 210 ASN cc_start: 0.8802 (m-40) cc_final: 0.8200 (t0) REVERT: e 472 PHE cc_start: 0.9077 (t80) cc_final: 0.8818 (t80) REVERT: e 482 THR cc_start: 0.9146 (m) cc_final: 0.8943 (m) REVERT: e 540 LEU cc_start: 0.9466 (mt) cc_final: 0.9257 (mt) REVERT: E 72 LYS cc_start: 0.8952 (mttm) cc_final: 0.8650 (mmtp) REVERT: E 106 GLN cc_start: 0.9139 (mt0) cc_final: 0.8840 (pp30) REVERT: E 107 LEU cc_start: 0.8752 (tp) cc_final: 0.8270 (tp) REVERT: E 127 SER cc_start: 0.9251 (t) cc_final: 0.9000 (p) REVERT: E 129 LEU cc_start: 0.9135 (mt) cc_final: 0.8654 (mm) REVERT: E 163 GLU cc_start: 0.9447 (mt-10) cc_final: 0.8918 (mp0) REVERT: E 254 MET cc_start: 0.0246 (mtt) cc_final: -0.1718 (tmm) REVERT: E 537 GLN cc_start: 0.9158 (tt0) cc_final: 0.8553 (tp40) REVERT: E 543 GLN cc_start: 0.9033 (tp40) cc_final: 0.8310 (tp-100) REVERT: g 24 ASN cc_start: 0.9314 (m-40) cc_final: 0.8564 (t0) REVERT: g 25 ILE cc_start: 0.9332 (mt) cc_final: 0.9118 (tp) REVERT: g 98 ILE cc_start: 0.9585 (mt) cc_final: 0.9077 (mm) REVERT: g 104 LEU cc_start: 0.9159 (tp) cc_final: 0.8659 (tp) REVERT: g 115 ASN cc_start: 0.9169 (t0) cc_final: 0.8806 (p0) REVERT: g 117 HIS cc_start: 0.7799 (t-90) cc_final: 0.7347 (t-90) REVERT: g 129 LEU cc_start: 0.9228 (tp) cc_final: 0.8885 (pp) REVERT: g 163 TYR cc_start: 0.6390 (t80) cc_final: 0.6104 (t80) REVERT: g 173 GLU cc_start: 0.8797 (tt0) cc_final: 0.8479 (mm-30) REVERT: g 481 MET cc_start: 0.9340 (tpp) cc_final: 0.8966 (tpt) REVERT: g 509 MET cc_start: 0.9069 (mmm) cc_final: 0.8812 (mmt) REVERT: g 525 ILE cc_start: 0.9494 (mt) cc_final: 0.9258 (tt) REVERT: g 544 ILE cc_start: 0.8297 (mm) cc_final: 0.7987 (mm) REVERT: g 571 LYS cc_start: 0.9350 (mttt) cc_final: 0.8882 (ptpt) REVERT: g 575 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8358 (pt0) REVERT: G 44 MET cc_start: 0.7735 (mmp) cc_final: 0.7158 (mmm) REVERT: G 76 LYS cc_start: 0.8169 (mttt) cc_final: 0.7938 (mtmm) REVERT: G 115 ASN cc_start: 0.8668 (t0) cc_final: 0.8401 (t0) REVERT: G 130 THR cc_start: 0.9318 (m) cc_final: 0.8945 (p) REVERT: G 173 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8751 (mm-30) REVERT: G 193 GLU cc_start: 0.3166 (tt0) cc_final: 0.2543 (mm-30) REVERT: G 207 GLU cc_start: 0.8361 (tp30) cc_final: 0.7820 (tm-30) REVERT: G 234 MET cc_start: 0.1995 (ttm) cc_final: -0.0651 (ptm) REVERT: G 298 GLU cc_start: 0.7082 (tt0) cc_final: 0.6795 (mm-30) REVERT: G 357 VAL cc_start: 0.5052 (m) cc_final: 0.4832 (p) REVERT: G 454 ARG cc_start: 0.8880 (mtm-85) cc_final: 0.8642 (ptt90) REVERT: G 466 VAL cc_start: 0.8824 (t) cc_final: 0.8262 (p) REVERT: G 511 CYS cc_start: 0.8919 (t) cc_final: 0.7513 (t) REVERT: G 512 ILE cc_start: 0.8823 (mm) cc_final: 0.8583 (mm) REVERT: G 514 ARG cc_start: 0.9009 (ttp-170) cc_final: 0.8631 (ttp80) REVERT: G 519 ASN cc_start: 0.8693 (m-40) cc_final: 0.8214 (t0) REVERT: G 571 LYS cc_start: 0.9178 (tttm) cc_final: 0.8821 (mtmm) REVERT: G 583 VAL cc_start: 0.8495 (t) cc_final: 0.8272 (p) REVERT: h 70 LEU cc_start: 0.9248 (tp) cc_final: 0.8700 (pp) REVERT: h 71 LYS cc_start: 0.8931 (mttt) cc_final: 0.8407 (mmtm) REVERT: h 87 SER cc_start: 0.9525 (t) cc_final: 0.8771 (m) REVERT: h 160 ARG cc_start: 0.8750 (mtt180) cc_final: 0.7779 (ptt180) REVERT: h 166 MET cc_start: 0.7382 (mtt) cc_final: 0.6357 (ttp) REVERT: h 362 TYR cc_start: 0.8071 (m-80) cc_final: 0.7436 (m-80) REVERT: h 454 CYS cc_start: 0.8583 (m) cc_final: 0.8313 (p) REVERT: h 502 VAL cc_start: 0.9070 (t) cc_final: 0.8738 (p) REVERT: h 504 ILE cc_start: 0.9482 (mt) cc_final: 0.9186 (tp) REVERT: h 511 THR cc_start: 0.9305 (m) cc_final: 0.8451 (t) REVERT: H 33 CYS cc_start: 0.9371 (m) cc_final: 0.9054 (t) REVERT: H 90 GLN cc_start: 0.8413 (tp40) cc_final: 0.8171 (tm-30) REVERT: H 98 THR cc_start: 0.8643 (p) cc_final: 0.7859 (t) REVERT: H 111 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7728 (mm-30) REVERT: H 125 ILE cc_start: 0.9424 (mt) cc_final: 0.9000 (tp) REVERT: H 135 LEU cc_start: 0.8267 (mt) cc_final: 0.8054 (tt) REVERT: H 138 GLU cc_start: 0.9315 (tt0) cc_final: 0.9111 (pt0) REVERT: H 204 ILE cc_start: 0.7304 (mt) cc_final: 0.7059 (mm) REVERT: H 306 PHE cc_start: 0.8264 (t80) cc_final: 0.7561 (m-10) REVERT: H 444 LYS cc_start: 0.9341 (tttt) cc_final: 0.8539 (tptt) REVERT: H 467 LYS cc_start: 0.8981 (mttt) cc_final: 0.8502 (ptmt) REVERT: H 477 LYS cc_start: 0.7496 (mttt) cc_final: 0.7226 (mttt) REVERT: q 39 HIS cc_start: 0.9126 (t-170) cc_final: 0.8492 (t70) REVERT: q 49 CYS cc_start: 0.7686 (m) cc_final: 0.6671 (m) REVERT: q 52 ASN cc_start: 0.8478 (m-40) cc_final: 0.7973 (t0) REVERT: q 87 MET cc_start: 0.8614 (mtm) cc_final: 0.8246 (mmt) REVERT: q 111 LEU cc_start: 0.9653 (mt) cc_final: 0.8994 (mt) REVERT: q 114 SER cc_start: 0.9081 (m) cc_final: 0.8442 (p) REVERT: q 120 MET cc_start: 0.7296 (ttp) cc_final: 0.6930 (ttm) REVERT: q 128 ILE cc_start: 0.9393 (mt) cc_final: 0.8907 (mt) REVERT: q 131 TYR cc_start: 0.8789 (m-10) cc_final: 0.8548 (m-10) REVERT: q 155 ASP cc_start: 0.8761 (t0) cc_final: 0.8477 (t0) REVERT: q 171 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7827 (mmtp) REVERT: q 174 SER cc_start: 0.8720 (m) cc_final: 0.8303 (t) REVERT: q 361 MET cc_start: 0.7610 (mtt) cc_final: 0.7157 (ttt) REVERT: q 393 ASN cc_start: 0.8465 (m-40) cc_final: 0.8209 (p0) REVERT: q 428 ILE cc_start: 0.9356 (mm) cc_final: 0.9124 (mm) REVERT: q 456 PHE cc_start: 0.9135 (m-10) cc_final: 0.8843 (m-80) REVERT: q 466 THR cc_start: 0.9452 (p) cc_final: 0.9004 (t) REVERT: q 473 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8391 (pt0) REVERT: q 519 ASP cc_start: 0.9021 (m-30) cc_final: 0.8785 (t0) REVERT: q 524 LYS cc_start: 0.9343 (mmmt) cc_final: 0.9103 (mmmm) REVERT: q 525 LYS cc_start: 0.8936 (tttt) cc_final: 0.8540 (tptt) REVERT: q 539 LEU cc_start: 0.9597 (mt) cc_final: 0.9260 (pp) REVERT: Q 109 GLU cc_start: 0.9422 (tp30) cc_final: 0.8941 (tp30) REVERT: Q 120 MET cc_start: 0.7594 (ttm) cc_final: 0.7255 (ttm) REVERT: Q 141 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7939 (tm-30) REVERT: Q 145 MET cc_start: 0.8611 (mmm) cc_final: 0.7173 (mmp) REVERT: Q 157 ASN cc_start: 0.9225 (m-40) cc_final: 0.8896 (m-40) REVERT: Q 171 LYS cc_start: 0.8356 (tptt) cc_final: 0.7753 (tppt) REVERT: Q 204 VAL cc_start: 0.9000 (t) cc_final: 0.8633 (p) REVERT: Q 224 LYS cc_start: 0.7943 (mttt) cc_final: 0.7614 (mmmt) REVERT: Q 230 ARG cc_start: 0.1516 (mtp85) cc_final: 0.1163 (mmp-170) REVERT: Q 361 MET cc_start: 0.8243 (mtt) cc_final: 0.7901 (mmt) REVERT: Q 380 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7445 (tpt170) REVERT: Q 384 ILE cc_start: 0.5055 (mt) cc_final: 0.4600 (mt) REVERT: Q 387 ARG cc_start: 0.9028 (mtt90) cc_final: 0.8750 (mtt90) REVERT: Q 418 LYS cc_start: 0.7636 (mttt) cc_final: 0.7183 (mtpt) REVERT: Q 445 LEU cc_start: 0.9419 (mt) cc_final: 0.9038 (mm) REVERT: Q 456 PHE cc_start: 0.8739 (m-10) cc_final: 0.8487 (m-80) REVERT: Q 472 ASN cc_start: 0.8227 (m-40) cc_final: 0.8007 (m-40) REVERT: Q 497 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7839 (mmmt) REVERT: Q 525 LYS cc_start: 0.9054 (tttt) cc_final: 0.8744 (tptt) REVERT: Q 533 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8917 (tm-30) REVERT: Q 545 ILE cc_start: 0.8575 (mt) cc_final: 0.8346 (mt) REVERT: z 83 GLN cc_start: 0.8674 (mm-40) cc_final: 0.7928 (tm-30) REVERT: z 85 GLU cc_start: 0.9269 (mt-10) cc_final: 0.9048 (pp20) REVERT: z 124 ILE cc_start: 0.9380 (mt) cc_final: 0.9157 (mm) REVERT: z 152 GLN cc_start: 0.8242 (mt0) cc_final: 0.8003 (pm20) REVERT: z 158 LEU cc_start: 0.9175 (mt) cc_final: 0.8948 (mt) REVERT: z 380 ILE cc_start: 0.8780 (mt) cc_final: 0.8508 (mt) REVERT: z 390 GLN cc_start: 0.8798 (tt0) cc_final: 0.8154 (tp40) REVERT: z 419 TYR cc_start: 0.8758 (m-80) cc_final: 0.8526 (m-10) REVERT: z 452 LEU cc_start: 0.9324 (mt) cc_final: 0.8853 (mm) REVERT: z 527 LEU cc_start: 0.9504 (mt) cc_final: 0.9284 (mt) REVERT: z 529 LEU cc_start: 0.8855 (mt) cc_final: 0.8645 (mt) REVERT: Z 37 LEU cc_start: 0.7669 (tp) cc_final: 0.6811 (tp) REVERT: Z 62 LEU cc_start: 0.8058 (mt) cc_final: 0.7768 (mt) REVERT: Z 104 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7188 (tp40) REVERT: Z 106 HIS cc_start: 0.8079 (t70) cc_final: 0.7735 (t-90) REVERT: Z 124 ILE cc_start: 0.9521 (mt) cc_final: 0.9242 (tp) REVERT: Z 128 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8844 (tp30) REVERT: Z 193 MET cc_start: 0.8255 (mtt) cc_final: 0.7977 (mtm) REVERT: Z 202 LEU cc_start: 0.8456 (tp) cc_final: 0.8230 (mm) REVERT: Z 362 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7907 (mm-30) REVERT: Z 364 PHE cc_start: 0.6084 (m-10) cc_final: 0.5883 (m-80) REVERT: Z 366 TYR cc_start: 0.6466 (m-10) cc_final: 0.6252 (m-10) REVERT: Z 412 ILE cc_start: 0.9520 (mt) cc_final: 0.9142 (mt) REVERT: Z 418 PHE cc_start: 0.9432 (t80) cc_final: 0.9219 (t80) REVERT: Z 420 ILE cc_start: 0.9178 (mt) cc_final: 0.8966 (mm) REVERT: Z 466 PRO cc_start: 0.8754 (Cg_endo) cc_final: 0.8174 (Cg_exo) REVERT: Z 470 LEU cc_start: 0.9150 (mt) cc_final: 0.8720 (pp) REVERT: Z 482 ASP cc_start: 0.8932 (m-30) cc_final: 0.8686 (p0) REVERT: Z 515 ASN cc_start: 0.9496 (m-40) cc_final: 0.8976 (t0) REVERT: Z 529 LEU cc_start: 0.8448 (mt) cc_final: 0.7888 (mt) outliers start: 1 outliers final: 0 residues processed: 2489 average time/residue: 0.6370 time to fit residues: 2576.1715 Evaluate side-chains 1302 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1302 time to evaluate : 5.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 678 optimal weight: 0.0980 chunk 609 optimal weight: 0.0030 chunk 338 optimal weight: 0.3980 chunk 208 optimal weight: 0.8980 chunk 411 optimal weight: 1.9990 chunk 325 optimal weight: 20.0000 chunk 630 optimal weight: 0.3980 chunk 243 optimal weight: 5.9990 chunk 383 optimal weight: 3.9990 chunk 469 optimal weight: 10.0000 chunk 730 optimal weight: 0.2980 overall best weight: 0.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 89 GLN A 190 GLN A 465 ASN A 499 ASN b 84 GLN ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 375 GLN ** b 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN B 192 HIS ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 284 ASN d 289 GLN d 461 ASN ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 284 ASN e 106 GLN e 397 GLN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 461 GLN e 536 GLN E 132 GLN E 353 HIS E 432 ASN E 466 GLN E 509 ASN E 536 GLN E 543 GLN g 188 GLN g 519 ASN g 530 GLN G 24 ASN G 188 GLN G 465 ASN G 530 GLN G 535 HIS h 58 GLN h 90 GLN h 172 HIS ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 GLN H 406 ASN q 482 HIS Q 27 GLN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS Q 314 ASN ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 22 ASN z 69 GLN z 201 HIS ** z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 356 GLN ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 ASN Z 104 GLN Z 430 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 62618 Z= 0.187 Angle : 0.623 9.957 84459 Z= 0.326 Chirality : 0.045 0.284 10166 Planarity : 0.004 0.108 10848 Dihedral : 3.473 28.850 8568 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.92 % Favored : 98.04 % Rotamer: Outliers : 0.15 % Allowed : 2.31 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.08), residues: 8065 helix: -1.15 (0.07), residues: 3844 sheet: -0.59 (0.19), residues: 619 loop : -0.92 (0.09), residues: 3602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 275 HIS 0.014 0.001 HIS e 50 PHE 0.037 0.002 PHE h 492 TYR 0.026 0.001 TYR e 381 ARG 0.009 0.001 ARG q 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1643 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1633 time to evaluate : 5.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 73 LEU cc_start: 0.8847 (mt) cc_final: 0.8174 (mt) REVERT: a 81 LYS cc_start: 0.9604 (mttt) cc_final: 0.9397 (mttp) REVERT: a 96 ASP cc_start: 0.5208 (t0) cc_final: 0.4503 (m-30) REVERT: a 135 GLU cc_start: 0.8394 (tp30) cc_final: 0.7183 (tp30) REVERT: a 142 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8716 (tm-30) REVERT: a 179 MET cc_start: 0.7521 (mtp) cc_final: 0.7081 (ptt) REVERT: a 258 MET cc_start: 0.0087 (mmm) cc_final: -0.0701 (mmt) REVERT: a 316 MET cc_start: 0.4256 (tmm) cc_final: 0.3242 (tpt) REVERT: a 399 GLU cc_start: 0.6706 (tt0) cc_final: 0.6324 (pp20) REVERT: a 432 TYR cc_start: 0.7857 (t80) cc_final: 0.7646 (t80) REVERT: a 433 LEU cc_start: 0.9585 (mt) cc_final: 0.9268 (mp) REVERT: a 448 ILE cc_start: 0.9200 (mt) cc_final: 0.8838 (tp) REVERT: a 460 LYS cc_start: 0.8608 (tptt) cc_final: 0.8292 (tptt) REVERT: a 469 ASP cc_start: 0.8314 (t0) cc_final: 0.7447 (t70) REVERT: a 472 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8770 (mm-30) REVERT: a 497 TYR cc_start: 0.7871 (m-80) cc_final: 0.7609 (m-80) REVERT: a 530 SER cc_start: 0.9552 (m) cc_final: 0.9199 (p) REVERT: a 532 LEU cc_start: 0.9370 (mm) cc_final: 0.8835 (tt) REVERT: A 25 ILE cc_start: 0.8221 (tp) cc_final: 0.8020 (tp) REVERT: A 88 GLN cc_start: 0.8920 (tp-100) cc_final: 0.8494 (mp10) REVERT: A 111 ARG cc_start: 0.9133 (mmt180) cc_final: 0.8889 (tpp80) REVERT: A 131 VAL cc_start: 0.9471 (t) cc_final: 0.9230 (t) REVERT: A 135 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8433 (mm-30) REVERT: A 204 ASN cc_start: 0.7839 (t0) cc_final: 0.7514 (m110) REVERT: A 233 MET cc_start: 0.0551 (mtm) cc_final: -0.1194 (ptt) REVERT: A 307 LEU cc_start: 0.4577 (mt) cc_final: 0.4268 (pp) REVERT: A 320 ARG cc_start: 0.8745 (mtt180) cc_final: 0.8485 (mtt90) REVERT: A 433 LEU cc_start: 0.9641 (mt) cc_final: 0.9329 (pp) REVERT: A 471 SER cc_start: 0.9448 (m) cc_final: 0.8671 (t) REVERT: A 533 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8888 (mm-30) REVERT: b 45 LEU cc_start: 0.8934 (tp) cc_final: 0.8270 (pp) REVERT: b 59 ASP cc_start: 0.8722 (t0) cc_final: 0.8358 (t0) REVERT: b 62 THR cc_start: 0.9150 (t) cc_final: 0.8896 (t) REVERT: b 135 LEU cc_start: 0.9562 (mt) cc_final: 0.9278 (mt) REVERT: b 148 MET cc_start: 0.8509 (ppp) cc_final: 0.8183 (ppp) REVERT: b 158 LYS cc_start: 0.9523 (mttt) cc_final: 0.9314 (mmmt) REVERT: b 238 LEU cc_start: 0.5316 (mt) cc_final: 0.5114 (mt) REVERT: b 267 GLU cc_start: 0.6946 (tt0) cc_final: 0.6734 (tm-30) REVERT: b 347 MET cc_start: 0.7196 (mmm) cc_final: 0.6537 (tmm) REVERT: b 409 MET cc_start: 0.8952 (tpp) cc_final: 0.8733 (ttm) REVERT: b 439 GLN cc_start: 0.8796 (mm110) cc_final: 0.8532 (mp10) REVERT: B 75 LYS cc_start: 0.8382 (mttt) cc_final: 0.7743 (tttt) REVERT: B 79 ASN cc_start: 0.9103 (m-40) cc_final: 0.8739 (m-40) REVERT: B 148 MET cc_start: 0.8408 (ppp) cc_final: 0.8075 (tmm) REVERT: B 354 LEU cc_start: 0.4002 (mt) cc_final: 0.2874 (tp) REVERT: B 409 MET cc_start: 0.9387 (tpp) cc_final: 0.9028 (ttm) REVERT: B 423 ASP cc_start: 0.7169 (m-30) cc_final: 0.5918 (m-30) REVERT: B 435 ARG cc_start: 0.9049 (mtm180) cc_final: 0.8794 (ptm160) REVERT: B 452 SER cc_start: 0.8307 (p) cc_final: 0.7951 (t) REVERT: B 472 LEU cc_start: 0.8706 (mt) cc_final: 0.8489 (mt) REVERT: B 489 GLU cc_start: 0.9418 (tp30) cc_final: 0.9187 (tp30) REVERT: d 209 MET cc_start: 0.3293 (mtm) cc_final: 0.3044 (ttm) REVERT: d 315 ASP cc_start: 0.2635 (m-30) cc_final: 0.2278 (t70) REVERT: d 419 ILE cc_start: 0.9408 (tp) cc_final: 0.9109 (tp) REVERT: d 422 SER cc_start: 0.9262 (t) cc_final: 0.8950 (p) REVERT: d 432 MET cc_start: 0.6972 (mmm) cc_final: 0.6398 (mmp) REVERT: d 513 GLU cc_start: 0.9558 (mm-30) cc_final: 0.8654 (mm-30) REVERT: d 516 LYS cc_start: 0.9280 (mtpp) cc_final: 0.8965 (mttm) REVERT: D 24 ASN cc_start: 0.8613 (m-40) cc_final: 0.8321 (m110) REVERT: D 44 MET cc_start: 0.8515 (mpp) cc_final: 0.8083 (mpp) REVERT: D 132 VAL cc_start: 0.9276 (t) cc_final: 0.9029 (p) REVERT: D 137 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8486 (tm-30) REVERT: D 138 MET cc_start: 0.7075 (ptp) cc_final: 0.6800 (tpp) REVERT: D 209 MET cc_start: 0.3046 (mmt) cc_final: 0.2722 (mmt) REVERT: D 304 PHE cc_start: 0.7090 (m-10) cc_final: 0.6205 (t80) REVERT: D 385 MET cc_start: 0.5707 (ppp) cc_final: 0.4292 (tpp) REVERT: D 448 GLU cc_start: 0.9261 (mt-10) cc_final: 0.9024 (mp0) REVERT: D 513 GLU cc_start: 0.9120 (mp0) cc_final: 0.8899 (mp0) REVERT: e 94 MET cc_start: 0.6528 (tpt) cc_final: 0.6234 (tpt) REVERT: e 113 ASP cc_start: 0.8511 (m-30) cc_final: 0.7473 (p0) REVERT: e 129 LEU cc_start: 0.9675 (mm) cc_final: 0.9365 (mm) REVERT: e 202 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7992 (tp30) REVERT: e 203 MET cc_start: 0.3508 (tmm) cc_final: 0.2324 (ptt) REVERT: e 210 ASN cc_start: 0.8714 (m-40) cc_final: 0.8160 (t0) REVERT: e 482 THR cc_start: 0.9300 (m) cc_final: 0.9042 (p) REVERT: e 495 LEU cc_start: 0.9035 (tp) cc_final: 0.8263 (mt) REVERT: e 540 LEU cc_start: 0.9518 (mt) cc_final: 0.9316 (mt) REVERT: E 63 THR cc_start: 0.9368 (p) cc_final: 0.9166 (t) REVERT: E 103 LEU cc_start: 0.9288 (mp) cc_final: 0.8854 (mp) REVERT: E 106 GLN cc_start: 0.9278 (mt0) cc_final: 0.9049 (pp30) REVERT: E 236 ASP cc_start: 0.7114 (p0) cc_final: 0.6816 (p0) REVERT: E 254 MET cc_start: 0.0253 (mtt) cc_final: -0.1756 (ttt) REVERT: E 379 ARG cc_start: 0.7119 (mmt-90) cc_final: 0.5962 (ptp-170) REVERT: E 420 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7801 (pp20) REVERT: E 543 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8774 (tp-100) REVERT: E 547 MET cc_start: 0.9325 (mtp) cc_final: 0.8993 (tmm) REVERT: E 553 ASN cc_start: 0.8234 (t0) cc_final: 0.7606 (t0) REVERT: E 555 ILE cc_start: 0.8635 (mm) cc_final: 0.8154 (mm) REVERT: g 24 ASN cc_start: 0.9220 (m-40) cc_final: 0.8770 (t0) REVERT: g 88 GLU cc_start: 0.9111 (mp0) cc_final: 0.8899 (mp0) REVERT: g 104 LEU cc_start: 0.9374 (tp) cc_final: 0.8959 (tp) REVERT: g 117 HIS cc_start: 0.7936 (t-90) cc_final: 0.7102 (t-90) REVERT: g 119 VAL cc_start: 0.9435 (t) cc_final: 0.9081 (p) REVERT: g 134 GLU cc_start: 0.9232 (pt0) cc_final: 0.8818 (pp20) REVERT: g 163 TYR cc_start: 0.6423 (t80) cc_final: 0.6123 (t80) REVERT: g 173 GLU cc_start: 0.8870 (tt0) cc_final: 0.8589 (mm-30) REVERT: g 440 MET cc_start: 0.5975 (pmm) cc_final: 0.4799 (pmm) REVERT: g 487 LEU cc_start: 0.9136 (mt) cc_final: 0.8884 (mt) REVERT: g 489 GLU cc_start: 0.9284 (mt-10) cc_final: 0.9062 (pp20) REVERT: g 492 LYS cc_start: 0.7875 (mmtm) cc_final: 0.7430 (mmtm) REVERT: g 497 ILE cc_start: 0.8720 (tp) cc_final: 0.8483 (tp) REVERT: g 509 MET cc_start: 0.8956 (mmm) cc_final: 0.8623 (mmt) REVERT: g 540 PHE cc_start: 0.7705 (p90) cc_final: 0.6902 (p90) REVERT: g 544 ILE cc_start: 0.8335 (mm) cc_final: 0.7906 (mm) REVERT: g 564 VAL cc_start: 0.9332 (t) cc_final: 0.9047 (t) REVERT: g 567 GLN cc_start: 0.9099 (mt0) cc_final: 0.8222 (pt0) REVERT: g 575 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8535 (pt0) REVERT: g 580 LEU cc_start: 0.9239 (mt) cc_final: 0.8983 (mt) REVERT: G 44 MET cc_start: 0.7325 (mmp) cc_final: 0.7065 (mmm) REVERT: G 115 ASN cc_start: 0.8709 (t0) cc_final: 0.8473 (t0) REVERT: G 123 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8594 (tp-100) REVERT: G 127 LYS cc_start: 0.9410 (tmtt) cc_final: 0.9049 (tmmt) REVERT: G 173 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8574 (mm-30) REVERT: G 176 LEU cc_start: 0.9374 (mm) cc_final: 0.8936 (pp) REVERT: G 234 MET cc_start: 0.2727 (ttm) cc_final: -0.0411 (ptm) REVERT: G 357 VAL cc_start: 0.5181 (m) cc_final: 0.4749 (p) REVERT: G 497 ILE cc_start: 0.8939 (tp) cc_final: 0.8585 (tp) REVERT: G 502 TYR cc_start: 0.8403 (t80) cc_final: 0.7926 (t80) REVERT: G 507 ASP cc_start: 0.9324 (m-30) cc_final: 0.8860 (m-30) REVERT: G 510 GLU cc_start: 0.8634 (pp20) cc_final: 0.8251 (pp20) REVERT: G 511 CYS cc_start: 0.9150 (t) cc_final: 0.8660 (t) REVERT: G 512 ILE cc_start: 0.9268 (mm) cc_final: 0.8762 (mm) REVERT: G 519 ASN cc_start: 0.8707 (m-40) cc_final: 0.8448 (t0) REVERT: h 70 LEU cc_start: 0.9301 (tp) cc_final: 0.9008 (tp) REVERT: h 87 SER cc_start: 0.8749 (t) cc_final: 0.8486 (p) REVERT: h 109 MET cc_start: 0.8322 (mtp) cc_final: 0.8117 (mtp) REVERT: h 126 MET cc_start: 0.8996 (ttm) cc_final: 0.8761 (ttm) REVERT: h 143 LEU cc_start: 0.9118 (mt) cc_final: 0.8802 (mt) REVERT: h 166 MET cc_start: 0.7160 (mtt) cc_final: 0.6317 (mtp) REVERT: h 171 ILE cc_start: 0.5030 (pt) cc_final: 0.4419 (pt) REVERT: h 362 TYR cc_start: 0.7505 (m-10) cc_final: 0.7302 (m-10) REVERT: h 440 ASN cc_start: 0.9529 (t0) cc_final: 0.9295 (t0) REVERT: h 447 GLU cc_start: 0.8951 (pp20) cc_final: 0.8515 (tm-30) REVERT: h 451 ARG cc_start: 0.9595 (tpp80) cc_final: 0.9054 (tpp80) REVERT: h 465 LEU cc_start: 0.8950 (mm) cc_final: 0.8729 (mp) REVERT: h 507 LEU cc_start: 0.9084 (mm) cc_final: 0.8422 (tp) REVERT: h 508 ASN cc_start: 0.9291 (m-40) cc_final: 0.9014 (m110) REVERT: H 98 THR cc_start: 0.9391 (p) cc_final: 0.8299 (t) REVERT: H 116 LEU cc_start: 0.8162 (tp) cc_final: 0.7815 (tp) REVERT: H 135 LEU cc_start: 0.8640 (mt) cc_final: 0.7844 (mt) REVERT: H 138 GLU cc_start: 0.9344 (tt0) cc_final: 0.9011 (pt0) REVERT: H 166 MET cc_start: 0.5517 (mmp) cc_final: 0.4893 (mmp) REVERT: H 306 PHE cc_start: 0.8335 (t80) cc_final: 0.7778 (m-10) REVERT: H 418 MET cc_start: 0.8366 (ttt) cc_final: 0.7667 (ttp) REVERT: H 444 LYS cc_start: 0.9024 (tttt) cc_final: 0.8786 (tptt) REVERT: H 449 ILE cc_start: 0.9204 (mp) cc_final: 0.8979 (mp) REVERT: H 508 ASN cc_start: 0.9128 (m-40) cc_final: 0.8502 (m110) REVERT: q 39 HIS cc_start: 0.8975 (t-170) cc_final: 0.8383 (t-170) REVERT: q 41 MET cc_start: 0.7842 (tmm) cc_final: 0.7594 (tmm) REVERT: q 49 CYS cc_start: 0.8518 (m) cc_final: 0.7310 (m) REVERT: q 52 ASN cc_start: 0.8894 (m-40) cc_final: 0.7911 (t0) REVERT: q 87 MET cc_start: 0.9088 (mtm) cc_final: 0.8704 (mmt) REVERT: q 94 ILE cc_start: 0.8757 (pt) cc_final: 0.8340 (pt) REVERT: q 96 MET cc_start: 0.8294 (ptp) cc_final: 0.6787 (ttm) REVERT: q 114 SER cc_start: 0.8879 (m) cc_final: 0.8593 (m) REVERT: q 115 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7796 (tm-30) REVERT: q 127 ILE cc_start: 0.9628 (mt) cc_final: 0.9230 (mt) REVERT: q 131 TYR cc_start: 0.8572 (m-10) cc_final: 0.8178 (m-10) REVERT: q 144 GLU cc_start: 0.8616 (pp20) cc_final: 0.8058 (mp0) REVERT: q 174 SER cc_start: 0.8805 (m) cc_final: 0.8338 (t) REVERT: q 226 MET cc_start: 0.4860 (mmp) cc_final: 0.1039 (tpt) REVERT: q 361 MET cc_start: 0.7662 (mtt) cc_final: 0.7209 (ttt) REVERT: q 452 PHE cc_start: 0.9057 (t80) cc_final: 0.8854 (t80) REVERT: q 456 PHE cc_start: 0.9100 (m-10) cc_final: 0.8632 (m-80) REVERT: q 466 THR cc_start: 0.9615 (p) cc_final: 0.9398 (t) REVERT: q 520 MET cc_start: 0.6886 (tpp) cc_final: 0.6575 (tpp) REVERT: q 521 LEU cc_start: 0.8841 (tt) cc_final: 0.8514 (tp) REVERT: q 533 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8933 (tm-30) REVERT: q 546 MET cc_start: 0.7784 (mmt) cc_final: 0.7451 (mmp) REVERT: Q 27 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6156 (pp30) REVERT: Q 36 ARG cc_start: 0.9450 (ttt180) cc_final: 0.9215 (ttp80) REVERT: Q 83 LYS cc_start: 0.9389 (mmtt) cc_final: 0.9188 (mmmt) REVERT: Q 109 GLU cc_start: 0.9403 (tp30) cc_final: 0.9085 (tp30) REVERT: Q 133 MET cc_start: 0.9581 (tpp) cc_final: 0.9279 (tpt) REVERT: Q 155 ASP cc_start: 0.8652 (t70) cc_final: 0.8395 (t70) REVERT: Q 230 ARG cc_start: 0.1617 (mtp85) cc_final: 0.1163 (mmp-170) REVERT: Q 380 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7557 (tpt170) REVERT: Q 437 TYR cc_start: 0.7356 (m-80) cc_final: 0.6942 (m-80) REVERT: Q 470 ASP cc_start: 0.8792 (t0) cc_final: 0.8388 (t70) REVERT: Q 473 GLU cc_start: 0.9113 (pt0) cc_final: 0.8332 (pt0) REVERT: Q 497 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7986 (mmtm) REVERT: Q 533 GLU cc_start: 0.9396 (mm-30) cc_final: 0.8952 (tm-30) REVERT: z 36 ASN cc_start: 0.9245 (p0) cc_final: 0.8867 (p0) REVERT: z 40 LYS cc_start: 0.9093 (mmpt) cc_final: 0.8861 (mmmt) REVERT: z 83 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8156 (tm-30) REVERT: z 92 THR cc_start: 0.7277 (p) cc_final: 0.6962 (p) REVERT: z 130 MET cc_start: 0.9368 (mmp) cc_final: 0.9113 (mmm) REVERT: z 152 GLN cc_start: 0.8638 (mt0) cc_final: 0.8081 (mm110) REVERT: z 198 GLN cc_start: 0.8637 (pp30) cc_final: 0.8267 (pp30) REVERT: z 201 HIS cc_start: 0.9037 (m-70) cc_final: 0.8785 (m90) REVERT: z 215 LEU cc_start: 0.8102 (tp) cc_final: 0.7717 (tp) REVERT: z 390 GLN cc_start: 0.9038 (tt0) cc_final: 0.8498 (tp-100) REVERT: z 472 MET cc_start: 0.8613 (ttp) cc_final: 0.8331 (tmm) REVERT: z 526 ASN cc_start: 0.9385 (m-40) cc_final: 0.9077 (m-40) REVERT: z 529 LEU cc_start: 0.8871 (mt) cc_final: 0.8588 (mt) REVERT: z 531 ASP cc_start: 0.6800 (m-30) cc_final: 0.5892 (m-30) REVERT: Z 37 LEU cc_start: 0.8029 (tp) cc_final: 0.7714 (tp) REVERT: Z 106 HIS cc_start: 0.8318 (t70) cc_final: 0.8112 (t-90) REVERT: Z 118 ILE cc_start: 0.8389 (mt) cc_final: 0.7859 (mt) REVERT: Z 119 THR cc_start: 0.9495 (t) cc_final: 0.9052 (p) REVERT: Z 128 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8767 (tp30) REVERT: Z 136 PHE cc_start: 0.8136 (t80) cc_final: 0.7549 (t80) REVERT: Z 168 GLU cc_start: 0.9606 (mp0) cc_final: 0.9361 (pm20) REVERT: Z 176 ASP cc_start: 0.8568 (m-30) cc_final: 0.8246 (m-30) REVERT: Z 193 MET cc_start: 0.8123 (mtt) cc_final: 0.7191 (mtm) REVERT: Z 282 ASN cc_start: 0.8465 (m-40) cc_final: 0.8235 (p0) REVERT: Z 366 TYR cc_start: 0.7133 (m-80) cc_final: 0.6700 (m-80) REVERT: Z 376 CYS cc_start: 0.8521 (m) cc_final: 0.8209 (m) REVERT: Z 393 ASP cc_start: 0.9634 (m-30) cc_final: 0.9247 (m-30) REVERT: Z 404 ASN cc_start: 0.9531 (m-40) cc_final: 0.9277 (m110) REVERT: Z 418 PHE cc_start: 0.9187 (t80) cc_final: 0.8829 (t80) REVERT: Z 439 LYS cc_start: 0.9166 (mppt) cc_final: 0.8953 (mttm) REVERT: Z 468 ASP cc_start: 0.9253 (t0) cc_final: 0.8614 (p0) REVERT: Z 504 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8461 (mm-30) REVERT: Z 515 ASN cc_start: 0.9546 (m-40) cc_final: 0.9304 (t0) REVERT: Z 523 ILE cc_start: 0.9671 (mm) cc_final: 0.9422 (mm) REVERT: Z 533 LEU cc_start: 0.8964 (mm) cc_final: 0.8676 (mt) outliers start: 10 outliers final: 2 residues processed: 1641 average time/residue: 0.5876 time to fit residues: 1627.8569 Evaluate side-chains 1175 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1172 time to evaluate : 5.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 405 optimal weight: 0.9980 chunk 226 optimal weight: 0.8980 chunk 607 optimal weight: 7.9990 chunk 497 optimal weight: 0.0570 chunk 201 optimal weight: 0.9980 chunk 731 optimal weight: 9.9990 chunk 790 optimal weight: 0.9980 chunk 651 optimal weight: 0.0670 chunk 725 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 586 optimal weight: 0.3980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 141 ASN B 420 GLN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 GLN d 284 ASN D 112 ASN D 284 ASN ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 251 HIS ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN g 85 GLN ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 HIS g 455 ASN g 519 ASN g 530 GLN g 567 GLN G 106 GLN G 568 GLN h 406 ASN ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN H 268 GLN H 328 GLN H 526 ASN q 132 ASN q 482 HIS ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 298 GLN ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 GLN ** Z 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 142 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 62618 Z= 0.165 Angle : 0.563 11.147 84459 Z= 0.290 Chirality : 0.044 0.309 10166 Planarity : 0.003 0.071 10848 Dihedral : 3.505 26.691 8568 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.22 % Favored : 97.73 % Rotamer: Outliers : 0.07 % Allowed : 2.41 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.09), residues: 8065 helix: -0.36 (0.08), residues: 3872 sheet: -0.44 (0.19), residues: 625 loop : -0.78 (0.10), residues: 3568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 325 HIS 0.013 0.001 HIS B 155 PHE 0.021 0.001 PHE b 433 TYR 0.023 0.001 TYR e 381 ARG 0.010 0.000 ARG g 582 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1474 time to evaluate : 5.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 LYS cc_start: 0.8856 (pttm) cc_final: 0.8644 (ptpp) REVERT: a 44 LEU cc_start: 0.9458 (tp) cc_final: 0.9245 (tp) REVERT: a 73 LEU cc_start: 0.8801 (mt) cc_final: 0.8076 (mt) REVERT: a 81 LYS cc_start: 0.9603 (mttt) cc_final: 0.9360 (mttp) REVERT: a 108 LEU cc_start: 0.9595 (mt) cc_final: 0.9312 (mt) REVERT: a 109 LEU cc_start: 0.8976 (mt) cc_final: 0.8731 (mt) REVERT: a 135 GLU cc_start: 0.8396 (tp30) cc_final: 0.7155 (tp30) REVERT: a 142 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8772 (pp20) REVERT: a 179 MET cc_start: 0.7552 (mtp) cc_final: 0.7073 (ptt) REVERT: a 399 GLU cc_start: 0.6887 (tt0) cc_final: 0.6452 (pp20) REVERT: a 433 LEU cc_start: 0.9499 (mt) cc_final: 0.9299 (mp) REVERT: a 448 ILE cc_start: 0.9219 (mt) cc_final: 0.8881 (tt) REVERT: a 460 LYS cc_start: 0.8666 (tptt) cc_final: 0.8264 (tptt) REVERT: a 469 ASP cc_start: 0.8381 (t0) cc_final: 0.7486 (t70) REVERT: a 472 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8797 (mm-30) REVERT: a 497 TYR cc_start: 0.7889 (m-80) cc_final: 0.7609 (m-80) REVERT: a 530 SER cc_start: 0.9473 (m) cc_final: 0.9254 (p) REVERT: a 532 LEU cc_start: 0.9410 (mm) cc_final: 0.8835 (tt) REVERT: a 542 ASP cc_start: 0.8658 (m-30) cc_final: 0.6598 (m-30) REVERT: A 111 ARG cc_start: 0.9142 (mmt180) cc_final: 0.8858 (tpp80) REVERT: A 119 LYS cc_start: 0.9319 (mppt) cc_final: 0.9117 (mmtm) REVERT: A 131 VAL cc_start: 0.9455 (t) cc_final: 0.9118 (t) REVERT: A 204 ASN cc_start: 0.7801 (t0) cc_final: 0.7557 (m110) REVERT: A 233 MET cc_start: 0.0619 (mtm) cc_final: -0.1119 (ptt) REVERT: A 307 LEU cc_start: 0.4608 (mt) cc_final: 0.4288 (pp) REVERT: A 320 ARG cc_start: 0.8739 (mtt180) cc_final: 0.8487 (mtt90) REVERT: A 533 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8913 (mm-30) REVERT: b 45 LEU cc_start: 0.8870 (tp) cc_final: 0.8349 (pp) REVERT: b 46 LEU cc_start: 0.8994 (mm) cc_final: 0.8743 (mm) REVERT: b 59 ASP cc_start: 0.8695 (t0) cc_final: 0.8301 (t0) REVERT: b 135 LEU cc_start: 0.9498 (mt) cc_final: 0.9089 (mt) REVERT: b 148 MET cc_start: 0.8542 (ppp) cc_final: 0.8281 (ppp) REVERT: b 158 LYS cc_start: 0.9480 (mttt) cc_final: 0.9264 (mmmt) REVERT: b 347 MET cc_start: 0.7122 (mmm) cc_final: 0.6635 (tmm) REVERT: b 384 LEU cc_start: 0.9492 (tp) cc_final: 0.9185 (mt) REVERT: b 409 MET cc_start: 0.9222 (tpp) cc_final: 0.8950 (ttm) REVERT: b 439 GLN cc_start: 0.8941 (mm110) cc_final: 0.8422 (mp10) REVERT: B 44 LYS cc_start: 0.7554 (tptp) cc_final: 0.6904 (mmmt) REVERT: B 75 LYS cc_start: 0.8441 (mttt) cc_final: 0.7806 (tttt) REVERT: B 79 ASN cc_start: 0.9057 (m-40) cc_final: 0.8745 (m-40) REVERT: B 155 HIS cc_start: 0.9120 (m90) cc_final: 0.8809 (m90) REVERT: B 354 LEU cc_start: 0.4056 (mt) cc_final: 0.3438 (mt) REVERT: B 409 MET cc_start: 0.9397 (tpp) cc_final: 0.9077 (ttm) REVERT: B 435 ARG cc_start: 0.9122 (mtm180) cc_final: 0.8862 (ptm160) REVERT: B 452 SER cc_start: 0.8861 (p) cc_final: 0.8303 (t) REVERT: B 472 LEU cc_start: 0.8850 (mt) cc_final: 0.8502 (mt) REVERT: d 209 MET cc_start: 0.3268 (mtm) cc_final: 0.2974 (ttp) REVERT: d 284 ASN cc_start: 0.7686 (m-40) cc_final: 0.7466 (m110) REVERT: d 311 MET cc_start: 0.1868 (mmm) cc_final: 0.1570 (mmm) REVERT: d 315 ASP cc_start: 0.2745 (m-30) cc_final: 0.2303 (t70) REVERT: d 433 GLU cc_start: 0.8082 (pm20) cc_final: 0.7350 (tp30) REVERT: d 464 LYS cc_start: 0.9635 (mmmt) cc_final: 0.9333 (mmmm) REVERT: d 513 GLU cc_start: 0.9536 (mm-30) cc_final: 0.8663 (mm-30) REVERT: d 516 LYS cc_start: 0.9321 (mtpp) cc_final: 0.8962 (mttm) REVERT: D 137 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8487 (tm-30) REVERT: D 138 MET cc_start: 0.7064 (ptp) cc_final: 0.6816 (mmt) REVERT: D 209 MET cc_start: 0.3125 (mmt) cc_final: 0.2846 (mmt) REVERT: D 304 PHE cc_start: 0.7093 (m-10) cc_final: 0.6148 (t80) REVERT: D 385 MET cc_start: 0.6125 (ppp) cc_final: 0.5304 (tpp) REVERT: D 513 GLU cc_start: 0.9212 (mp0) cc_final: 0.8783 (mp0) REVERT: e 94 MET cc_start: 0.6704 (tpt) cc_final: 0.6277 (tpt) REVERT: e 107 LEU cc_start: 0.9437 (tp) cc_final: 0.9190 (tp) REVERT: e 113 ASP cc_start: 0.8541 (m-30) cc_final: 0.7582 (p0) REVERT: e 129 LEU cc_start: 0.9639 (mm) cc_final: 0.9404 (mm) REVERT: e 131 ASP cc_start: 0.8945 (t70) cc_final: 0.8657 (m-30) REVERT: e 151 ASP cc_start: 0.9326 (t0) cc_final: 0.8863 (m-30) REVERT: e 202 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7997 (tp30) REVERT: e 203 MET cc_start: 0.3130 (tmm) cc_final: 0.1987 (ptt) REVERT: e 210 ASN cc_start: 0.8719 (m-40) cc_final: 0.8171 (t0) REVERT: e 464 ILE cc_start: 0.8728 (mt) cc_final: 0.8443 (mt) REVERT: e 482 THR cc_start: 0.9211 (m) cc_final: 0.8992 (p) REVERT: e 492 ILE cc_start: 0.8655 (mt) cc_final: 0.8348 (mm) REVERT: e 495 LEU cc_start: 0.8983 (tp) cc_final: 0.8456 (mt) REVERT: E 63 THR cc_start: 0.9387 (p) cc_final: 0.9108 (t) REVERT: E 102 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8941 (mmtt) REVERT: E 103 LEU cc_start: 0.9330 (mp) cc_final: 0.9100 (mp) REVERT: E 106 GLN cc_start: 0.9270 (mt0) cc_final: 0.8907 (pp30) REVERT: E 107 LEU cc_start: 0.9177 (mt) cc_final: 0.8965 (mt) REVERT: E 226 MET cc_start: 0.5392 (pmm) cc_final: 0.4104 (pmm) REVERT: E 254 MET cc_start: 0.0435 (mtt) cc_final: -0.1669 (ttt) REVERT: E 392 MET cc_start: 0.7371 (mpp) cc_final: 0.7163 (mmp) REVERT: E 481 MET cc_start: 0.9188 (mmm) cc_final: 0.8863 (tpt) REVERT: E 491 PRO cc_start: 0.9461 (Cg_endo) cc_final: 0.9211 (Cg_exo) REVERT: E 522 MET cc_start: 0.8638 (ttm) cc_final: 0.8198 (ttt) REVERT: E 526 PHE cc_start: 0.6318 (m-10) cc_final: 0.6078 (m-10) REVERT: E 547 MET cc_start: 0.9178 (mtp) cc_final: 0.8917 (tmm) REVERT: E 548 ILE cc_start: 0.9219 (tp) cc_final: 0.8885 (tt) REVERT: E 553 ASN cc_start: 0.8325 (t0) cc_final: 0.7669 (t0) REVERT: E 555 ILE cc_start: 0.8574 (mm) cc_final: 0.8086 (mm) REVERT: g 24 ASN cc_start: 0.9303 (m-40) cc_final: 0.8956 (t0) REVERT: g 44 MET cc_start: 0.8980 (mpp) cc_final: 0.8004 (mmm) REVERT: g 102 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8301 (mm-30) REVERT: g 110 TYR cc_start: 0.8479 (m-80) cc_final: 0.8135 (m-80) REVERT: g 113 GLU cc_start: 0.9147 (pp20) cc_final: 0.8943 (pp20) REVERT: g 117 HIS cc_start: 0.8108 (t-90) cc_final: 0.7533 (t-90) REVERT: g 133 LEU cc_start: 0.9479 (mt) cc_final: 0.9234 (mt) REVERT: g 163 TYR cc_start: 0.6568 (t80) cc_final: 0.6290 (t80) REVERT: g 173 GLU cc_start: 0.9075 (tt0) cc_final: 0.8775 (mm-30) REVERT: g 440 MET cc_start: 0.5524 (pmm) cc_final: 0.5209 (pmm) REVERT: g 487 LEU cc_start: 0.9279 (mt) cc_final: 0.9060 (mt) REVERT: g 492 LYS cc_start: 0.8246 (mmtm) cc_final: 0.7669 (mmtm) REVERT: g 497 ILE cc_start: 0.8713 (tp) cc_final: 0.8392 (tp) REVERT: g 540 PHE cc_start: 0.7785 (p90) cc_final: 0.7106 (p90) REVERT: g 544 ILE cc_start: 0.8611 (mm) cc_final: 0.8125 (mm) REVERT: g 564 VAL cc_start: 0.9366 (t) cc_final: 0.8985 (t) REVERT: g 567 GLN cc_start: 0.8987 (mt0) cc_final: 0.7961 (pt0) REVERT: g 568 GLN cc_start: 0.9301 (mm-40) cc_final: 0.8921 (mm110) REVERT: g 571 LYS cc_start: 0.9310 (ptpp) cc_final: 0.8481 (ptpt) REVERT: g 575 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8754 (pt0) REVERT: G 44 MET cc_start: 0.7621 (mmp) cc_final: 0.7354 (mmm) REVERT: G 52 MET cc_start: 0.8447 (tmm) cc_final: 0.8171 (tmm) REVERT: G 117 HIS cc_start: 0.9090 (t-90) cc_final: 0.8810 (t-90) REVERT: G 123 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8544 (tp-100) REVERT: G 127 LYS cc_start: 0.9348 (tmtt) cc_final: 0.8910 (tmmt) REVERT: G 173 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8488 (mm-30) REVERT: G 234 MET cc_start: 0.2679 (ttm) cc_final: -0.0542 (ptm) REVERT: G 357 VAL cc_start: 0.4528 (m) cc_final: 0.4141 (p) REVERT: G 502 TYR cc_start: 0.8161 (t80) cc_final: 0.7855 (t80) REVERT: G 507 ASP cc_start: 0.9318 (m-30) cc_final: 0.8752 (m-30) REVERT: G 511 CYS cc_start: 0.9198 (t) cc_final: 0.8740 (t) REVERT: G 512 ILE cc_start: 0.9053 (mm) cc_final: 0.8791 (mm) REVERT: G 519 ASN cc_start: 0.8838 (m-40) cc_final: 0.8487 (t0) REVERT: G 571 LYS cc_start: 0.9203 (mttp) cc_final: 0.8735 (mttp) REVERT: h 64 ASN cc_start: 0.6773 (t0) cc_final: 0.6569 (t0) REVERT: h 70 LEU cc_start: 0.9353 (tp) cc_final: 0.8810 (pp) REVERT: h 126 MET cc_start: 0.8735 (ttm) cc_final: 0.8356 (tmm) REVERT: h 355 MET cc_start: 0.3147 (ptt) cc_final: 0.2914 (ptp) REVERT: h 362 TYR cc_start: 0.7587 (m-10) cc_final: 0.7274 (m-10) REVERT: h 440 ASN cc_start: 0.9599 (t0) cc_final: 0.9362 (t0) REVERT: h 451 ARG cc_start: 0.9607 (tpp80) cc_final: 0.9261 (tpp80) REVERT: h 465 LEU cc_start: 0.9221 (mm) cc_final: 0.8981 (tt) REVERT: h 466 ASN cc_start: 0.8829 (m-40) cc_final: 0.8472 (m-40) REVERT: h 504 ILE cc_start: 0.9538 (mt) cc_final: 0.9200 (tp) REVERT: H 109 MET cc_start: 0.9603 (mmp) cc_final: 0.9376 (mmp) REVERT: H 135 LEU cc_start: 0.8782 (mt) cc_final: 0.8121 (mp) REVERT: H 166 MET cc_start: 0.5447 (mmp) cc_final: 0.4987 (mmp) REVERT: H 202 LYS cc_start: 0.7936 (mmpt) cc_final: 0.7435 (mmtm) REVERT: H 306 PHE cc_start: 0.8614 (t80) cc_final: 0.7721 (m-80) REVERT: H 402 ARG cc_start: 0.9299 (mpt180) cc_final: 0.8819 (mmt90) REVERT: H 418 MET cc_start: 0.8470 (ttt) cc_final: 0.7829 (ptm) REVERT: H 449 ILE cc_start: 0.9285 (mp) cc_final: 0.9061 (mp) REVERT: H 477 LYS cc_start: 0.7838 (pttm) cc_final: 0.7496 (pptt) REVERT: H 508 ASN cc_start: 0.9145 (m-40) cc_final: 0.8501 (m110) REVERT: q 39 HIS cc_start: 0.8843 (t-170) cc_final: 0.8298 (t70) REVERT: q 41 MET cc_start: 0.8295 (tmm) cc_final: 0.7834 (tmm) REVERT: q 49 CYS cc_start: 0.8471 (m) cc_final: 0.7822 (m) REVERT: q 52 ASN cc_start: 0.8875 (m-40) cc_final: 0.7552 (t0) REVERT: q 87 MET cc_start: 0.9141 (mtm) cc_final: 0.8833 (mmt) REVERT: q 94 ILE cc_start: 0.8602 (pt) cc_final: 0.8291 (pt) REVERT: q 115 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7916 (tm-30) REVERT: q 128 ILE cc_start: 0.9451 (mt) cc_final: 0.9164 (mt) REVERT: q 144 GLU cc_start: 0.8464 (pp20) cc_final: 0.8169 (mp0) REVERT: q 153 LYS cc_start: 0.7482 (tptt) cc_final: 0.7191 (tptp) REVERT: q 155 ASP cc_start: 0.8471 (t70) cc_final: 0.8203 (t0) REVERT: q 174 SER cc_start: 0.8807 (m) cc_final: 0.8343 (t) REVERT: q 213 MET cc_start: 0.1867 (mmp) cc_final: 0.0547 (mmm) REVERT: q 226 MET cc_start: 0.4425 (mmp) cc_final: 0.0908 (tpt) REVERT: q 361 MET cc_start: 0.7656 (mtt) cc_final: 0.7267 (ttt) REVERT: q 452 PHE cc_start: 0.9068 (t80) cc_final: 0.8733 (t80) REVERT: q 456 PHE cc_start: 0.9174 (m-10) cc_final: 0.8685 (m-80) REVERT: q 521 LEU cc_start: 0.8879 (tt) cc_final: 0.8644 (tt) REVERT: q 525 LYS cc_start: 0.9315 (ptpt) cc_final: 0.8992 (mtmm) REVERT: q 533 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8959 (tm-30) REVERT: q 546 MET cc_start: 0.7691 (mmt) cc_final: 0.7407 (mmp) REVERT: Q 30 LYS cc_start: 0.8696 (pttm) cc_final: 0.8319 (ptpt) REVERT: Q 41 MET cc_start: 0.8428 (tmm) cc_final: 0.8133 (tmm) REVERT: Q 83 LYS cc_start: 0.9410 (mmmt) cc_final: 0.9019 (mmmm) REVERT: Q 103 VAL cc_start: 0.9468 (p) cc_final: 0.9167 (t) REVERT: Q 109 GLU cc_start: 0.9355 (tp30) cc_final: 0.9103 (tp30) REVERT: Q 155 ASP cc_start: 0.8634 (t70) cc_final: 0.8402 (t70) REVERT: Q 230 ARG cc_start: 0.1467 (mtp85) cc_final: 0.1002 (mmp-170) REVERT: Q 361 MET cc_start: 0.7805 (ppp) cc_final: 0.7383 (ptt) REVERT: Q 380 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7547 (tpt170) REVERT: Q 457 GLU cc_start: 0.9090 (mp0) cc_final: 0.8876 (mp0) REVERT: Q 470 ASP cc_start: 0.8685 (t0) cc_final: 0.8355 (t70) REVERT: Q 473 GLU cc_start: 0.9126 (pt0) cc_final: 0.8396 (pt0) REVERT: Q 533 GLU cc_start: 0.9365 (mm-30) cc_final: 0.8947 (tm-30) REVERT: Q 545 ILE cc_start: 0.8555 (mm) cc_final: 0.8216 (mm) REVERT: z 36 ASN cc_start: 0.9210 (p0) cc_final: 0.8952 (p0) REVERT: z 40 LYS cc_start: 0.9122 (mmpt) cc_final: 0.8844 (mmmt) REVERT: z 83 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8006 (tm-30) REVERT: z 92 THR cc_start: 0.6810 (p) cc_final: 0.6317 (p) REVERT: z 128 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8485 (tt0) REVERT: z 130 MET cc_start: 0.9313 (mmp) cc_final: 0.8994 (mmm) REVERT: z 152 GLN cc_start: 0.8654 (mt0) cc_final: 0.8200 (mm-40) REVERT: z 185 GLN cc_start: 0.8316 (tt0) cc_final: 0.7999 (mp10) REVERT: z 201 HIS cc_start: 0.8981 (m-70) cc_final: 0.8750 (m90) REVERT: z 215 LEU cc_start: 0.8077 (tp) cc_final: 0.7693 (tp) REVERT: z 330 LEU cc_start: 0.8855 (tp) cc_final: 0.8504 (mp) REVERT: z 390 GLN cc_start: 0.9074 (tt0) cc_final: 0.8424 (tp-100) REVERT: z 412 ILE cc_start: 0.9491 (mm) cc_final: 0.9135 (mm) REVERT: z 445 GLU cc_start: 0.9065 (mp0) cc_final: 0.8800 (mm-30) REVERT: z 523 ILE cc_start: 0.9420 (tp) cc_final: 0.9202 (tp) REVERT: z 526 ASN cc_start: 0.9328 (m-40) cc_final: 0.9039 (m-40) REVERT: Z 37 LEU cc_start: 0.7869 (tp) cc_final: 0.6894 (tp) REVERT: Z 108 PHE cc_start: 0.8972 (m-80) cc_final: 0.8499 (m-80) REVERT: Z 111 GLU cc_start: 0.7753 (pt0) cc_final: 0.7487 (mp0) REVERT: Z 118 ILE cc_start: 0.8685 (mt) cc_final: 0.8367 (mm) REVERT: Z 119 THR cc_start: 0.9483 (t) cc_final: 0.9175 (p) REVERT: Z 128 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8761 (tp30) REVERT: Z 136 PHE cc_start: 0.8382 (t80) cc_final: 0.7400 (t80) REVERT: Z 168 GLU cc_start: 0.9572 (mp0) cc_final: 0.9223 (pm20) REVERT: Z 176 ASP cc_start: 0.8522 (m-30) cc_final: 0.8287 (m-30) REVERT: Z 189 LEU cc_start: 0.8224 (tp) cc_final: 0.7941 (tp) REVERT: Z 282 ASN cc_start: 0.8422 (m-40) cc_final: 0.8102 (p0) REVERT: Z 366 TYR cc_start: 0.7014 (m-80) cc_final: 0.6575 (m-10) REVERT: Z 393 ASP cc_start: 0.9358 (m-30) cc_final: 0.9127 (p0) REVERT: Z 404 ASN cc_start: 0.9538 (m-40) cc_final: 0.9213 (m110) REVERT: Z 418 PHE cc_start: 0.8890 (t80) cc_final: 0.8687 (t80) REVERT: Z 465 ASP cc_start: 0.9313 (t0) cc_final: 0.8636 (t0) REVERT: Z 468 ASP cc_start: 0.9224 (t0) cc_final: 0.8731 (p0) REVERT: Z 482 ASP cc_start: 0.8549 (m-30) cc_final: 0.8312 (m-30) REVERT: Z 504 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8482 (mm-30) REVERT: Z 523 ILE cc_start: 0.9653 (mm) cc_final: 0.9376 (mm) REVERT: Z 533 LEU cc_start: 0.8879 (mm) cc_final: 0.8584 (mt) outliers start: 5 outliers final: 1 residues processed: 1477 average time/residue: 0.5645 time to fit residues: 1420.0487 Evaluate side-chains 1125 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1124 time to evaluate : 5.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 722 optimal weight: 10.0000 chunk 549 optimal weight: 0.9990 chunk 379 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 349 optimal weight: 8.9990 chunk 491 optimal weight: 9.9990 chunk 734 optimal weight: 0.9990 chunk 777 optimal weight: 10.0000 chunk 383 optimal weight: 7.9990 chunk 695 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 89 GLN a 113 ASN a 141 ASN ** a 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 465 ASN A 113 ASN b 172 HIS ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN D 284 ASN D 436 GLN ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 251 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 HIS g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 567 GLN G 231 HIS h 174 ASN ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 GLN H 245 ASN H 436 GLN H 452 GLN H 526 ASN ** q 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 ASN q 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 329 GLN ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 62618 Z= 0.263 Angle : 0.645 14.618 84459 Z= 0.334 Chirality : 0.045 0.467 10166 Planarity : 0.004 0.068 10848 Dihedral : 3.757 25.736 8568 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 0.13 % Allowed : 2.31 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.09), residues: 8065 helix: 0.09 (0.08), residues: 3912 sheet: -0.33 (0.19), residues: 610 loop : -0.73 (0.10), residues: 3543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 440 HIS 0.008 0.001 HIS E 142 PHE 0.022 0.002 PHE Z 309 TYR 0.031 0.002 TYR B 124 ARG 0.019 0.001 ARG Q 334 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1414 time to evaluate : 5.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 44 LEU cc_start: 0.9460 (tp) cc_final: 0.9192 (tp) REVERT: a 73 LEU cc_start: 0.8840 (mt) cc_final: 0.8092 (mt) REVERT: a 81 LYS cc_start: 0.9612 (mttt) cc_final: 0.9387 (mptt) REVERT: a 109 LEU cc_start: 0.8999 (mt) cc_final: 0.8798 (mt) REVERT: a 142 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8824 (tm-30) REVERT: a 359 ASP cc_start: 0.7672 (m-30) cc_final: 0.7335 (p0) REVERT: a 399 GLU cc_start: 0.6748 (tt0) cc_final: 0.6310 (pp20) REVERT: a 448 ILE cc_start: 0.9334 (mt) cc_final: 0.9038 (tt) REVERT: a 450 GLU cc_start: 0.9376 (mm-30) cc_final: 0.8941 (mm-30) REVERT: a 451 PHE cc_start: 0.9444 (t80) cc_final: 0.9145 (t80) REVERT: a 460 LYS cc_start: 0.8842 (tptt) cc_final: 0.8582 (mmtt) REVERT: a 497 TYR cc_start: 0.8019 (m-80) cc_final: 0.7664 (m-80) REVERT: a 530 SER cc_start: 0.9569 (m) cc_final: 0.9225 (p) REVERT: a 532 LEU cc_start: 0.9463 (mm) cc_final: 0.8846 (tt) REVERT: A 52 MET cc_start: 0.5686 (tpt) cc_final: 0.5447 (tpt) REVERT: A 70 LEU cc_start: 0.9627 (tp) cc_final: 0.9409 (pp) REVERT: A 111 ARG cc_start: 0.9125 (mmt180) cc_final: 0.8544 (tpp80) REVERT: A 119 LYS cc_start: 0.9335 (mppt) cc_final: 0.9101 (mppt) REVERT: A 179 MET cc_start: 0.5215 (pmm) cc_final: 0.3760 (pmm) REVERT: A 204 ASN cc_start: 0.7861 (t0) cc_final: 0.7592 (m110) REVERT: A 233 MET cc_start: 0.2203 (mtm) cc_final: 0.1034 (ptm) REVERT: A 307 LEU cc_start: 0.4660 (mt) cc_final: 0.4345 (pp) REVERT: A 398 MET cc_start: 0.6946 (ttt) cc_final: 0.6329 (ptm) REVERT: A 448 ILE cc_start: 0.9473 (mm) cc_final: 0.9246 (mt) REVERT: A 469 ASP cc_start: 0.8906 (t0) cc_final: 0.8700 (t0) REVERT: A 502 LEU cc_start: 0.8426 (mt) cc_final: 0.7827 (mt) REVERT: A 518 LEU cc_start: 0.8971 (mm) cc_final: 0.8700 (mm) REVERT: A 533 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8895 (mm-30) REVERT: b 45 LEU cc_start: 0.9330 (tp) cc_final: 0.8572 (pp) REVERT: b 46 LEU cc_start: 0.9246 (mm) cc_final: 0.8784 (mm) REVERT: b 59 ASP cc_start: 0.8887 (t0) cc_final: 0.8467 (t0) REVERT: b 121 ILE cc_start: 0.8985 (mt) cc_final: 0.8492 (mt) REVERT: b 148 MET cc_start: 0.8722 (ppp) cc_final: 0.8011 (ppp) REVERT: b 158 LYS cc_start: 0.9426 (mttt) cc_final: 0.9105 (mmmt) REVERT: b 347 MET cc_start: 0.7275 (mmm) cc_final: 0.6661 (tmm) REVERT: b 388 LEU cc_start: 0.9726 (tp) cc_final: 0.9391 (pp) REVERT: b 409 MET cc_start: 0.9332 (tpp) cc_final: 0.9129 (ttt) REVERT: b 431 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9049 (mm-30) REVERT: b 439 GLN cc_start: 0.9099 (mm110) cc_final: 0.8631 (mp10) REVERT: B 70 ASP cc_start: 0.5846 (p0) cc_final: 0.5600 (p0) REVERT: B 103 LEU cc_start: 0.9033 (mt) cc_final: 0.8825 (tp) REVERT: B 116 HIS cc_start: 0.8462 (t70) cc_final: 0.8180 (t-90) REVERT: B 155 HIS cc_start: 0.9298 (m90) cc_final: 0.9056 (m-70) REVERT: B 354 LEU cc_start: 0.4296 (mt) cc_final: 0.3521 (mt) REVERT: B 386 ASP cc_start: 0.8701 (m-30) cc_final: 0.7454 (t70) REVERT: B 409 MET cc_start: 0.9417 (tpp) cc_final: 0.9148 (ttm) REVERT: B 452 SER cc_start: 0.9293 (p) cc_final: 0.8884 (t) REVERT: B 472 LEU cc_start: 0.8759 (mt) cc_final: 0.8365 (mt) REVERT: B 476 ASN cc_start: 0.8970 (m-40) cc_final: 0.8148 (p0) REVERT: d 39 LEU cc_start: 0.8721 (tp) cc_final: 0.8497 (tp) REVERT: d 209 MET cc_start: 0.3175 (mtm) cc_final: 0.2542 (ttp) REVERT: d 311 MET cc_start: 0.2437 (mmm) cc_final: 0.1987 (mmm) REVERT: d 315 ASP cc_start: 0.3014 (m-30) cc_final: 0.2200 (t70) REVERT: d 433 GLU cc_start: 0.8393 (pm20) cc_final: 0.7759 (tp30) REVERT: d 464 LYS cc_start: 0.9700 (mmmt) cc_final: 0.9488 (mmmt) REVERT: d 513 GLU cc_start: 0.9588 (mm-30) cc_final: 0.8777 (mm-30) REVERT: d 516 LYS cc_start: 0.9479 (mtpp) cc_final: 0.8978 (mttm) REVERT: d 518 ILE cc_start: 0.8943 (mm) cc_final: 0.8729 (mm) REVERT: D 44 MET cc_start: 0.8512 (mpp) cc_final: 0.7956 (mpp) REVERT: D 133 ASP cc_start: 0.9405 (m-30) cc_final: 0.9130 (t0) REVERT: D 137 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8717 (tm-30) REVERT: D 138 MET cc_start: 0.7244 (ptp) cc_final: 0.6940 (mmt) REVERT: D 209 MET cc_start: 0.3525 (mmt) cc_final: 0.3054 (mmt) REVERT: D 304 PHE cc_start: 0.7262 (m-10) cc_final: 0.6231 (t80) REVERT: D 432 MET cc_start: 0.5323 (ppp) cc_final: 0.5012 (ppp) REVERT: D 436 GLN cc_start: 0.8314 (tt0) cc_final: 0.7920 (tt0) REVERT: D 470 ARG cc_start: 0.9185 (tpt90) cc_final: 0.8514 (tpt90) REVERT: D 509 THR cc_start: 0.9310 (t) cc_final: 0.9092 (t) REVERT: D 513 GLU cc_start: 0.9372 (mp0) cc_final: 0.8925 (mp0) REVERT: e 94 MET cc_start: 0.7137 (tpt) cc_final: 0.6889 (tpt) REVERT: e 107 LEU cc_start: 0.9436 (tp) cc_final: 0.9223 (tp) REVERT: e 109 LYS cc_start: 0.9511 (mmpt) cc_final: 0.9302 (mmmt) REVERT: e 113 ASP cc_start: 0.8522 (m-30) cc_final: 0.7616 (p0) REVERT: e 131 ASP cc_start: 0.9129 (t70) cc_final: 0.8765 (m-30) REVERT: e 132 GLN cc_start: 0.9206 (tp-100) cc_final: 0.8840 (tp40) REVERT: e 134 LEU cc_start: 0.8844 (tp) cc_final: 0.8499 (tp) REVERT: e 146 ILE cc_start: 0.9695 (mm) cc_final: 0.8412 (mm) REVERT: e 150 PHE cc_start: 0.8957 (m-10) cc_final: 0.8508 (m-80) REVERT: e 210 ASN cc_start: 0.8809 (m-40) cc_final: 0.8291 (t0) REVERT: e 238 LYS cc_start: 0.8752 (mttt) cc_final: 0.8510 (ttpp) REVERT: e 472 PHE cc_start: 0.9259 (t80) cc_final: 0.8879 (t80) REVERT: e 495 LEU cc_start: 0.9082 (tp) cc_final: 0.8451 (mt) REVERT: E 63 THR cc_start: 0.9485 (p) cc_final: 0.9145 (t) REVERT: E 107 LEU cc_start: 0.9291 (mt) cc_final: 0.8942 (mt) REVERT: E 113 ASP cc_start: 0.9048 (m-30) cc_final: 0.8520 (t0) REVERT: E 163 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8975 (mp0) REVERT: E 203 MET cc_start: 0.5200 (ptp) cc_final: 0.4260 (mpp) REVERT: E 379 ARG cc_start: 0.6848 (tpt170) cc_final: 0.5553 (ptp-170) REVERT: E 418 GLU cc_start: 0.8313 (tt0) cc_final: 0.8074 (tt0) REVERT: E 481 MET cc_start: 0.9304 (mmm) cc_final: 0.8904 (tpt) REVERT: E 522 MET cc_start: 0.8596 (ttm) cc_final: 0.8333 (ttm) REVERT: E 526 PHE cc_start: 0.7000 (m-10) cc_final: 0.6709 (m-10) REVERT: g 24 ASN cc_start: 0.9416 (m-40) cc_final: 0.9116 (t0) REVERT: g 102 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8422 (mm-30) REVERT: g 117 HIS cc_start: 0.8748 (t-90) cc_final: 0.8540 (t-90) REVERT: g 126 LYS cc_start: 0.9514 (mmmt) cc_final: 0.9309 (mmmt) REVERT: g 134 GLU cc_start: 0.9322 (pt0) cc_final: 0.8820 (pp20) REVERT: g 163 TYR cc_start: 0.6926 (t80) cc_final: 0.6717 (t80) REVERT: g 173 GLU cc_start: 0.9220 (tt0) cc_final: 0.8917 (mm-30) REVERT: g 440 MET cc_start: 0.4594 (pmm) cc_final: 0.4095 (pmm) REVERT: g 481 MET cc_start: 0.9022 (tpt) cc_final: 0.8619 (tpt) REVERT: g 492 LYS cc_start: 0.8333 (mmtm) cc_final: 0.7684 (mmtm) REVERT: g 497 ILE cc_start: 0.8919 (tp) cc_final: 0.8360 (tp) REVERT: g 540 PHE cc_start: 0.7980 (p90) cc_final: 0.7219 (p90) REVERT: g 564 VAL cc_start: 0.9460 (t) cc_final: 0.9199 (t) REVERT: g 575 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8837 (pt0) REVERT: G 52 MET cc_start: 0.8546 (tmm) cc_final: 0.8314 (tmm) REVERT: G 117 HIS cc_start: 0.9101 (t-90) cc_final: 0.8844 (t-90) REVERT: G 123 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8589 (tp-100) REVERT: G 127 LYS cc_start: 0.9335 (tmtt) cc_final: 0.8874 (tmmt) REVERT: G 176 LEU cc_start: 0.9455 (mm) cc_final: 0.9004 (pp) REVERT: G 234 MET cc_start: 0.3174 (ttm) cc_final: 0.0091 (ptm) REVERT: G 359 MET cc_start: 0.5260 (ppp) cc_final: 0.4715 (mpp) REVERT: G 502 TYR cc_start: 0.8410 (t80) cc_final: 0.7917 (t80) REVERT: G 507 ASP cc_start: 0.9306 (m-30) cc_final: 0.8999 (m-30) REVERT: G 511 CYS cc_start: 0.9349 (t) cc_final: 0.9031 (t) REVERT: G 514 ARG cc_start: 0.9204 (ttm110) cc_final: 0.8878 (ttp-110) REVERT: G 564 VAL cc_start: 0.9027 (t) cc_final: 0.8444 (t) REVERT: G 567 GLN cc_start: 0.9111 (mt0) cc_final: 0.8888 (mt0) REVERT: G 585 ASP cc_start: 0.8056 (p0) cc_final: 0.6919 (p0) REVERT: h 104 LEU cc_start: 0.9119 (mm) cc_final: 0.8917 (mm) REVERT: h 146 ASP cc_start: 0.7554 (t0) cc_final: 0.7340 (t0) REVERT: h 355 MET cc_start: 0.4221 (ptt) cc_final: 0.3972 (ptp) REVERT: h 436 GLN cc_start: 0.9519 (tm-30) cc_final: 0.9225 (tp40) REVERT: h 440 ASN cc_start: 0.9559 (t0) cc_final: 0.9339 (t0) REVERT: h 455 GLU cc_start: 0.9447 (tp30) cc_final: 0.9232 (tp30) REVERT: h 460 ASP cc_start: 0.8603 (p0) cc_final: 0.8225 (p0) REVERT: h 504 ILE cc_start: 0.9586 (mt) cc_final: 0.9269 (tp) REVERT: H 44 LEU cc_start: 0.9528 (tp) cc_final: 0.9306 (tp) REVERT: H 110 LYS cc_start: 0.9164 (ptpp) cc_final: 0.8862 (pttt) REVERT: H 117 GLU cc_start: 0.9225 (pm20) cc_final: 0.8984 (pm20) REVERT: H 166 MET cc_start: 0.5476 (mmp) cc_final: 0.5194 (mmp) REVERT: H 362 TYR cc_start: 0.6375 (m-10) cc_final: 0.6142 (m-10) REVERT: H 384 GLN cc_start: 0.8963 (mp10) cc_final: 0.8746 (mp10) REVERT: H 398 MET cc_start: 0.8642 (mtm) cc_final: 0.7972 (mpp) REVERT: H 402 ARG cc_start: 0.9379 (mpt180) cc_final: 0.9005 (mmt90) REVERT: H 436 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8985 (tm-30) REVERT: H 449 ILE cc_start: 0.9391 (mp) cc_final: 0.9150 (mp) REVERT: H 452 GLN cc_start: 0.9223 (mm110) cc_final: 0.8719 (tp40) REVERT: H 494 LYS cc_start: 0.9110 (mmmt) cc_final: 0.8613 (mptt) REVERT: q 39 HIS cc_start: 0.9171 (t-170) cc_final: 0.8812 (t-170) REVERT: q 41 MET cc_start: 0.8403 (tmm) cc_final: 0.7907 (tmm) REVERT: q 49 CYS cc_start: 0.8718 (m) cc_final: 0.7852 (m) REVERT: q 52 ASN cc_start: 0.8822 (m-40) cc_final: 0.8584 (m-40) REVERT: q 94 ILE cc_start: 0.8576 (pt) cc_final: 0.8373 (mm) REVERT: q 96 MET cc_start: 0.8211 (ptm) cc_final: 0.6748 (pmm) REVERT: q 114 SER cc_start: 0.9112 (m) cc_final: 0.8905 (m) REVERT: q 115 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7995 (tm-30) REVERT: q 126 GLU cc_start: 0.9198 (mp0) cc_final: 0.8929 (mp0) REVERT: q 153 LYS cc_start: 0.7964 (tptt) cc_final: 0.7700 (tptp) REVERT: q 155 ASP cc_start: 0.8764 (t70) cc_final: 0.8503 (t0) REVERT: q 213 MET cc_start: 0.2486 (mmp) cc_final: 0.0673 (mmm) REVERT: q 226 MET cc_start: 0.5142 (mmp) cc_final: 0.4863 (mmp) REVERT: q 361 MET cc_start: 0.7714 (mtt) cc_final: 0.7378 (ttt) REVERT: q 452 PHE cc_start: 0.9217 (t80) cc_final: 0.8579 (t80) REVERT: q 456 PHE cc_start: 0.9201 (m-10) cc_final: 0.8609 (m-80) REVERT: q 519 ASP cc_start: 0.8229 (t0) cc_final: 0.7926 (t0) REVERT: q 520 MET cc_start: 0.7216 (tpt) cc_final: 0.6900 (tpp) REVERT: q 533 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9032 (tm-30) REVERT: q 546 MET cc_start: 0.7792 (mmt) cc_final: 0.7490 (mmp) REVERT: Q 39 HIS cc_start: 0.9439 (t70) cc_final: 0.9205 (t70) REVERT: Q 41 MET cc_start: 0.8660 (tmm) cc_final: 0.8411 (tmm) REVERT: Q 49 CYS cc_start: 0.8742 (m) cc_final: 0.8265 (m) REVERT: Q 83 LYS cc_start: 0.9370 (mmmt) cc_final: 0.8984 (mmmm) REVERT: Q 92 GLN cc_start: 0.8924 (tt0) cc_final: 0.8714 (tt0) REVERT: Q 109 GLU cc_start: 0.9306 (tp30) cc_final: 0.9100 (tp30) REVERT: Q 113 VAL cc_start: 0.9568 (p) cc_final: 0.9360 (p) REVERT: Q 126 GLU cc_start: 0.9475 (tm-30) cc_final: 0.9067 (tm-30) REVERT: Q 129 GLN cc_start: 0.9697 (tm-30) cc_final: 0.9390 (pp30) REVERT: Q 145 MET cc_start: 0.8658 (mmm) cc_final: 0.8170 (mmm) REVERT: Q 161 LYS cc_start: 0.9270 (mttt) cc_final: 0.8665 (mtmm) REVERT: Q 162 MET cc_start: 0.9043 (tmm) cc_final: 0.8709 (tmm) REVERT: Q 361 MET cc_start: 0.8008 (ppp) cc_final: 0.7429 (mtm) REVERT: Q 428 ILE cc_start: 0.9386 (tt) cc_final: 0.9105 (tt) REVERT: Q 470 ASP cc_start: 0.9071 (t0) cc_final: 0.8595 (t70) REVERT: Q 473 GLU cc_start: 0.9309 (pt0) cc_final: 0.8549 (pt0) REVERT: Q 533 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8944 (tm-30) REVERT: z 36 ASN cc_start: 0.9084 (p0) cc_final: 0.8803 (p0) REVERT: z 40 LYS cc_start: 0.9267 (mmpt) cc_final: 0.9007 (mmmt) REVERT: z 128 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8377 (mt-10) REVERT: z 152 GLN cc_start: 0.8696 (mt0) cc_final: 0.8162 (mm-40) REVERT: z 158 LEU cc_start: 0.9045 (mt) cc_final: 0.8792 (mt) REVERT: z 163 ASP cc_start: 0.7955 (m-30) cc_final: 0.7722 (t0) REVERT: z 185 GLN cc_start: 0.8570 (tt0) cc_final: 0.8343 (pm20) REVERT: z 193 MET cc_start: 0.7716 (tpp) cc_final: 0.7513 (tpp) REVERT: z 201 HIS cc_start: 0.9209 (m-70) cc_final: 0.8967 (m90) REVERT: z 215 LEU cc_start: 0.8194 (tp) cc_final: 0.7729 (tp) REVERT: z 412 ILE cc_start: 0.9603 (mm) cc_final: 0.9246 (mm) REVERT: z 419 TYR cc_start: 0.9057 (m-10) cc_final: 0.8802 (m-10) REVERT: z 445 GLU cc_start: 0.9247 (mp0) cc_final: 0.8784 (mm-30) REVERT: z 467 LEU cc_start: 0.9008 (mm) cc_final: 0.8793 (mm) REVERT: z 523 ILE cc_start: 0.9434 (tp) cc_final: 0.9211 (tp) REVERT: z 526 ASN cc_start: 0.9394 (m-40) cc_final: 0.9093 (m-40) REVERT: z 527 LEU cc_start: 0.9622 (mt) cc_final: 0.9396 (mt) REVERT: z 529 LEU cc_start: 0.8909 (mt) cc_final: 0.8608 (mt) REVERT: Z 118 ILE cc_start: 0.8830 (mt) cc_final: 0.8544 (mm) REVERT: Z 119 THR cc_start: 0.9560 (t) cc_final: 0.9316 (p) REVERT: Z 128 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8792 (tp30) REVERT: Z 168 GLU cc_start: 0.9609 (mp0) cc_final: 0.9292 (pm20) REVERT: Z 189 LEU cc_start: 0.8303 (tp) cc_final: 0.8024 (tp) REVERT: Z 193 MET cc_start: 0.7094 (mtm) cc_final: 0.6816 (ttt) REVERT: Z 199 MET cc_start: 0.7906 (ppp) cc_final: 0.7568 (ppp) REVERT: Z 224 MET cc_start: 0.2184 (mmm) cc_final: 0.1937 (mmm) REVERT: Z 366 TYR cc_start: 0.7198 (m-10) cc_final: 0.6612 (m-10) REVERT: Z 393 ASP cc_start: 0.9459 (m-30) cc_final: 0.8836 (p0) REVERT: Z 418 PHE cc_start: 0.9157 (t80) cc_final: 0.8728 (t80) REVERT: Z 465 ASP cc_start: 0.9377 (t0) cc_final: 0.9158 (t0) REVERT: Z 482 ASP cc_start: 0.8641 (m-30) cc_final: 0.8386 (m-30) REVERT: Z 504 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8585 (mm-30) REVERT: Z 527 LEU cc_start: 0.9155 (mt) cc_final: 0.8737 (mt) outliers start: 9 outliers final: 0 residues processed: 1419 average time/residue: 0.5618 time to fit residues: 1367.2181 Evaluate side-chains 1100 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1099 time to evaluate : 5.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 647 optimal weight: 0.8980 chunk 441 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 578 optimal weight: 4.9990 chunk 320 optimal weight: 0.8980 chunk 663 optimal weight: 9.9990 chunk 537 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 697 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 380 HIS ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 HIS d 303 HIS D 112 ASN D 284 ASN ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 251 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 HIS g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 567 GLN G 519 ASN ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN H 436 GLN q 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 62618 Z= 0.172 Angle : 0.571 13.399 84459 Z= 0.292 Chirality : 0.044 0.267 10166 Planarity : 0.003 0.076 10848 Dihedral : 3.699 24.174 8568 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % Rotamer: Outliers : 0.01 % Allowed : 1.62 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.09), residues: 8065 helix: 0.32 (0.08), residues: 3904 sheet: -0.41 (0.19), residues: 649 loop : -0.68 (0.10), residues: 3512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 440 HIS 0.012 0.001 HIS d 303 PHE 0.027 0.001 PHE a 436 TYR 0.015 0.001 TYR b 464 ARG 0.008 0.000 ARG Q 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1408 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1407 time to evaluate : 5.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 44 LEU cc_start: 0.9420 (tp) cc_final: 0.9192 (tp) REVERT: a 73 LEU cc_start: 0.8732 (mt) cc_final: 0.7966 (mt) REVERT: a 81 LYS cc_start: 0.9629 (mttt) cc_final: 0.9372 (mptt) REVERT: a 108 LEU cc_start: 0.9583 (mt) cc_final: 0.9367 (mt) REVERT: a 109 LEU cc_start: 0.8939 (mt) cc_final: 0.8653 (mt) REVERT: a 142 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8807 (tm-30) REVERT: a 359 ASP cc_start: 0.7669 (m-30) cc_final: 0.7349 (p0) REVERT: a 399 GLU cc_start: 0.6958 (tt0) cc_final: 0.6477 (pp20) REVERT: a 448 ILE cc_start: 0.9316 (mt) cc_final: 0.9070 (tp) REVERT: a 451 PHE cc_start: 0.9375 (t80) cc_final: 0.9145 (t80) REVERT: a 460 LYS cc_start: 0.8844 (tptt) cc_final: 0.8514 (mmtt) REVERT: a 497 TYR cc_start: 0.8071 (m-80) cc_final: 0.7685 (m-80) REVERT: a 502 LEU cc_start: 0.8009 (mt) cc_final: 0.7521 (mt) REVERT: a 530 SER cc_start: 0.9512 (m) cc_final: 0.9105 (p) REVERT: a 532 LEU cc_start: 0.9425 (mm) cc_final: 0.8858 (tt) REVERT: a 542 ASP cc_start: 0.8750 (t70) cc_final: 0.8449 (t70) REVERT: A 204 ASN cc_start: 0.7832 (t0) cc_final: 0.7608 (m110) REVERT: A 227 THR cc_start: 0.6350 (p) cc_final: 0.6016 (p) REVERT: A 233 MET cc_start: 0.1805 (mtm) cc_final: 0.0859 (ptm) REVERT: A 307 LEU cc_start: 0.4785 (mt) cc_final: 0.4381 (pp) REVERT: A 320 ARG cc_start: 0.7157 (mtt90) cc_final: 0.6110 (ppt170) REVERT: A 341 MET cc_start: 0.3396 (mpp) cc_final: 0.3078 (mmm) REVERT: A 477 LEU cc_start: 0.9432 (mt) cc_final: 0.9167 (mt) REVERT: A 518 LEU cc_start: 0.9033 (mm) cc_final: 0.8793 (mm) REVERT: A 533 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8823 (mm-30) REVERT: b 45 LEU cc_start: 0.9365 (tp) cc_final: 0.8501 (pp) REVERT: b 46 LEU cc_start: 0.9133 (mm) cc_final: 0.8636 (mt) REVERT: b 59 ASP cc_start: 0.8675 (t0) cc_final: 0.8429 (t0) REVERT: b 78 VAL cc_start: 0.9055 (t) cc_final: 0.8750 (t) REVERT: b 115 ILE cc_start: 0.8172 (mm) cc_final: 0.7915 (mm) REVERT: b 121 ILE cc_start: 0.9080 (mt) cc_final: 0.8834 (mt) REVERT: b 148 MET cc_start: 0.8532 (ppp) cc_final: 0.8008 (ppp) REVERT: b 158 LYS cc_start: 0.9384 (mttt) cc_final: 0.9044 (mmmt) REVERT: b 347 MET cc_start: 0.7221 (mmm) cc_final: 0.6649 (tmm) REVERT: b 409 MET cc_start: 0.9377 (tpp) cc_final: 0.9156 (ttm) REVERT: b 439 GLN cc_start: 0.9030 (mm110) cc_final: 0.8629 (mp10) REVERT: b 472 LEU cc_start: 0.8735 (mt) cc_final: 0.8259 (mt) REVERT: B 64 LEU cc_start: 0.9440 (mt) cc_final: 0.9162 (pp) REVERT: B 155 HIS cc_start: 0.9298 (m90) cc_final: 0.9023 (m90) REVERT: B 315 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 354 LEU cc_start: 0.4830 (mt) cc_final: 0.4139 (mt) REVERT: B 386 ASP cc_start: 0.8670 (m-30) cc_final: 0.7455 (t70) REVERT: B 409 MET cc_start: 0.9395 (tpp) cc_final: 0.9111 (ttm) REVERT: B 415 VAL cc_start: 0.9450 (t) cc_final: 0.9239 (p) REVERT: B 452 SER cc_start: 0.9151 (p) cc_final: 0.8645 (t) REVERT: B 472 LEU cc_start: 0.8741 (mt) cc_final: 0.8299 (mt) REVERT: B 476 ASN cc_start: 0.9022 (m-40) cc_final: 0.8195 (p0) REVERT: d 39 LEU cc_start: 0.8685 (tp) cc_final: 0.8418 (tp) REVERT: d 80 GLU cc_start: 0.8607 (pp20) cc_final: 0.8270 (pm20) REVERT: d 166 TYR cc_start: 0.7029 (m-80) cc_final: 0.6759 (m-10) REVERT: d 209 MET cc_start: 0.3180 (mtm) cc_final: 0.2682 (ttp) REVERT: d 311 MET cc_start: 0.2214 (mmm) cc_final: 0.1786 (mmm) REVERT: d 315 ASP cc_start: 0.3167 (m-30) cc_final: 0.2336 (t70) REVERT: d 411 ILE cc_start: 0.9016 (pt) cc_final: 0.8563 (mm) REVERT: d 433 GLU cc_start: 0.8493 (pm20) cc_final: 0.7275 (tp30) REVERT: d 464 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9429 (mmmt) REVERT: d 513 GLU cc_start: 0.9597 (mm-30) cc_final: 0.8620 (mm-30) REVERT: d 516 LYS cc_start: 0.9471 (mtpp) cc_final: 0.8840 (mttm) REVERT: D 44 MET cc_start: 0.8419 (mpp) cc_final: 0.7855 (mpp) REVERT: D 56 ILE cc_start: 0.7460 (pt) cc_final: 0.7202 (pt) REVERT: D 110 LEU cc_start: 0.8287 (mt) cc_final: 0.8059 (mt) REVERT: D 133 ASP cc_start: 0.9442 (m-30) cc_final: 0.9130 (t0) REVERT: D 137 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8749 (tm-30) REVERT: D 138 MET cc_start: 0.7201 (ptp) cc_final: 0.6964 (mmt) REVERT: D 209 MET cc_start: 0.3699 (mmt) cc_final: 0.3374 (mmt) REVERT: D 385 MET cc_start: 0.5514 (ppp) cc_final: 0.4539 (tpp) REVERT: D 470 ARG cc_start: 0.9164 (tpt90) cc_final: 0.8353 (ptt180) REVERT: D 509 THR cc_start: 0.9384 (t) cc_final: 0.9077 (t) REVERT: D 513 GLU cc_start: 0.9539 (mm-30) cc_final: 0.9244 (mp0) REVERT: e 113 ASP cc_start: 0.8618 (m-30) cc_final: 0.7759 (p0) REVERT: e 131 ASP cc_start: 0.9100 (t70) cc_final: 0.8819 (m-30) REVERT: e 132 GLN cc_start: 0.9241 (tp-100) cc_final: 0.9011 (tp40) REVERT: e 134 LEU cc_start: 0.8910 (tp) cc_final: 0.8657 (tp) REVERT: e 146 ILE cc_start: 0.9700 (mm) cc_final: 0.8636 (mm) REVERT: e 150 PHE cc_start: 0.8978 (m-10) cc_final: 0.8609 (m-80) REVERT: e 203 MET cc_start: 0.4018 (tmm) cc_final: 0.3034 (ptt) REVERT: e 210 ASN cc_start: 0.8785 (m-40) cc_final: 0.8266 (t0) REVERT: e 254 MET cc_start: 0.4162 (mtt) cc_final: 0.3853 (mtt) REVERT: e 472 PHE cc_start: 0.9213 (t80) cc_final: 0.8992 (t80) REVERT: e 492 ILE cc_start: 0.8832 (mt) cc_final: 0.8518 (mm) REVERT: e 495 LEU cc_start: 0.9105 (tp) cc_final: 0.8502 (mt) REVERT: E 63 THR cc_start: 0.9357 (p) cc_final: 0.9122 (t) REVERT: E 113 ASP cc_start: 0.9067 (m-30) cc_final: 0.8695 (t0) REVERT: E 163 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9036 (mp0) REVERT: E 203 MET cc_start: 0.5245 (ptp) cc_final: 0.4209 (mpp) REVERT: E 379 ARG cc_start: 0.7783 (mmt180) cc_final: 0.6824 (ptp-170) REVERT: E 467 TYR cc_start: 0.8723 (m-80) cc_final: 0.8506 (m-80) REVERT: E 481 MET cc_start: 0.9352 (mmm) cc_final: 0.9134 (tpt) REVERT: E 522 MET cc_start: 0.8495 (ttm) cc_final: 0.8113 (ttt) REVERT: E 526 PHE cc_start: 0.7011 (m-10) cc_final: 0.6700 (m-10) REVERT: E 550 LYS cc_start: 0.9370 (tppt) cc_final: 0.8967 (tppt) REVERT: g 24 ASN cc_start: 0.9402 (m-40) cc_final: 0.9091 (t0) REVERT: g 102 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8357 (mm-30) REVERT: g 117 HIS cc_start: 0.8630 (t-90) cc_final: 0.8422 (t-90) REVERT: g 126 LYS cc_start: 0.9525 (mmmt) cc_final: 0.9298 (mmmt) REVERT: g 134 GLU cc_start: 0.9297 (pt0) cc_final: 0.8717 (pp20) REVERT: g 137 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8328 (mtmm) REVERT: g 163 TYR cc_start: 0.6814 (t80) cc_final: 0.6586 (t80) REVERT: g 173 GLU cc_start: 0.9222 (tt0) cc_final: 0.8950 (mm-30) REVERT: g 440 MET cc_start: 0.4383 (pmm) cc_final: 0.4011 (pmm) REVERT: g 481 MET cc_start: 0.9048 (tpt) cc_final: 0.8566 (tpt) REVERT: g 497 ILE cc_start: 0.8829 (tp) cc_final: 0.8449 (tp) REVERT: g 510 GLU cc_start: 0.8875 (tm-30) cc_final: 0.7795 (tm-30) REVERT: g 514 ARG cc_start: 0.9302 (ttm-80) cc_final: 0.8927 (tpp80) REVERT: g 540 PHE cc_start: 0.7872 (p90) cc_final: 0.7078 (p90) REVERT: g 571 LYS cc_start: 0.9287 (ptpp) cc_final: 0.8810 (ptpp) REVERT: g 575 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8835 (pt0) REVERT: G 52 MET cc_start: 0.8630 (tmm) cc_final: 0.8424 (tmm) REVERT: G 127 LYS cc_start: 0.9202 (tmtt) cc_final: 0.8785 (ttpt) REVERT: G 176 LEU cc_start: 0.9435 (mm) cc_final: 0.8994 (pp) REVERT: G 234 MET cc_start: 0.2996 (ttm) cc_final: 0.0427 (ptm) REVERT: G 359 MET cc_start: 0.5103 (ppp) cc_final: 0.4520 (mpp) REVERT: G 502 TYR cc_start: 0.8362 (t80) cc_final: 0.8125 (t80) REVERT: G 507 ASP cc_start: 0.9276 (m-30) cc_final: 0.8855 (m-30) REVERT: G 514 ARG cc_start: 0.9070 (ttm110) cc_final: 0.8718 (ttp-110) REVERT: G 563 GLU cc_start: 0.7819 (pm20) cc_final: 0.7041 (pm20) REVERT: G 564 VAL cc_start: 0.8993 (t) cc_final: 0.8269 (t) REVERT: G 567 GLN cc_start: 0.9168 (mt0) cc_final: 0.8424 (mt0) REVERT: h 64 ASN cc_start: 0.7916 (t0) cc_final: 0.7714 (t0) REVERT: h 70 LEU cc_start: 0.9238 (tp) cc_final: 0.9024 (tp) REVERT: h 376 LEU cc_start: 0.8889 (tt) cc_final: 0.8640 (mp) REVERT: h 417 GLU cc_start: 0.9236 (mp0) cc_final: 0.8992 (mp0) REVERT: h 436 GLN cc_start: 0.9502 (tm-30) cc_final: 0.9132 (tp40) REVERT: h 440 ASN cc_start: 0.9577 (t0) cc_final: 0.9359 (t0) REVERT: h 447 GLU cc_start: 0.9330 (pp20) cc_final: 0.8631 (tm-30) REVERT: h 451 ARG cc_start: 0.9582 (tpp80) cc_final: 0.8890 (tpp80) REVERT: h 455 GLU cc_start: 0.9439 (tp30) cc_final: 0.9198 (tp30) REVERT: h 460 ASP cc_start: 0.8610 (p0) cc_final: 0.8253 (p0) REVERT: h 465 LEU cc_start: 0.9586 (mp) cc_final: 0.9094 (mt) REVERT: h 503 LYS cc_start: 0.9267 (mmtt) cc_final: 0.8855 (mmtp) REVERT: h 504 ILE cc_start: 0.9589 (mt) cc_final: 0.8916 (tp) REVERT: h 508 ASN cc_start: 0.9339 (m-40) cc_final: 0.8956 (m110) REVERT: H 166 MET cc_start: 0.5504 (mmp) cc_final: 0.5226 (mmp) REVERT: H 202 LYS cc_start: 0.8179 (mmpt) cc_final: 0.7629 (mmtm) REVERT: H 362 TYR cc_start: 0.6329 (m-10) cc_final: 0.6044 (m-10) REVERT: H 398 MET cc_start: 0.8628 (mtm) cc_final: 0.8217 (mpp) REVERT: H 402 ARG cc_start: 0.9355 (mpt180) cc_final: 0.8933 (mmt-90) REVERT: H 418 MET cc_start: 0.8789 (ttt) cc_final: 0.8162 (ptm) REVERT: H 444 LYS cc_start: 0.9386 (tmtt) cc_final: 0.9117 (tptt) REVERT: H 449 ILE cc_start: 0.9394 (mp) cc_final: 0.9144 (mp) REVERT: H 494 LYS cc_start: 0.9143 (mmmt) cc_final: 0.8631 (mptt) REVERT: q 39 HIS cc_start: 0.9101 (t-170) cc_final: 0.8689 (t-170) REVERT: q 41 MET cc_start: 0.8263 (tmm) cc_final: 0.7795 (tmm) REVERT: q 49 CYS cc_start: 0.8615 (m) cc_final: 0.7762 (m) REVERT: q 52 ASN cc_start: 0.8701 (m-40) cc_final: 0.8342 (m-40) REVERT: q 96 MET cc_start: 0.8262 (ptm) cc_final: 0.7061 (pmm) REVERT: q 115 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8089 (tm-30) REVERT: q 133 MET cc_start: 0.9246 (tpt) cc_final: 0.9032 (tpt) REVERT: q 140 LYS cc_start: 0.8990 (mmtm) cc_final: 0.8453 (mttt) REVERT: q 153 LYS cc_start: 0.7910 (tptt) cc_final: 0.7670 (tptp) REVERT: q 155 ASP cc_start: 0.8815 (t70) cc_final: 0.8546 (t0) REVERT: q 213 MET cc_start: 0.2375 (mmp) cc_final: 0.1493 (tpp) REVERT: q 361 MET cc_start: 0.7720 (mtt) cc_final: 0.7304 (ttt) REVERT: q 451 GLN cc_start: 0.9450 (tp-100) cc_final: 0.9177 (tp40) REVERT: q 452 PHE cc_start: 0.9159 (t80) cc_final: 0.8664 (t80) REVERT: q 456 PHE cc_start: 0.9153 (m-10) cc_final: 0.8381 (m-80) REVERT: q 473 GLU cc_start: 0.8944 (tt0) cc_final: 0.8729 (tt0) REVERT: q 520 MET cc_start: 0.7607 (tpt) cc_final: 0.7374 (tpt) REVERT: q 533 GLU cc_start: 0.9394 (mt-10) cc_final: 0.9057 (tm-30) REVERT: Q 39 HIS cc_start: 0.9424 (t70) cc_final: 0.9142 (t70) REVERT: Q 41 MET cc_start: 0.8643 (tmm) cc_final: 0.8412 (tmm) REVERT: Q 49 CYS cc_start: 0.8743 (m) cc_final: 0.8146 (m) REVERT: Q 91 GLN cc_start: 0.9265 (mm-40) cc_final: 0.9046 (mm-40) REVERT: Q 109 GLU cc_start: 0.9316 (tp30) cc_final: 0.9064 (tp30) REVERT: Q 113 VAL cc_start: 0.9533 (p) cc_final: 0.9274 (p) REVERT: Q 155 ASP cc_start: 0.8566 (t70) cc_final: 0.8287 (t70) REVERT: Q 161 LYS cc_start: 0.9266 (mttt) cc_final: 0.8707 (mtmm) REVERT: Q 162 MET cc_start: 0.9060 (tmm) cc_final: 0.8814 (tmm) REVERT: Q 202 PHE cc_start: 0.7347 (t80) cc_final: 0.7126 (t80) REVERT: Q 230 ARG cc_start: 0.1548 (ttt180) cc_final: -0.0062 (mmp-170) REVERT: Q 374 GLU cc_start: 0.5659 (mt-10) cc_final: 0.5042 (pm20) REVERT: Q 380 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7504 (mmp80) REVERT: Q 473 GLU cc_start: 0.9288 (pt0) cc_final: 0.8836 (pt0) REVERT: Q 545 ILE cc_start: 0.8758 (mm) cc_final: 0.8353 (mm) REVERT: z 36 ASN cc_start: 0.9029 (p0) cc_final: 0.8814 (p0) REVERT: z 37 LEU cc_start: 0.9458 (tp) cc_final: 0.9050 (mt) REVERT: z 40 LYS cc_start: 0.9272 (mmpt) cc_final: 0.8992 (mmmt) REVERT: z 128 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8344 (mt-10) REVERT: z 152 GLN cc_start: 0.8875 (mt0) cc_final: 0.8409 (mm-40) REVERT: z 158 LEU cc_start: 0.9079 (mt) cc_final: 0.8808 (mt) REVERT: z 185 GLN cc_start: 0.8609 (tt0) cc_final: 0.8393 (pm20) REVERT: z 192 HIS cc_start: 0.8379 (m-70) cc_final: 0.8128 (m90) REVERT: z 201 HIS cc_start: 0.9195 (m-70) cc_final: 0.8869 (m90) REVERT: z 215 LEU cc_start: 0.8084 (tp) cc_final: 0.7616 (tp) REVERT: z 392 LYS cc_start: 0.9452 (ptmm) cc_final: 0.9195 (ptmm) REVERT: z 412 ILE cc_start: 0.9571 (mm) cc_final: 0.9189 (mm) REVERT: z 419 TYR cc_start: 0.9029 (m-10) cc_final: 0.8800 (m-10) REVERT: z 445 GLU cc_start: 0.9297 (mp0) cc_final: 0.8861 (mm-30) REVERT: z 452 LEU cc_start: 0.9526 (mt) cc_final: 0.9221 (mt) REVERT: z 523 ILE cc_start: 0.9426 (tp) cc_final: 0.9211 (tp) REVERT: z 527 LEU cc_start: 0.9637 (mt) cc_final: 0.9381 (mt) REVERT: z 529 LEU cc_start: 0.8952 (mt) cc_final: 0.8653 (mt) REVERT: Z 22 ASN cc_start: 0.8632 (m110) cc_final: 0.8324 (m110) REVERT: Z 118 ILE cc_start: 0.8781 (mt) cc_final: 0.8543 (mm) REVERT: Z 119 THR cc_start: 0.9598 (t) cc_final: 0.9322 (p) REVERT: Z 128 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8755 (tp30) REVERT: Z 168 GLU cc_start: 0.9564 (mp0) cc_final: 0.9239 (pm20) REVERT: Z 176 ASP cc_start: 0.8727 (m-30) cc_final: 0.8458 (m-30) REVERT: Z 193 MET cc_start: 0.7052 (mtm) cc_final: 0.6797 (ttt) REVERT: Z 224 MET cc_start: 0.2178 (mmm) cc_final: 0.1940 (mmm) REVERT: Z 366 TYR cc_start: 0.7187 (m-10) cc_final: 0.6625 (m-10) REVERT: Z 376 CYS cc_start: 0.8871 (p) cc_final: 0.8424 (p) REVERT: Z 378 ILE cc_start: 0.9178 (mm) cc_final: 0.8977 (mm) REVERT: Z 393 ASP cc_start: 0.9237 (m-30) cc_final: 0.8811 (p0) REVERT: Z 418 PHE cc_start: 0.9087 (t80) cc_final: 0.8770 (t80) REVERT: Z 431 MET cc_start: 0.6977 (mmm) cc_final: 0.6736 (tpt) REVERT: Z 465 ASP cc_start: 0.9350 (t0) cc_final: 0.9149 (t0) REVERT: Z 482 ASP cc_start: 0.8800 (m-30) cc_final: 0.8524 (m-30) REVERT: Z 504 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8577 (mm-30) REVERT: Z 523 ILE cc_start: 0.9663 (mm) cc_final: 0.9418 (mm) outliers start: 1 outliers final: 1 residues processed: 1408 average time/residue: 0.5455 time to fit residues: 1329.3634 Evaluate side-chains 1123 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1122 time to evaluate : 5.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 261 optimal weight: 0.6980 chunk 699 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 456 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 777 optimal weight: 7.9990 chunk 645 optimal weight: 7.9990 chunk 360 optimal weight: 7.9990 chunk 64 optimal weight: 0.3980 chunk 257 optimal weight: 3.9990 chunk 408 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 113 ASN a 380 HIS ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 118 GLN d 240 GLN ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN e 132 GLN ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 474 GLN E 353 HIS E 543 GLN g 123 GLN g 237 HIS g 499 GLN g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN h 90 GLN ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 276 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 62618 Z= 0.157 Angle : 0.563 13.028 84459 Z= 0.287 Chirality : 0.043 0.251 10166 Planarity : 0.003 0.046 10848 Dihedral : 3.678 22.081 8568 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.50 % Rotamer: Outliers : 0.07 % Allowed : 1.39 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.09), residues: 8065 helix: 0.46 (0.08), residues: 3931 sheet: -0.28 (0.20), residues: 625 loop : -0.67 (0.10), residues: 3509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 440 HIS 0.012 0.001 HIS d 473 PHE 0.027 0.001 PHE Q 137 TYR 0.021 0.001 TYR Q 496 ARG 0.008 0.000 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1401 time to evaluate : 5.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 44 LEU cc_start: 0.9394 (tp) cc_final: 0.9108 (tp) REVERT: a 73 LEU cc_start: 0.8714 (mt) cc_final: 0.7968 (mt) REVERT: a 81 LYS cc_start: 0.9659 (mttt) cc_final: 0.9399 (mptt) REVERT: a 109 LEU cc_start: 0.8961 (mt) cc_final: 0.8711 (mt) REVERT: a 135 GLU cc_start: 0.8342 (tp30) cc_final: 0.7671 (tp30) REVERT: a 142 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8861 (tm-30) REVERT: a 175 PHE cc_start: 0.7952 (t80) cc_final: 0.7736 (t80) REVERT: a 258 MET cc_start: 0.1122 (mmm) cc_final: 0.0524 (mmt) REVERT: a 399 GLU cc_start: 0.7007 (tt0) cc_final: 0.6502 (pp20) REVERT: a 448 ILE cc_start: 0.9316 (mt) cc_final: 0.9078 (tp) REVERT: a 451 PHE cc_start: 0.9316 (t80) cc_final: 0.9072 (t80) REVERT: a 460 LYS cc_start: 0.8752 (tptt) cc_final: 0.8516 (tptt) REVERT: a 497 TYR cc_start: 0.8176 (m-80) cc_final: 0.7789 (m-80) REVERT: a 502 LEU cc_start: 0.7972 (mt) cc_final: 0.7564 (mt) REVERT: a 530 SER cc_start: 0.9358 (m) cc_final: 0.9139 (p) REVERT: a 532 LEU cc_start: 0.9420 (mm) cc_final: 0.8919 (tt) REVERT: A 111 ARG cc_start: 0.9009 (mmm-85) cc_final: 0.8749 (tpp80) REVERT: A 119 LYS cc_start: 0.9294 (mppt) cc_final: 0.9075 (mppt) REVERT: A 184 LEU cc_start: 0.7988 (tp) cc_final: 0.7758 (tp) REVERT: A 320 ARG cc_start: 0.7128 (mtt90) cc_final: 0.6787 (ptp90) REVERT: A 341 MET cc_start: 0.3486 (mpp) cc_final: 0.3055 (mmm) REVERT: A 444 GLU cc_start: 0.9498 (pm20) cc_final: 0.9272 (pm20) REVERT: A 457 ILE cc_start: 0.9189 (pt) cc_final: 0.8907 (pt) REVERT: A 477 LEU cc_start: 0.9298 (mt) cc_final: 0.8914 (mt) REVERT: A 518 LEU cc_start: 0.9046 (mm) cc_final: 0.8723 (mm) REVERT: A 533 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8791 (mm-30) REVERT: b 42 MET cc_start: 0.7852 (mpp) cc_final: 0.7367 (mpp) REVERT: b 45 LEU cc_start: 0.9386 (tp) cc_final: 0.8473 (pp) REVERT: b 46 LEU cc_start: 0.9148 (mm) cc_final: 0.8619 (mt) REVERT: b 55 MET cc_start: 0.6464 (mtt) cc_final: 0.6217 (mtt) REVERT: b 59 ASP cc_start: 0.8696 (t0) cc_final: 0.8448 (t0) REVERT: b 115 ILE cc_start: 0.8096 (mm) cc_final: 0.7869 (mm) REVERT: b 121 ILE cc_start: 0.9154 (mt) cc_final: 0.8895 (mt) REVERT: b 148 MET cc_start: 0.8539 (ppp) cc_final: 0.8009 (ppp) REVERT: b 158 LYS cc_start: 0.9336 (mttt) cc_final: 0.8998 (mmmm) REVERT: b 431 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8976 (mm-30) REVERT: b 439 GLN cc_start: 0.9039 (mm110) cc_final: 0.8687 (mp10) REVERT: b 472 LEU cc_start: 0.8728 (mt) cc_final: 0.8306 (mt) REVERT: B 64 LEU cc_start: 0.9474 (mt) cc_final: 0.9188 (pp) REVERT: B 155 HIS cc_start: 0.9346 (m90) cc_final: 0.9079 (m90) REVERT: B 196 ILE cc_start: 0.8314 (mm) cc_final: 0.7900 (mm) REVERT: B 354 LEU cc_start: 0.4615 (mt) cc_final: 0.3913 (mt) REVERT: B 386 ASP cc_start: 0.8630 (m-30) cc_final: 0.7452 (t70) REVERT: B 409 MET cc_start: 0.9418 (tpp) cc_final: 0.9118 (ttm) REVERT: B 415 VAL cc_start: 0.9453 (t) cc_final: 0.9236 (p) REVERT: B 452 SER cc_start: 0.9051 (p) cc_final: 0.8558 (t) REVERT: B 472 LEU cc_start: 0.8726 (mt) cc_final: 0.8256 (mt) REVERT: B 476 ASN cc_start: 0.9136 (m-40) cc_final: 0.8389 (p0) REVERT: d 44 MET cc_start: 0.8385 (tmm) cc_final: 0.7420 (tmm) REVERT: d 80 GLU cc_start: 0.8611 (pp20) cc_final: 0.8275 (pm20) REVERT: d 166 TYR cc_start: 0.7076 (m-80) cc_final: 0.6710 (m-10) REVERT: d 209 MET cc_start: 0.3509 (mtm) cc_final: 0.3134 (ttp) REVERT: d 311 MET cc_start: 0.2180 (mmm) cc_final: 0.1912 (mmm) REVERT: d 315 ASP cc_start: 0.3216 (m-30) cc_final: 0.2377 (t70) REVERT: d 411 ILE cc_start: 0.9012 (pt) cc_final: 0.8555 (mm) REVERT: d 433 GLU cc_start: 0.7782 (pm20) cc_final: 0.7292 (tp30) REVERT: d 513 GLU cc_start: 0.9619 (mm-30) cc_final: 0.8759 (mm-30) REVERT: d 516 LYS cc_start: 0.9492 (mtpp) cc_final: 0.8854 (mttm) REVERT: D 110 LEU cc_start: 0.8376 (mt) cc_final: 0.8163 (mt) REVERT: D 133 ASP cc_start: 0.9471 (m-30) cc_final: 0.9090 (t0) REVERT: D 209 MET cc_start: 0.4065 (mmt) cc_final: 0.3567 (mmt) REVERT: D 385 MET cc_start: 0.6030 (ppp) cc_final: 0.5207 (tpp) REVERT: D 470 ARG cc_start: 0.9156 (tpt90) cc_final: 0.8349 (ptt180) REVERT: D 509 THR cc_start: 0.9417 (t) cc_final: 0.9037 (t) REVERT: D 513 GLU cc_start: 0.9564 (mm-30) cc_final: 0.9263 (mp0) REVERT: e 109 LYS cc_start: 0.9451 (mmpt) cc_final: 0.8865 (mttt) REVERT: e 113 ASP cc_start: 0.8456 (m-30) cc_final: 0.7639 (p0) REVERT: e 131 ASP cc_start: 0.9052 (t70) cc_final: 0.8785 (m-30) REVERT: e 134 LEU cc_start: 0.8981 (tp) cc_final: 0.8749 (tp) REVERT: e 146 ILE cc_start: 0.9707 (mm) cc_final: 0.8659 (mm) REVERT: e 150 PHE cc_start: 0.9013 (m-10) cc_final: 0.8587 (m-80) REVERT: e 202 GLU cc_start: 0.8000 (pp20) cc_final: 0.7279 (tp30) REVERT: e 203 MET cc_start: 0.4020 (tmm) cc_final: 0.2968 (ptt) REVERT: e 210 ASN cc_start: 0.8764 (m-40) cc_final: 0.8249 (t0) REVERT: e 254 MET cc_start: 0.4146 (mtt) cc_final: 0.3743 (mtt) REVERT: e 472 PHE cc_start: 0.9237 (t80) cc_final: 0.9034 (t80) REVERT: e 492 ILE cc_start: 0.8952 (mt) cc_final: 0.8728 (mm) REVERT: e 495 LEU cc_start: 0.9129 (tp) cc_final: 0.8426 (mt) REVERT: e 536 GLN cc_start: 0.8934 (mp10) cc_final: 0.8612 (mp10) REVERT: e 554 VAL cc_start: 0.7351 (p) cc_final: 0.6930 (p) REVERT: E 50 HIS cc_start: 0.8832 (m90) cc_final: 0.8573 (m90) REVERT: E 63 THR cc_start: 0.9429 (p) cc_final: 0.9142 (t) REVERT: E 113 ASP cc_start: 0.9110 (m-30) cc_final: 0.8726 (t0) REVERT: E 203 MET cc_start: 0.5543 (ptp) cc_final: 0.4352 (mpp) REVERT: E 414 MET cc_start: 0.8525 (tpp) cc_final: 0.8291 (tmm) REVERT: E 481 MET cc_start: 0.9301 (mmm) cc_final: 0.8821 (tpt) REVERT: E 522 MET cc_start: 0.8394 (ttm) cc_final: 0.7897 (ttt) REVERT: E 526 PHE cc_start: 0.6989 (m-10) cc_final: 0.6675 (m-10) REVERT: E 550 LYS cc_start: 0.9282 (tppt) cc_final: 0.8995 (tppt) REVERT: E 553 ASN cc_start: 0.8445 (m-40) cc_final: 0.7969 (m-40) REVERT: g 24 ASN cc_start: 0.9393 (m-40) cc_final: 0.9187 (t0) REVERT: g 102 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8278 (mm-30) REVERT: g 117 HIS cc_start: 0.8512 (t-90) cc_final: 0.8266 (t-90) REVERT: g 134 GLU cc_start: 0.9312 (pt0) cc_final: 0.8747 (pp20) REVERT: g 137 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8280 (mtmm) REVERT: g 163 TYR cc_start: 0.6821 (t80) cc_final: 0.6579 (t80) REVERT: g 173 GLU cc_start: 0.9221 (tt0) cc_final: 0.8953 (mm-30) REVERT: g 440 MET cc_start: 0.4452 (pmm) cc_final: 0.4133 (pmm) REVERT: g 465 ASN cc_start: 0.8613 (m-40) cc_final: 0.8366 (m-40) REVERT: g 481 MET cc_start: 0.9092 (tpt) cc_final: 0.8551 (tpt) REVERT: g 497 ILE cc_start: 0.8745 (tp) cc_final: 0.8131 (tp) REVERT: g 509 MET cc_start: 0.9335 (mmp) cc_final: 0.9112 (mmm) REVERT: g 510 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8295 (tm-30) REVERT: g 514 ARG cc_start: 0.9348 (ttm-80) cc_final: 0.9068 (tpp80) REVERT: g 540 PHE cc_start: 0.7958 (p90) cc_final: 0.7125 (p90) REVERT: g 564 VAL cc_start: 0.9450 (t) cc_final: 0.8992 (p) REVERT: g 571 LYS cc_start: 0.9287 (ptpp) cc_final: 0.8839 (ptpt) REVERT: g 575 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8797 (pt0) REVERT: G 44 MET cc_start: 0.8177 (tpt) cc_final: 0.7553 (tpt) REVERT: G 49 LEU cc_start: 0.8985 (mt) cc_final: 0.8715 (tt) REVERT: G 176 LEU cc_start: 0.9392 (mm) cc_final: 0.8985 (pp) REVERT: G 234 MET cc_start: 0.3361 (ttm) cc_final: 0.0480 (ptm) REVERT: G 507 ASP cc_start: 0.9143 (m-30) cc_final: 0.8912 (m-30) REVERT: G 514 ARG cc_start: 0.9030 (ttm110) cc_final: 0.8716 (ttp-110) REVERT: G 563 GLU cc_start: 0.7860 (pm20) cc_final: 0.7036 (pm20) REVERT: G 567 GLN cc_start: 0.9144 (mt0) cc_final: 0.8367 (mt0) REVERT: G 568 GLN cc_start: 0.9292 (mp10) cc_final: 0.8911 (pm20) REVERT: G 571 LYS cc_start: 0.9342 (mttp) cc_final: 0.8936 (mttp) REVERT: h 52 LEU cc_start: 0.8825 (tp) cc_final: 0.8596 (tt) REVERT: h 70 LEU cc_start: 0.9299 (tp) cc_final: 0.8108 (tp) REVERT: h 84 VAL cc_start: 0.9565 (t) cc_final: 0.8025 (t) REVERT: h 323 MET cc_start: 0.7225 (mtp) cc_final: 0.6967 (mmm) REVERT: h 362 TYR cc_start: 0.7518 (m-10) cc_final: 0.7246 (m-10) REVERT: h 376 LEU cc_start: 0.8897 (tt) cc_final: 0.8616 (mp) REVERT: h 436 GLN cc_start: 0.9513 (tm-30) cc_final: 0.9199 (tp40) REVERT: h 440 ASN cc_start: 0.9577 (t0) cc_final: 0.9368 (t0) REVERT: h 447 GLU cc_start: 0.9329 (pp20) cc_final: 0.9033 (tm-30) REVERT: h 455 GLU cc_start: 0.9432 (tp30) cc_final: 0.9194 (tp30) REVERT: h 460 ASP cc_start: 0.8500 (p0) cc_final: 0.8179 (p0) REVERT: h 503 LYS cc_start: 0.9308 (mmtt) cc_final: 0.8937 (mmtp) REVERT: h 504 ILE cc_start: 0.9619 (mt) cc_final: 0.8957 (tp) REVERT: h 508 ASN cc_start: 0.9378 (m-40) cc_final: 0.8954 (m110) REVERT: H 44 LEU cc_start: 0.9526 (tp) cc_final: 0.9322 (tp) REVERT: H 109 MET cc_start: 0.9638 (mmp) cc_final: 0.9362 (mmp) REVERT: H 110 LYS cc_start: 0.9147 (pttm) cc_final: 0.8919 (ptpt) REVERT: H 138 GLU cc_start: 0.9295 (pt0) cc_final: 0.8971 (pp20) REVERT: H 166 MET cc_start: 0.5470 (mmp) cc_final: 0.5214 (mmp) REVERT: H 202 LYS cc_start: 0.8220 (mmpt) cc_final: 0.7724 (mmtm) REVERT: H 362 TYR cc_start: 0.6256 (m-10) cc_final: 0.5986 (m-10) REVERT: H 398 MET cc_start: 0.8668 (mtm) cc_final: 0.8231 (mpp) REVERT: H 402 ARG cc_start: 0.9370 (mpt180) cc_final: 0.8924 (mmt-90) REVERT: H 418 MET cc_start: 0.8824 (ttt) cc_final: 0.8302 (ptm) REVERT: H 419 GLU cc_start: 0.8693 (tp30) cc_final: 0.8351 (tp30) REVERT: H 449 ILE cc_start: 0.9421 (mp) cc_final: 0.9170 (mp) REVERT: H 494 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8619 (mptt) REVERT: q 39 HIS cc_start: 0.9205 (t-170) cc_final: 0.8500 (t-170) REVERT: q 41 MET cc_start: 0.8168 (tmm) cc_final: 0.7725 (tmm) REVERT: q 49 CYS cc_start: 0.8407 (m) cc_final: 0.7544 (m) REVERT: q 52 ASN cc_start: 0.8686 (m-40) cc_final: 0.8374 (m-40) REVERT: q 91 GLN cc_start: 0.9291 (tt0) cc_final: 0.9090 (tt0) REVERT: q 96 MET cc_start: 0.8157 (ptm) cc_final: 0.7240 (pmm) REVERT: q 115 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8090 (tm-30) REVERT: q 126 GLU cc_start: 0.9151 (mp0) cc_final: 0.8893 (mp0) REVERT: q 153 LYS cc_start: 0.8077 (tptt) cc_final: 0.7828 (tptp) REVERT: q 155 ASP cc_start: 0.8912 (t70) cc_final: 0.8658 (t0) REVERT: q 213 MET cc_start: 0.2304 (mmp) cc_final: 0.1536 (tpp) REVERT: q 226 MET cc_start: 0.3948 (mmp) cc_final: 0.1296 (tpt) REVERT: q 361 MET cc_start: 0.7825 (mtt) cc_final: 0.7368 (ttt) REVERT: q 362 GLU cc_start: 0.7395 (tt0) cc_final: 0.6866 (mm-30) REVERT: q 452 PHE cc_start: 0.9138 (t80) cc_final: 0.8454 (t80) REVERT: q 456 PHE cc_start: 0.9279 (m-10) cc_final: 0.8499 (m-80) REVERT: q 473 GLU cc_start: 0.8990 (tt0) cc_final: 0.8760 (tt0) REVERT: q 533 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9089 (tm-30) REVERT: Q 38 LEU cc_start: 0.9620 (tp) cc_final: 0.9396 (tp) REVERT: Q 39 HIS cc_start: 0.9382 (t70) cc_final: 0.9091 (t70) REVERT: Q 49 CYS cc_start: 0.8734 (m) cc_final: 0.8153 (m) REVERT: Q 53 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8231 (mmtm) REVERT: Q 109 GLU cc_start: 0.9308 (tp30) cc_final: 0.8982 (tp30) REVERT: Q 113 VAL cc_start: 0.9414 (p) cc_final: 0.9090 (p) REVERT: Q 155 ASP cc_start: 0.8555 (t70) cc_final: 0.8270 (t70) REVERT: Q 161 LYS cc_start: 0.9395 (mttt) cc_final: 0.8990 (mtmm) REVERT: Q 162 MET cc_start: 0.8908 (tmm) cc_final: 0.8580 (tmm) REVERT: Q 202 PHE cc_start: 0.7486 (t80) cc_final: 0.7071 (t80) REVERT: Q 230 ARG cc_start: 0.1565 (ttt180) cc_final: -0.0215 (mmp-170) REVERT: Q 361 MET cc_start: 0.7821 (ppp) cc_final: 0.7239 (mtm) REVERT: Q 374 GLU cc_start: 0.5582 (mt-10) cc_final: 0.4854 (pm20) REVERT: Q 428 ILE cc_start: 0.9290 (tt) cc_final: 0.9019 (tt) REVERT: Q 470 ASP cc_start: 0.9025 (t0) cc_final: 0.8547 (t70) REVERT: Q 472 ASN cc_start: 0.8524 (m-40) cc_final: 0.8192 (m-40) REVERT: Q 473 GLU cc_start: 0.9263 (pt0) cc_final: 0.8402 (pt0) REVERT: Q 533 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8576 (tm-30) REVERT: z 37 LEU cc_start: 0.9445 (tp) cc_final: 0.9044 (mt) REVERT: z 40 LYS cc_start: 0.9314 (mmpt) cc_final: 0.9105 (mmmt) REVERT: z 83 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8095 (tm-30) REVERT: z 104 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8659 (tm-30) REVERT: z 128 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8319 (mt-10) REVERT: z 130 MET cc_start: 0.9340 (mmp) cc_final: 0.8727 (mmm) REVERT: z 152 GLN cc_start: 0.8887 (mt0) cc_final: 0.8382 (mm-40) REVERT: z 158 LEU cc_start: 0.9072 (mt) cc_final: 0.8791 (mt) REVERT: z 201 HIS cc_start: 0.9169 (m-70) cc_final: 0.8868 (m90) REVERT: z 215 LEU cc_start: 0.8100 (tp) cc_final: 0.7770 (mm) REVERT: z 246 GLU cc_start: 0.5674 (tt0) cc_final: 0.5436 (mp0) REVERT: z 386 TYR cc_start: 0.8407 (p90) cc_final: 0.7917 (p90) REVERT: z 392 LYS cc_start: 0.9457 (ptmm) cc_final: 0.9220 (ptmm) REVERT: z 412 ILE cc_start: 0.9596 (mm) cc_final: 0.9293 (mm) REVERT: z 419 TYR cc_start: 0.9103 (m-10) cc_final: 0.8635 (m-10) REVERT: z 445 GLU cc_start: 0.9239 (mp0) cc_final: 0.8759 (mm-30) REVERT: z 526 ASN cc_start: 0.9487 (m110) cc_final: 0.9245 (m-40) REVERT: z 527 LEU cc_start: 0.9587 (mt) cc_final: 0.9344 (mt) REVERT: z 529 LEU cc_start: 0.8919 (mt) cc_final: 0.8540 (mt) REVERT: Z 22 ASN cc_start: 0.8598 (m110) cc_final: 0.8363 (m110) REVERT: Z 118 ILE cc_start: 0.8796 (mt) cc_final: 0.8543 (mm) REVERT: Z 119 THR cc_start: 0.9599 (t) cc_final: 0.9348 (p) REVERT: Z 128 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8752 (tp30) REVERT: Z 168 GLU cc_start: 0.9565 (mp0) cc_final: 0.9308 (mp0) REVERT: Z 176 ASP cc_start: 0.8748 (m-30) cc_final: 0.8489 (m-30) REVERT: Z 189 LEU cc_start: 0.8668 (tp) cc_final: 0.8396 (tp) REVERT: Z 193 MET cc_start: 0.7173 (mtm) cc_final: 0.6951 (ttp) REVERT: Z 366 TYR cc_start: 0.7154 (m-10) cc_final: 0.6563 (m-10) REVERT: Z 376 CYS cc_start: 0.9145 (p) cc_final: 0.8847 (p) REVERT: Z 378 ILE cc_start: 0.9204 (mm) cc_final: 0.8961 (mm) REVERT: Z 393 ASP cc_start: 0.9106 (m-30) cc_final: 0.8671 (p0) REVERT: Z 431 MET cc_start: 0.6883 (mmm) cc_final: 0.6658 (tpt) REVERT: Z 465 ASP cc_start: 0.9291 (t0) cc_final: 0.9085 (t0) REVERT: Z 482 ASP cc_start: 0.8810 (m-30) cc_final: 0.8501 (m-30) REVERT: Z 504 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8608 (mm-30) REVERT: Z 523 ILE cc_start: 0.9662 (mm) cc_final: 0.9427 (mm) REVERT: Z 526 ASN cc_start: 0.9146 (m-40) cc_final: 0.8548 (t0) outliers start: 5 outliers final: 2 residues processed: 1404 average time/residue: 0.5562 time to fit residues: 1345.2065 Evaluate side-chains 1113 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1111 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 749 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 443 optimal weight: 9.9990 chunk 568 optimal weight: 6.9990 chunk 440 optimal weight: 0.2980 chunk 654 optimal weight: 3.9990 chunk 434 optimal weight: 6.9990 chunk 774 optimal weight: 20.0000 chunk 484 optimal weight: 0.9990 chunk 472 optimal weight: 0.0270 chunk 357 optimal weight: 0.9990 overall best weight: 1.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 HIS D 112 ASN e 132 GLN ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 474 GLN E 138 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 HIS g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 543 GLN Q 27 GLN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 69 GLN z 142 ASN z 370 ASN ** z 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.6746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 62618 Z= 0.158 Angle : 0.568 12.245 84459 Z= 0.291 Chirality : 0.043 0.225 10166 Planarity : 0.003 0.107 10848 Dihedral : 3.696 23.840 8568 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 0.01 % Allowed : 1.08 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.09), residues: 8065 helix: 0.54 (0.08), residues: 3931 sheet: -0.24 (0.20), residues: 665 loop : -0.61 (0.10), residues: 3469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 440 HIS 0.011 0.001 HIS d 303 PHE 0.031 0.001 PHE Q 137 TYR 0.028 0.001 TYR a 432 ARG 0.008 0.000 ARG Z 318 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1390 time to evaluate : 5.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 44 LEU cc_start: 0.9408 (tp) cc_final: 0.9114 (tp) REVERT: a 73 LEU cc_start: 0.8777 (mt) cc_final: 0.7982 (mt) REVERT: a 81 LYS cc_start: 0.9653 (mttt) cc_final: 0.9399 (mptt) REVERT: a 119 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8667 (tppt) REVERT: a 175 PHE cc_start: 0.7968 (t80) cc_final: 0.7486 (t80) REVERT: a 179 MET cc_start: 0.7699 (mtp) cc_final: 0.7281 (mmm) REVERT: a 258 MET cc_start: 0.1153 (mmm) cc_final: 0.0557 (mmt) REVERT: a 399 GLU cc_start: 0.7026 (tt0) cc_final: 0.6526 (pp20) REVERT: a 432 TYR cc_start: 0.8351 (t80) cc_final: 0.8068 (t80) REVERT: a 448 ILE cc_start: 0.9421 (mt) cc_final: 0.9099 (tt) REVERT: a 451 PHE cc_start: 0.9388 (t80) cc_final: 0.9068 (t80) REVERT: a 460 LYS cc_start: 0.8841 (tptt) cc_final: 0.8450 (tptt) REVERT: a 497 TYR cc_start: 0.8136 (m-80) cc_final: 0.7692 (m-80) REVERT: a 502 LEU cc_start: 0.8060 (mt) cc_final: 0.7665 (mt) REVERT: a 530 SER cc_start: 0.9450 (m) cc_final: 0.9197 (p) REVERT: a 532 LEU cc_start: 0.9407 (mm) cc_final: 0.8894 (tt) REVERT: A 30 VAL cc_start: 0.9323 (p) cc_final: 0.9041 (m) REVERT: A 52 MET cc_start: 0.6239 (tpt) cc_final: 0.5840 (tpp) REVERT: A 111 ARG cc_start: 0.9123 (mmm-85) cc_final: 0.8762 (tpp80) REVERT: A 119 LYS cc_start: 0.9319 (mppt) cc_final: 0.9061 (mppt) REVERT: A 233 MET cc_start: 0.3037 (ptt) cc_final: 0.1518 (ptm) REVERT: A 307 LEU cc_start: 0.4630 (mt) cc_final: 0.4331 (pp) REVERT: A 320 ARG cc_start: 0.7115 (mtt90) cc_final: 0.6782 (ptp90) REVERT: A 444 GLU cc_start: 0.9493 (pm20) cc_final: 0.9229 (pm20) REVERT: A 477 LEU cc_start: 0.9326 (mt) cc_final: 0.8966 (mt) REVERT: A 506 ARG cc_start: 0.9220 (tmm-80) cc_final: 0.8915 (tmm-80) REVERT: A 533 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8790 (mm-30) REVERT: b 42 MET cc_start: 0.7917 (mpp) cc_final: 0.7279 (mpp) REVERT: b 45 LEU cc_start: 0.9272 (tp) cc_final: 0.8491 (pp) REVERT: b 46 LEU cc_start: 0.9087 (mm) cc_final: 0.8629 (mt) REVERT: b 55 MET cc_start: 0.6697 (mtt) cc_final: 0.6433 (mtt) REVERT: b 59 ASP cc_start: 0.8726 (t0) cc_final: 0.8480 (t0) REVERT: b 78 VAL cc_start: 0.9135 (t) cc_final: 0.8775 (t) REVERT: b 82 LYS cc_start: 0.9344 (mmtt) cc_final: 0.9087 (mmmm) REVERT: b 85 ASP cc_start: 0.9179 (m-30) cc_final: 0.8507 (t70) REVERT: b 121 ILE cc_start: 0.8830 (mt) cc_final: 0.8626 (mt) REVERT: b 144 HIS cc_start: 0.8098 (p90) cc_final: 0.7862 (p90) REVERT: b 148 MET cc_start: 0.8461 (ppp) cc_final: 0.7988 (ppp) REVERT: b 158 LYS cc_start: 0.9326 (mttt) cc_final: 0.8978 (mmmm) REVERT: b 439 GLN cc_start: 0.9122 (mm110) cc_final: 0.8788 (mp10) REVERT: b 472 LEU cc_start: 0.8875 (mt) cc_final: 0.8542 (mt) REVERT: B 64 LEU cc_start: 0.9452 (mt) cc_final: 0.9147 (pp) REVERT: B 155 HIS cc_start: 0.9341 (m90) cc_final: 0.9061 (m90) REVERT: B 196 ILE cc_start: 0.8310 (mm) cc_final: 0.7919 (mm) REVERT: B 315 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 354 LEU cc_start: 0.4661 (mt) cc_final: 0.3918 (mt) REVERT: B 386 ASP cc_start: 0.8603 (m-30) cc_final: 0.7460 (t70) REVERT: B 409 MET cc_start: 0.9420 (tpp) cc_final: 0.9128 (ttm) REVERT: B 415 VAL cc_start: 0.9435 (t) cc_final: 0.9210 (p) REVERT: B 452 SER cc_start: 0.9055 (p) cc_final: 0.8579 (t) REVERT: B 472 LEU cc_start: 0.8722 (mt) cc_final: 0.8261 (mt) REVERT: d 166 TYR cc_start: 0.7038 (m-80) cc_final: 0.6692 (m-10) REVERT: d 209 MET cc_start: 0.3529 (mtm) cc_final: 0.3147 (ttp) REVERT: d 311 MET cc_start: 0.2870 (mmm) cc_final: 0.2565 (mmm) REVERT: d 315 ASP cc_start: 0.3263 (m-30) cc_final: 0.2423 (t70) REVERT: d 411 ILE cc_start: 0.9010 (pt) cc_final: 0.8552 (mm) REVERT: d 433 GLU cc_start: 0.7839 (pm20) cc_final: 0.7410 (tp30) REVERT: d 464 LYS cc_start: 0.9591 (mmmt) cc_final: 0.8975 (tmmt) REVERT: D 44 MET cc_start: 0.8124 (mpp) cc_final: 0.7626 (mpp) REVERT: D 110 LEU cc_start: 0.8410 (mt) cc_final: 0.8196 (mt) REVERT: D 122 ASP cc_start: 0.8733 (t70) cc_final: 0.8410 (p0) REVERT: D 133 ASP cc_start: 0.9453 (m-30) cc_final: 0.9067 (t0) REVERT: D 138 MET cc_start: 0.5359 (mmt) cc_final: 0.5002 (mmt) REVERT: D 209 MET cc_start: 0.4430 (mmt) cc_final: 0.3969 (mmt) REVERT: D 385 MET cc_start: 0.6011 (ppp) cc_final: 0.5225 (tpp) REVERT: D 509 THR cc_start: 0.9432 (t) cc_final: 0.9049 (t) REVERT: D 513 GLU cc_start: 0.9562 (mm-30) cc_final: 0.9255 (mp0) REVERT: e 107 LEU cc_start: 0.9318 (tp) cc_final: 0.9095 (tp) REVERT: e 113 ASP cc_start: 0.8371 (m-30) cc_final: 0.7660 (p0) REVERT: e 125 LEU cc_start: 0.9487 (tp) cc_final: 0.9266 (tp) REVERT: e 131 ASP cc_start: 0.9045 (t70) cc_final: 0.8762 (m-30) REVERT: e 134 LEU cc_start: 0.9015 (tp) cc_final: 0.8796 (tp) REVERT: e 146 ILE cc_start: 0.9714 (mm) cc_final: 0.8600 (mm) REVERT: e 150 PHE cc_start: 0.9046 (m-10) cc_final: 0.8595 (m-80) REVERT: e 202 GLU cc_start: 0.7993 (pp20) cc_final: 0.7294 (tp30) REVERT: e 203 MET cc_start: 0.4050 (tmm) cc_final: 0.3040 (ptt) REVERT: e 210 ASN cc_start: 0.8769 (m-40) cc_final: 0.8256 (t0) REVERT: e 254 MET cc_start: 0.3898 (mtt) cc_final: 0.3505 (mtt) REVERT: e 472 PHE cc_start: 0.9207 (t80) cc_final: 0.8834 (t80) REVERT: e 495 LEU cc_start: 0.9160 (tp) cc_final: 0.8502 (mt) REVERT: e 554 VAL cc_start: 0.7435 (p) cc_final: 0.7053 (p) REVERT: E 50 HIS cc_start: 0.8826 (m90) cc_final: 0.8592 (m90) REVERT: E 63 THR cc_start: 0.9376 (p) cc_final: 0.9117 (t) REVERT: E 94 MET cc_start: 0.7503 (ttp) cc_final: 0.6773 (tmm) REVERT: E 113 ASP cc_start: 0.9141 (m-30) cc_final: 0.8811 (t0) REVERT: E 203 MET cc_start: 0.5824 (ptp) cc_final: 0.4805 (mpp) REVERT: E 368 ASP cc_start: 0.5593 (m-30) cc_final: 0.5141 (t70) REVERT: E 481 MET cc_start: 0.9311 (mmm) cc_final: 0.8848 (tpt) REVERT: E 522 MET cc_start: 0.8254 (ttm) cc_final: 0.8052 (ttt) REVERT: E 526 PHE cc_start: 0.6887 (m-10) cc_final: 0.6591 (m-10) REVERT: E 550 LYS cc_start: 0.9339 (tppt) cc_final: 0.9051 (tppt) REVERT: E 553 ASN cc_start: 0.8492 (m-40) cc_final: 0.8270 (m-40) REVERT: g 24 ASN cc_start: 0.9398 (m-40) cc_final: 0.9191 (t0) REVERT: g 38 CYS cc_start: 0.9447 (m) cc_final: 0.9113 (m) REVERT: g 102 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8213 (mm-30) REVERT: g 117 HIS cc_start: 0.8470 (t-90) cc_final: 0.8250 (t-90) REVERT: g 134 GLU cc_start: 0.9305 (pt0) cc_final: 0.8770 (pp20) REVERT: g 137 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8257 (mtmm) REVERT: g 163 TYR cc_start: 0.6810 (t80) cc_final: 0.6568 (t80) REVERT: g 173 GLU cc_start: 0.9239 (tt0) cc_final: 0.8970 (mm-30) REVERT: g 234 MET cc_start: 0.1379 (tmm) cc_final: 0.0964 (tmm) REVERT: g 440 MET cc_start: 0.4548 (pmm) cc_final: 0.4213 (pmm) REVERT: g 481 MET cc_start: 0.9047 (tpt) cc_final: 0.8529 (tpt) REVERT: g 497 ILE cc_start: 0.8644 (tp) cc_final: 0.7958 (tp) REVERT: g 512 ILE cc_start: 0.9391 (mp) cc_final: 0.9168 (mp) REVERT: g 540 PHE cc_start: 0.7954 (p90) cc_final: 0.7103 (p90) REVERT: g 568 GLN cc_start: 0.9598 (mp10) cc_final: 0.9317 (mp10) REVERT: g 575 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8792 (pt0) REVERT: g 585 ASP cc_start: 0.8743 (m-30) cc_final: 0.8425 (m-30) REVERT: G 45 LEU cc_start: 0.8926 (tp) cc_final: 0.8279 (tp) REVERT: G 49 LEU cc_start: 0.9055 (mt) cc_final: 0.8782 (tt) REVERT: G 52 MET cc_start: 0.8601 (tmm) cc_final: 0.8337 (tmm) REVERT: G 117 HIS cc_start: 0.8992 (t-90) cc_final: 0.8724 (t-90) REVERT: G 234 MET cc_start: 0.3400 (ttm) cc_final: 0.0437 (ptm) REVERT: G 512 ILE cc_start: 0.9131 (mm) cc_final: 0.8826 (mm) REVERT: G 563 GLU cc_start: 0.7963 (pm20) cc_final: 0.7346 (pm20) REVERT: G 567 GLN cc_start: 0.9134 (mt0) cc_final: 0.8443 (mt0) REVERT: h 52 LEU cc_start: 0.8897 (tp) cc_final: 0.8675 (tt) REVERT: h 64 ASN cc_start: 0.7891 (t0) cc_final: 0.7638 (t0) REVERT: h 70 LEU cc_start: 0.8998 (tp) cc_final: 0.8627 (tp) REVERT: h 71 LYS cc_start: 0.9277 (tppt) cc_final: 0.9008 (tppt) REVERT: h 323 MET cc_start: 0.7225 (mtp) cc_final: 0.6946 (mmm) REVERT: h 362 TYR cc_start: 0.7569 (m-10) cc_final: 0.7305 (m-10) REVERT: h 376 LEU cc_start: 0.8822 (tt) cc_final: 0.8452 (mp) REVERT: h 436 GLN cc_start: 0.9461 (tm-30) cc_final: 0.9107 (tp40) REVERT: h 440 ASN cc_start: 0.9580 (t0) cc_final: 0.9368 (t0) REVERT: h 447 GLU cc_start: 0.9319 (pp20) cc_final: 0.8909 (pp20) REVERT: h 451 ARG cc_start: 0.9551 (tpp80) cc_final: 0.9073 (tpp80) REVERT: h 455 GLU cc_start: 0.9433 (tp30) cc_final: 0.9196 (tp30) REVERT: h 460 ASP cc_start: 0.8501 (p0) cc_final: 0.8165 (p0) REVERT: h 465 LEU cc_start: 0.9581 (mp) cc_final: 0.9354 (mp) REVERT: h 503 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8839 (mmtp) REVERT: h 504 ILE cc_start: 0.9632 (mt) cc_final: 0.8970 (tp) REVERT: h 508 ASN cc_start: 0.9357 (m-40) cc_final: 0.8966 (m110) REVERT: H 44 LEU cc_start: 0.9513 (tp) cc_final: 0.9305 (tp) REVERT: H 110 LYS cc_start: 0.8789 (pttm) cc_final: 0.8581 (ptpp) REVERT: H 138 GLU cc_start: 0.9302 (pt0) cc_final: 0.8999 (pp20) REVERT: H 202 LYS cc_start: 0.8137 (mmpt) cc_final: 0.7621 (mmtm) REVERT: H 362 TYR cc_start: 0.6051 (m-10) cc_final: 0.5771 (m-10) REVERT: H 398 MET cc_start: 0.8736 (mtm) cc_final: 0.8343 (mpp) REVERT: H 402 ARG cc_start: 0.9432 (mpt180) cc_final: 0.8943 (mmt-90) REVERT: H 418 MET cc_start: 0.8865 (ttt) cc_final: 0.8350 (ptm) REVERT: H 419 GLU cc_start: 0.8885 (tp30) cc_final: 0.8539 (tp30) REVERT: H 437 MET cc_start: 0.9537 (mtm) cc_final: 0.9265 (tpt) REVERT: H 440 ASN cc_start: 0.9245 (m-40) cc_final: 0.8973 (m110) REVERT: H 449 ILE cc_start: 0.9410 (mp) cc_final: 0.9157 (mp) REVERT: H 494 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8642 (mptt) REVERT: q 39 HIS cc_start: 0.9310 (t-170) cc_final: 0.8832 (t-170) REVERT: q 41 MET cc_start: 0.8159 (tmm) cc_final: 0.7452 (tmm) REVERT: q 49 CYS cc_start: 0.8449 (m) cc_final: 0.7582 (m) REVERT: q 52 ASN cc_start: 0.8769 (m-40) cc_final: 0.8440 (m-40) REVERT: q 94 ILE cc_start: 0.8454 (mm) cc_final: 0.7883 (mm) REVERT: q 96 MET cc_start: 0.8098 (ptm) cc_final: 0.7193 (pmm) REVERT: q 115 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8282 (tm-30) REVERT: q 153 LYS cc_start: 0.8187 (tptt) cc_final: 0.7937 (tptp) REVERT: q 155 ASP cc_start: 0.8969 (t70) cc_final: 0.8731 (t0) REVERT: q 213 MET cc_start: 0.2325 (mmp) cc_final: 0.0270 (tpp) REVERT: q 361 MET cc_start: 0.7823 (mtt) cc_final: 0.7381 (ttt) REVERT: q 362 GLU cc_start: 0.7456 (tt0) cc_final: 0.7112 (mm-30) REVERT: q 452 PHE cc_start: 0.9105 (t80) cc_final: 0.8411 (t80) REVERT: q 456 PHE cc_start: 0.9305 (m-10) cc_final: 0.8516 (m-80) REVERT: q 473 GLU cc_start: 0.9044 (tt0) cc_final: 0.8637 (tt0) REVERT: q 520 MET cc_start: 0.7530 (tpt) cc_final: 0.7248 (tpt) REVERT: q 533 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9093 (tm-30) REVERT: Q 30 LYS cc_start: 0.8518 (pttm) cc_final: 0.8059 (ptpt) REVERT: Q 39 HIS cc_start: 0.9403 (t70) cc_final: 0.9093 (t-170) REVERT: Q 41 MET cc_start: 0.8565 (tmm) cc_final: 0.8325 (tmm) REVERT: Q 49 CYS cc_start: 0.8696 (m) cc_final: 0.8258 (m) REVERT: Q 87 MET cc_start: 0.9574 (mpp) cc_final: 0.9316 (mmt) REVERT: Q 96 MET cc_start: 0.7617 (ptp) cc_final: 0.7362 (ptp) REVERT: Q 109 GLU cc_start: 0.9295 (tp30) cc_final: 0.9021 (tp30) REVERT: Q 113 VAL cc_start: 0.9411 (p) cc_final: 0.9039 (p) REVERT: Q 155 ASP cc_start: 0.8615 (t70) cc_final: 0.8337 (t70) REVERT: Q 161 LYS cc_start: 0.9446 (mttt) cc_final: 0.8924 (mtmm) REVERT: Q 162 MET cc_start: 0.8932 (tmm) cc_final: 0.8591 (tmm) REVERT: Q 202 PHE cc_start: 0.7235 (t80) cc_final: 0.6951 (t80) REVERT: Q 361 MET cc_start: 0.7821 (ppp) cc_final: 0.7183 (mtm) REVERT: Q 374 GLU cc_start: 0.5593 (mt-10) cc_final: 0.4878 (pm20) REVERT: Q 428 ILE cc_start: 0.9277 (tt) cc_final: 0.9024 (tt) REVERT: Q 470 ASP cc_start: 0.9019 (t0) cc_final: 0.8557 (t70) REVERT: Q 472 ASN cc_start: 0.8500 (m-40) cc_final: 0.8126 (m-40) REVERT: Q 473 GLU cc_start: 0.9254 (pt0) cc_final: 0.8358 (pt0) REVERT: Q 533 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8577 (tm-30) REVERT: z 36 ASN cc_start: 0.9013 (p0) cc_final: 0.8772 (p0) REVERT: z 37 LEU cc_start: 0.9440 (tp) cc_final: 0.9043 (mt) REVERT: z 40 LYS cc_start: 0.9393 (mmpt) cc_final: 0.9126 (mmmt) REVERT: z 83 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8324 (tm-30) REVERT: z 128 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8311 (mt-10) REVERT: z 130 MET cc_start: 0.9328 (mmp) cc_final: 0.8713 (mmm) REVERT: z 158 LEU cc_start: 0.9063 (mt) cc_final: 0.8758 (mt) REVERT: z 197 MET cc_start: 0.8361 (ppp) cc_final: 0.7859 (ppp) REVERT: z 201 HIS cc_start: 0.9121 (m-70) cc_final: 0.8874 (m90) REVERT: z 215 LEU cc_start: 0.8198 (tp) cc_final: 0.7900 (mm) REVERT: z 386 TYR cc_start: 0.8457 (p90) cc_final: 0.7937 (p90) REVERT: z 392 LYS cc_start: 0.9475 (ptmm) cc_final: 0.9235 (ptmm) REVERT: z 412 ILE cc_start: 0.9601 (mm) cc_final: 0.9259 (mm) REVERT: z 419 TYR cc_start: 0.8996 (m-10) cc_final: 0.8649 (m-10) REVERT: z 445 GLU cc_start: 0.9214 (mp0) cc_final: 0.8812 (mm-30) REVERT: z 525 SER cc_start: 0.9453 (m) cc_final: 0.8971 (p) REVERT: z 526 ASN cc_start: 0.9493 (m110) cc_final: 0.9269 (m-40) REVERT: z 527 LEU cc_start: 0.9579 (mt) cc_final: 0.9307 (mt) REVERT: z 529 LEU cc_start: 0.8958 (mt) cc_final: 0.8544 (mt) REVERT: Z 22 ASN cc_start: 0.8590 (m110) cc_final: 0.8331 (m110) REVERT: Z 118 ILE cc_start: 0.8910 (mt) cc_final: 0.8609 (mm) REVERT: Z 128 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8744 (tp30) REVERT: Z 168 GLU cc_start: 0.9541 (mp0) cc_final: 0.9290 (pm20) REVERT: Z 176 ASP cc_start: 0.8799 (m-30) cc_final: 0.8558 (m-30) REVERT: Z 189 LEU cc_start: 0.8672 (tp) cc_final: 0.8394 (tp) REVERT: Z 193 MET cc_start: 0.7215 (mtm) cc_final: 0.7000 (ttp) REVERT: Z 366 TYR cc_start: 0.7173 (m-10) cc_final: 0.6613 (m-10) REVERT: Z 376 CYS cc_start: 0.9196 (p) cc_final: 0.8890 (p) REVERT: Z 378 ILE cc_start: 0.9180 (mm) cc_final: 0.8940 (mm) REVERT: Z 393 ASP cc_start: 0.9077 (m-30) cc_final: 0.8591 (p0) REVERT: Z 431 MET cc_start: 0.6788 (mmm) cc_final: 0.6543 (tpt) REVERT: Z 465 ASP cc_start: 0.9360 (t0) cc_final: 0.9108 (t0) REVERT: Z 482 ASP cc_start: 0.8893 (m-30) cc_final: 0.8576 (m-30) REVERT: Z 504 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8620 (mm-30) REVERT: Z 523 ILE cc_start: 0.9672 (mm) cc_final: 0.9427 (mm) REVERT: Z 526 ASN cc_start: 0.9186 (m-40) cc_final: 0.8634 (t0) outliers start: 1 outliers final: 0 residues processed: 1391 average time/residue: 0.5575 time to fit residues: 1334.9301 Evaluate side-chains 1099 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1099 time to evaluate : 5.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 479 optimal weight: 0.9980 chunk 309 optimal weight: 8.9990 chunk 462 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 492 optimal weight: 4.9990 chunk 527 optimal weight: 5.9990 chunk 383 optimal weight: 5.9990 chunk 72 optimal weight: 0.2980 chunk 609 optimal weight: 0.0570 overall best weight: 1.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 113 ASN ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 118 GLN D 112 ASN e 138 GLN ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN G 535 HIS ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 529 ASN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 391 GLN z 22 ASN z 230 ASN z 298 GLN z 481 GLN ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 62618 Z= 0.171 Angle : 0.582 14.210 84459 Z= 0.296 Chirality : 0.043 0.226 10166 Planarity : 0.003 0.097 10848 Dihedral : 3.733 20.103 8568 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.09), residues: 8065 helix: 0.58 (0.08), residues: 3932 sheet: -0.31 (0.20), residues: 669 loop : -0.59 (0.10), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 440 HIS 0.007 0.001 HIS E 424 PHE 0.031 0.001 PHE Q 137 TYR 0.015 0.001 TYR a 432 ARG 0.011 0.000 ARG G 514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1376 time to evaluate : 5.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 34 MET cc_start: 0.8693 (ppp) cc_final: 0.8466 (tmm) REVERT: a 44 LEU cc_start: 0.9404 (tp) cc_final: 0.9099 (tp) REVERT: a 51 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7941 (mmtp) REVERT: a 73 LEU cc_start: 0.8674 (mt) cc_final: 0.7802 (mt) REVERT: a 109 LEU cc_start: 0.9074 (mt) cc_final: 0.8855 (mt) REVERT: a 119 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8709 (tppt) REVERT: a 125 ILE cc_start: 0.9472 (tp) cc_final: 0.9199 (tp) REVERT: a 135 GLU cc_start: 0.8450 (tp30) cc_final: 0.7762 (tp30) REVERT: a 164 MET cc_start: 0.6457 (mmp) cc_final: 0.6186 (mmm) REVERT: a 175 PHE cc_start: 0.7992 (t80) cc_final: 0.7786 (t80) REVERT: a 193 LYS cc_start: 0.7095 (mttt) cc_final: 0.6866 (mtmm) REVERT: a 258 MET cc_start: 0.1414 (mmm) cc_final: 0.0778 (mmt) REVERT: a 399 GLU cc_start: 0.7052 (tt0) cc_final: 0.6580 (pp20) REVERT: a 436 PHE cc_start: 0.8206 (t80) cc_final: 0.7463 (t80) REVERT: a 451 PHE cc_start: 0.9404 (t80) cc_final: 0.9199 (t80) REVERT: a 460 LYS cc_start: 0.8890 (tptt) cc_final: 0.8573 (tptt) REVERT: a 469 ASP cc_start: 0.8933 (t0) cc_final: 0.7726 (t0) REVERT: a 472 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8579 (mm-30) REVERT: a 497 TYR cc_start: 0.8029 (m-80) cc_final: 0.7560 (m-80) REVERT: a 502 LEU cc_start: 0.7880 (mt) cc_final: 0.7499 (mt) REVERT: a 532 LEU cc_start: 0.9389 (mm) cc_final: 0.8910 (tt) REVERT: A 30 VAL cc_start: 0.9370 (p) cc_final: 0.9074 (m) REVERT: A 41 LYS cc_start: 0.8957 (pttt) cc_final: 0.8739 (mttt) REVERT: A 52 MET cc_start: 0.6514 (tpt) cc_final: 0.6056 (tpp) REVERT: A 111 ARG cc_start: 0.9190 (mmm-85) cc_final: 0.8532 (mmm-85) REVERT: A 114 GLU cc_start: 0.9310 (tm-30) cc_final: 0.9104 (tm-30) REVERT: A 119 LYS cc_start: 0.9304 (mppt) cc_final: 0.9050 (mppt) REVERT: A 233 MET cc_start: 0.3262 (ptt) cc_final: 0.2042 (ptm) REVERT: A 307 LEU cc_start: 0.4722 (mt) cc_final: 0.4346 (pp) REVERT: A 320 ARG cc_start: 0.7124 (mtt90) cc_final: 0.6821 (ptp90) REVERT: A 341 MET cc_start: 0.3659 (mpp) cc_final: 0.3459 (mmm) REVERT: A 393 TYR cc_start: 0.8431 (m-80) cc_final: 0.8168 (m-80) REVERT: A 444 GLU cc_start: 0.9482 (pm20) cc_final: 0.9208 (pm20) REVERT: A 477 LEU cc_start: 0.9334 (mt) cc_final: 0.8970 (mt) REVERT: A 533 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8688 (mm-30) REVERT: b 42 MET cc_start: 0.8187 (mpp) cc_final: 0.7406 (mpp) REVERT: b 45 LEU cc_start: 0.9439 (tp) cc_final: 0.8511 (pp) REVERT: b 46 LEU cc_start: 0.9202 (mm) cc_final: 0.8622 (mt) REVERT: b 55 MET cc_start: 0.6873 (mtt) cc_final: 0.6615 (mtt) REVERT: b 59 ASP cc_start: 0.8782 (t0) cc_final: 0.8540 (t0) REVERT: b 78 VAL cc_start: 0.9156 (t) cc_final: 0.8798 (t) REVERT: b 115 ILE cc_start: 0.7991 (mm) cc_final: 0.7774 (mm) REVERT: b 144 HIS cc_start: 0.8114 (p90) cc_final: 0.7878 (p90) REVERT: b 148 MET cc_start: 0.8441 (ppp) cc_final: 0.8013 (ppp) REVERT: b 181 ILE cc_start: 0.7611 (pt) cc_final: 0.7346 (pt) REVERT: b 388 LEU cc_start: 0.9631 (tp) cc_final: 0.9425 (tp) REVERT: b 425 LYS cc_start: 0.9176 (ptmt) cc_final: 0.8718 (ttpp) REVERT: b 426 LYS cc_start: 0.9325 (mtmm) cc_final: 0.9098 (mppt) REVERT: b 439 GLN cc_start: 0.9180 (mm110) cc_final: 0.8803 (mp10) REVERT: b 472 LEU cc_start: 0.8641 (mt) cc_final: 0.8304 (mt) REVERT: B 64 LEU cc_start: 0.9442 (mt) cc_final: 0.9159 (pp) REVERT: B 155 HIS cc_start: 0.9346 (m90) cc_final: 0.9121 (m90) REVERT: B 196 ILE cc_start: 0.8303 (mm) cc_final: 0.7843 (mm) REVERT: B 315 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 354 LEU cc_start: 0.4605 (mt) cc_final: 0.3956 (mt) REVERT: B 386 ASP cc_start: 0.8566 (m-30) cc_final: 0.7422 (t70) REVERT: B 409 MET cc_start: 0.9404 (tpp) cc_final: 0.9069 (ttm) REVERT: B 452 SER cc_start: 0.9076 (p) cc_final: 0.8562 (t) REVERT: B 472 LEU cc_start: 0.8712 (mt) cc_final: 0.8234 (mt) REVERT: d 166 TYR cc_start: 0.6798 (m-80) cc_final: 0.6382 (m-10) REVERT: d 209 MET cc_start: 0.3939 (mtm) cc_final: 0.3488 (ttm) REVERT: d 311 MET cc_start: 0.3801 (mmm) cc_final: 0.3420 (mmm) REVERT: d 315 ASP cc_start: 0.3060 (m-30) cc_final: 0.2160 (t70) REVERT: d 411 ILE cc_start: 0.9061 (pt) cc_final: 0.8576 (mm) REVERT: d 433 GLU cc_start: 0.7921 (pm20) cc_final: 0.7529 (tp30) REVERT: d 464 LYS cc_start: 0.9658 (mmmt) cc_final: 0.8947 (ptmm) REVERT: D 44 MET cc_start: 0.8165 (mpp) cc_final: 0.7666 (mpp) REVERT: D 47 MET cc_start: 0.5438 (tpt) cc_final: 0.5126 (tpt) REVERT: D 122 ASP cc_start: 0.8793 (t70) cc_final: 0.8466 (p0) REVERT: D 133 ASP cc_start: 0.9437 (m-30) cc_final: 0.9167 (t0) REVERT: D 138 MET cc_start: 0.5623 (mmt) cc_final: 0.5277 (mmt) REVERT: D 209 MET cc_start: 0.4579 (mmt) cc_final: 0.4138 (mmt) REVERT: D 385 MET cc_start: 0.5996 (ppp) cc_final: 0.5261 (tpp) REVERT: D 438 PHE cc_start: 0.9495 (m-10) cc_final: 0.9259 (m-80) REVERT: D 470 ARG cc_start: 0.9185 (tpt90) cc_final: 0.8567 (tpt90) REVERT: D 509 THR cc_start: 0.9380 (t) cc_final: 0.9063 (t) REVERT: D 513 GLU cc_start: 0.9589 (mm-30) cc_final: 0.9190 (mp0) REVERT: e 104 LEU cc_start: 0.8967 (mt) cc_final: 0.8665 (mt) REVERT: e 107 LEU cc_start: 0.9309 (tp) cc_final: 0.9088 (tp) REVERT: e 113 ASP cc_start: 0.8295 (m-30) cc_final: 0.7605 (p0) REVERT: e 125 LEU cc_start: 0.9504 (tp) cc_final: 0.9271 (tp) REVERT: e 146 ILE cc_start: 0.9720 (mm) cc_final: 0.8709 (mm) REVERT: e 150 PHE cc_start: 0.9075 (m-10) cc_final: 0.8495 (m-80) REVERT: e 202 GLU cc_start: 0.8037 (pp20) cc_final: 0.7281 (tp30) REVERT: e 203 MET cc_start: 0.4192 (tmm) cc_final: 0.3174 (ptt) REVERT: e 210 ASN cc_start: 0.8720 (m-40) cc_final: 0.8216 (t0) REVERT: e 254 MET cc_start: 0.3993 (mtt) cc_final: 0.3599 (mtt) REVERT: e 462 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7220 (mmt90) REVERT: e 472 PHE cc_start: 0.9239 (t80) cc_final: 0.9033 (t80) REVERT: e 495 LEU cc_start: 0.9173 (tp) cc_final: 0.8485 (mt) REVERT: e 536 GLN cc_start: 0.8943 (mp10) cc_final: 0.8542 (mp10) REVERT: E 50 HIS cc_start: 0.8878 (m90) cc_final: 0.8629 (m90) REVERT: E 63 THR cc_start: 0.9423 (p) cc_final: 0.9131 (t) REVERT: E 94 MET cc_start: 0.7677 (ttp) cc_final: 0.6689 (tmm) REVERT: E 113 ASP cc_start: 0.9161 (m-30) cc_final: 0.8859 (t0) REVERT: E 163 GLU cc_start: 0.9389 (mt-10) cc_final: 0.9079 (mp0) REVERT: E 203 MET cc_start: 0.5996 (ptp) cc_final: 0.4906 (mpp) REVERT: E 224 ILE cc_start: 0.6217 (mm) cc_final: 0.5835 (mm) REVERT: E 368 ASP cc_start: 0.5649 (m-30) cc_final: 0.5128 (t70) REVERT: E 481 MET cc_start: 0.9334 (mmm) cc_final: 0.8847 (tpt) REVERT: E 522 MET cc_start: 0.8244 (ttm) cc_final: 0.7842 (ttt) REVERT: E 526 PHE cc_start: 0.7050 (m-10) cc_final: 0.6759 (m-10) REVERT: E 539 LEU cc_start: 0.9406 (tp) cc_final: 0.9117 (tp) REVERT: E 542 THR cc_start: 0.9361 (m) cc_final: 0.9082 (t) REVERT: E 553 ASN cc_start: 0.8587 (m-40) cc_final: 0.6815 (m-40) REVERT: g 24 ASN cc_start: 0.9462 (m-40) cc_final: 0.9203 (t0) REVERT: g 38 CYS cc_start: 0.9421 (m) cc_final: 0.9149 (m) REVERT: g 102 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8164 (mm-30) REVERT: g 117 HIS cc_start: 0.8479 (t-90) cc_final: 0.8274 (t-90) REVERT: g 134 GLU cc_start: 0.9300 (pt0) cc_final: 0.8826 (pp20) REVERT: g 163 TYR cc_start: 0.6818 (t80) cc_final: 0.6565 (t80) REVERT: g 173 GLU cc_start: 0.9220 (tt0) cc_final: 0.8986 (mm-30) REVERT: g 440 MET cc_start: 0.5033 (pmm) cc_final: 0.4732 (pmm) REVERT: g 481 MET cc_start: 0.9022 (tpt) cc_final: 0.8349 (tpt) REVERT: g 497 ILE cc_start: 0.8727 (tp) cc_final: 0.8027 (tp) REVERT: g 509 MET cc_start: 0.9422 (mmp) cc_final: 0.9121 (tpp) REVERT: g 540 PHE cc_start: 0.7981 (p90) cc_final: 0.7082 (p90) REVERT: g 585 ASP cc_start: 0.8688 (m-30) cc_final: 0.8141 (m-30) REVERT: G 45 LEU cc_start: 0.8974 (tp) cc_final: 0.8703 (tp) REVERT: G 52 MET cc_start: 0.8629 (tmm) cc_final: 0.8369 (tmm) REVERT: G 117 HIS cc_start: 0.8938 (t-90) cc_final: 0.8698 (t-90) REVERT: G 134 GLU cc_start: 0.9295 (mt-10) cc_final: 0.9004 (mm-30) REVERT: G 234 MET cc_start: 0.3439 (ttm) cc_final: 0.0560 (ptm) REVERT: G 511 CYS cc_start: 0.9033 (p) cc_final: 0.8725 (p) REVERT: G 563 GLU cc_start: 0.8195 (pm20) cc_final: 0.7603 (pm20) REVERT: G 567 GLN cc_start: 0.9144 (mt0) cc_final: 0.8346 (mt0) REVERT: h 70 LEU cc_start: 0.9068 (tp) cc_final: 0.8836 (tp) REVERT: h 71 LYS cc_start: 0.9296 (tppt) cc_final: 0.9013 (tppt) REVERT: h 104 LEU cc_start: 0.9263 (mm) cc_final: 0.8993 (mm) REVERT: h 376 LEU cc_start: 0.8868 (tt) cc_final: 0.8495 (mp) REVERT: h 436 GLN cc_start: 0.9364 (tm-30) cc_final: 0.9112 (tp40) REVERT: h 440 ASN cc_start: 0.9570 (t0) cc_final: 0.9365 (t0) REVERT: h 455 GLU cc_start: 0.9431 (tp30) cc_final: 0.9221 (tp30) REVERT: h 460 ASP cc_start: 0.8420 (p0) cc_final: 0.8113 (p0) REVERT: h 465 LEU cc_start: 0.9559 (mp) cc_final: 0.9276 (mp) REVERT: h 504 ILE cc_start: 0.9605 (mt) cc_final: 0.9045 (tp) REVERT: h 508 ASN cc_start: 0.9360 (m-40) cc_final: 0.8942 (m110) REVERT: H 44 LEU cc_start: 0.9516 (tp) cc_final: 0.9304 (tp) REVERT: H 51 ILE cc_start: 0.9021 (mm) cc_final: 0.8586 (mm) REVERT: H 110 LYS cc_start: 0.8588 (pttm) cc_final: 0.8280 (ptpp) REVERT: H 126 MET cc_start: 0.9157 (tpp) cc_final: 0.8553 (tpp) REVERT: H 138 GLU cc_start: 0.9326 (pt0) cc_final: 0.9021 (pp20) REVERT: H 166 MET cc_start: 0.5353 (mmp) cc_final: 0.4961 (mmp) REVERT: H 202 LYS cc_start: 0.8158 (mmpt) cc_final: 0.7705 (mmtm) REVERT: H 362 TYR cc_start: 0.5955 (m-10) cc_final: 0.5632 (m-10) REVERT: H 398 MET cc_start: 0.8890 (mtm) cc_final: 0.8392 (mpp) REVERT: H 418 MET cc_start: 0.8940 (ttt) cc_final: 0.8333 (ptm) REVERT: H 419 GLU cc_start: 0.8870 (tp30) cc_final: 0.8490 (tp30) REVERT: H 437 MET cc_start: 0.9507 (mtm) cc_final: 0.9269 (ttp) REVERT: H 440 ASN cc_start: 0.9224 (m-40) cc_final: 0.8976 (m110) REVERT: H 444 LYS cc_start: 0.9562 (tmtt) cc_final: 0.9327 (tptt) REVERT: H 449 ILE cc_start: 0.9411 (mp) cc_final: 0.9154 (mp) REVERT: H 494 LYS cc_start: 0.9200 (mmmt) cc_final: 0.8643 (mptt) REVERT: q 39 HIS cc_start: 0.9355 (t-170) cc_final: 0.8928 (t-170) REVERT: q 49 CYS cc_start: 0.8473 (m) cc_final: 0.7629 (m) REVERT: q 52 ASN cc_start: 0.8761 (m-40) cc_final: 0.8424 (m-40) REVERT: q 91 GLN cc_start: 0.9298 (tt0) cc_final: 0.8698 (tp40) REVERT: q 94 ILE cc_start: 0.8459 (mm) cc_final: 0.7941 (mm) REVERT: q 96 MET cc_start: 0.8276 (ptm) cc_final: 0.7277 (pmm) REVERT: q 115 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8316 (tm-30) REVERT: q 127 ILE cc_start: 0.9762 (mt) cc_final: 0.9516 (mt) REVERT: q 140 LYS cc_start: 0.9254 (mmtm) cc_final: 0.9028 (mttt) REVERT: q 213 MET cc_start: 0.2822 (mmp) cc_final: 0.0574 (tpp) REVERT: q 361 MET cc_start: 0.7827 (mtt) cc_final: 0.7414 (ttt) REVERT: q 362 GLU cc_start: 0.7522 (tt0) cc_final: 0.7215 (mm-30) REVERT: q 470 ASP cc_start: 0.9264 (t0) cc_final: 0.9054 (t0) REVERT: q 473 GLU cc_start: 0.9139 (tt0) cc_final: 0.8756 (tt0) REVERT: q 519 ASP cc_start: 0.8199 (t0) cc_final: 0.7516 (t0) REVERT: q 520 MET cc_start: 0.7580 (tpt) cc_final: 0.7347 (tpt) REVERT: q 533 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9124 (tm-30) REVERT: q 542 ASP cc_start: 0.8957 (p0) cc_final: 0.8730 (p0) REVERT: Q 30 LYS cc_start: 0.8555 (pttm) cc_final: 0.8160 (ptpt) REVERT: Q 38 LEU cc_start: 0.9620 (tp) cc_final: 0.9420 (tp) REVERT: Q 39 HIS cc_start: 0.9395 (t70) cc_final: 0.9069 (t-170) REVERT: Q 41 MET cc_start: 0.8590 (tmm) cc_final: 0.8359 (tmm) REVERT: Q 49 CYS cc_start: 0.8805 (m) cc_final: 0.8339 (m) REVERT: Q 109 GLU cc_start: 0.9288 (tp30) cc_final: 0.9008 (tp30) REVERT: Q 113 VAL cc_start: 0.9410 (p) cc_final: 0.9053 (p) REVERT: Q 155 ASP cc_start: 0.8642 (t70) cc_final: 0.8391 (t70) REVERT: Q 161 LYS cc_start: 0.9373 (mttt) cc_final: 0.8815 (mtmm) REVERT: Q 162 MET cc_start: 0.8923 (tmm) cc_final: 0.8599 (tmm) REVERT: Q 175 GLU cc_start: 0.7949 (pm20) cc_final: 0.7393 (mp0) REVERT: Q 202 PHE cc_start: 0.7466 (t80) cc_final: 0.7104 (t80) REVERT: Q 230 ARG cc_start: 0.1388 (ttt180) cc_final: -0.0187 (mmp-170) REVERT: Q 374 GLU cc_start: 0.5647 (mt-10) cc_final: 0.4699 (pm20) REVERT: Q 470 ASP cc_start: 0.9073 (t0) cc_final: 0.8603 (t70) REVERT: Q 472 ASN cc_start: 0.8573 (m-40) cc_final: 0.8124 (m-40) REVERT: Q 473 GLU cc_start: 0.9236 (pt0) cc_final: 0.8357 (pt0) REVERT: Q 533 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8658 (tm-30) REVERT: z 37 LEU cc_start: 0.9422 (tp) cc_final: 0.9020 (mt) REVERT: z 40 LYS cc_start: 0.9407 (mmpt) cc_final: 0.9098 (mmmt) REVERT: z 83 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8479 (tm-30) REVERT: z 100 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8578 (mm-30) REVERT: z 128 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8265 (mt-10) REVERT: z 130 MET cc_start: 0.9363 (mmp) cc_final: 0.8768 (mmm) REVERT: z 158 LEU cc_start: 0.9090 (mt) cc_final: 0.8858 (mt) REVERT: z 197 MET cc_start: 0.8327 (ppp) cc_final: 0.7714 (ppp) REVERT: z 201 HIS cc_start: 0.9153 (m-70) cc_final: 0.8889 (m90) REVERT: z 215 LEU cc_start: 0.8276 (tp) cc_final: 0.8020 (mm) REVERT: z 386 TYR cc_start: 0.8525 (p90) cc_final: 0.8010 (p90) REVERT: z 392 LYS cc_start: 0.9480 (ptmm) cc_final: 0.9229 (ptmm) REVERT: z 412 ILE cc_start: 0.9621 (mm) cc_final: 0.9332 (mm) REVERT: z 419 TYR cc_start: 0.9152 (m-10) cc_final: 0.8742 (m-10) REVERT: z 445 GLU cc_start: 0.9283 (mp0) cc_final: 0.8950 (mm-30) REVERT: z 467 LEU cc_start: 0.8991 (mm) cc_final: 0.8672 (mm) REVERT: z 525 SER cc_start: 0.9489 (m) cc_final: 0.8955 (p) REVERT: z 526 ASN cc_start: 0.9526 (m110) cc_final: 0.9284 (m-40) REVERT: z 527 LEU cc_start: 0.9608 (mt) cc_final: 0.9333 (mt) REVERT: z 529 LEU cc_start: 0.8997 (mt) cc_final: 0.8597 (mt) REVERT: Z 22 ASN cc_start: 0.8592 (m110) cc_final: 0.8375 (m110) REVERT: Z 118 ILE cc_start: 0.8980 (mt) cc_final: 0.8611 (mm) REVERT: Z 119 THR cc_start: 0.9676 (p) cc_final: 0.9387 (p) REVERT: Z 128 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8732 (tp30) REVERT: Z 168 GLU cc_start: 0.9545 (mp0) cc_final: 0.9298 (pm20) REVERT: Z 176 ASP cc_start: 0.8852 (m-30) cc_final: 0.8628 (m-30) REVERT: Z 189 LEU cc_start: 0.8690 (tp) cc_final: 0.8430 (tp) REVERT: Z 193 MET cc_start: 0.7232 (mtm) cc_final: 0.6958 (ttp) REVERT: Z 366 TYR cc_start: 0.7392 (m-10) cc_final: 0.6815 (m-10) REVERT: Z 376 CYS cc_start: 0.9263 (p) cc_final: 0.9033 (p) REVERT: Z 378 ILE cc_start: 0.9197 (mm) cc_final: 0.8964 (mm) REVERT: Z 431 MET cc_start: 0.6782 (mmm) cc_final: 0.6514 (tpt) REVERT: Z 460 LYS cc_start: 0.9403 (mmmm) cc_final: 0.9157 (tppt) REVERT: Z 465 ASP cc_start: 0.9331 (t0) cc_final: 0.9078 (t0) REVERT: Z 482 ASP cc_start: 0.8890 (m-30) cc_final: 0.8574 (m-30) REVERT: Z 504 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8647 (mm-30) REVERT: Z 523 ILE cc_start: 0.9684 (mm) cc_final: 0.9458 (mm) outliers start: 0 outliers final: 0 residues processed: 1376 average time/residue: 0.5610 time to fit residues: 1333.1671 Evaluate side-chains 1096 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1096 time to evaluate : 5.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 704 optimal weight: 6.9990 chunk 742 optimal weight: 6.9990 chunk 677 optimal weight: 6.9990 chunk 722 optimal weight: 3.9990 chunk 434 optimal weight: 2.9990 chunk 314 optimal weight: 10.0000 chunk 567 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 652 optimal weight: 7.9990 chunk 682 optimal weight: 1.9990 chunk 719 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN b 58 ASN ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 ASN b 375 GLN b 385 HIS ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 HIS D 112 ASN D 149 GLN D 461 ASN ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 353 HIS ** e 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 432 ASN ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 GLN ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN ** h 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 188 HIS ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 373 GLN ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 543 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 245 HIS ** z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 185 GLN Z 329 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.8132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 62618 Z= 0.272 Angle : 0.710 13.946 84459 Z= 0.369 Chirality : 0.047 0.265 10166 Planarity : 0.004 0.105 10848 Dihedral : 4.370 27.396 8568 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.92 % Favored : 96.03 % Rotamer: Outliers : 0.03 % Allowed : 0.57 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.09), residues: 8065 helix: 0.28 (0.08), residues: 3910 sheet: -0.59 (0.20), residues: 626 loop : -0.79 (0.10), residues: 3529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 500 HIS 0.010 0.002 HIS d 303 PHE 0.034 0.002 PHE Q 137 TYR 0.028 0.002 TYR Q 437 ARG 0.013 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1352 time to evaluate : 5.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 28 GLN cc_start: 0.9060 (tp40) cc_final: 0.8810 (tp40) REVERT: a 44 LEU cc_start: 0.9368 (tp) cc_final: 0.9150 (tp) REVERT: a 109 LEU cc_start: 0.9083 (mt) cc_final: 0.8846 (mt) REVERT: a 119 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8775 (tppt) REVERT: a 135 GLU cc_start: 0.8579 (tp30) cc_final: 0.7886 (tp30) REVERT: a 175 PHE cc_start: 0.7999 (t80) cc_final: 0.7639 (t80) REVERT: a 179 MET cc_start: 0.7487 (mtp) cc_final: 0.7172 (mmm) REVERT: a 193 LYS cc_start: 0.7924 (mttt) cc_final: 0.7623 (mtmm) REVERT: a 258 MET cc_start: 0.2434 (mmm) cc_final: 0.1808 (mmm) REVERT: a 398 MET cc_start: 0.5826 (ttt) cc_final: 0.4886 (mmt) REVERT: a 399 GLU cc_start: 0.7192 (tt0) cc_final: 0.6696 (pp20) REVERT: a 436 PHE cc_start: 0.8330 (t80) cc_final: 0.7648 (t80) REVERT: a 450 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8812 (mm-30) REVERT: a 451 PHE cc_start: 0.9518 (t80) cc_final: 0.9228 (t80) REVERT: a 497 TYR cc_start: 0.8136 (m-80) cc_final: 0.7541 (m-80) REVERT: a 502 LEU cc_start: 0.8071 (mt) cc_final: 0.7794 (mt) REVERT: A 30 VAL cc_start: 0.9366 (p) cc_final: 0.9108 (m) REVERT: A 108 LEU cc_start: 0.9552 (mt) cc_final: 0.9303 (mt) REVERT: A 179 MET cc_start: 0.5085 (pmm) cc_final: 0.4769 (pmm) REVERT: A 233 MET cc_start: 0.3968 (ptt) cc_final: 0.3153 (ptt) REVERT: A 320 ARG cc_start: 0.7158 (mtt90) cc_final: 0.6856 (ptp90) REVERT: A 393 TYR cc_start: 0.7976 (m-80) cc_final: 0.7670 (m-10) REVERT: A 398 MET cc_start: 0.7380 (ttt) cc_final: 0.6780 (ptm) REVERT: A 477 LEU cc_start: 0.9424 (mt) cc_final: 0.9056 (mt) REVERT: A 533 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8730 (mm-30) REVERT: b 46 LEU cc_start: 0.9289 (mm) cc_final: 0.9051 (mt) REVERT: b 59 ASP cc_start: 0.8999 (t0) cc_final: 0.8705 (t0) REVERT: b 62 THR cc_start: 0.9270 (t) cc_final: 0.9049 (t) REVERT: b 78 VAL cc_start: 0.9289 (t) cc_final: 0.8994 (t) REVERT: b 82 LYS cc_start: 0.9419 (mmtt) cc_final: 0.9161 (mmmm) REVERT: b 85 ASP cc_start: 0.9369 (m-30) cc_final: 0.8656 (t0) REVERT: b 148 MET cc_start: 0.8580 (ppp) cc_final: 0.8215 (ppp) REVERT: b 388 LEU cc_start: 0.9536 (tp) cc_final: 0.9306 (tp) REVERT: b 425 LYS cc_start: 0.9309 (ptmt) cc_final: 0.8840 (pttt) REVERT: b 439 GLN cc_start: 0.9360 (mm110) cc_final: 0.8956 (mp10) REVERT: b 443 ILE cc_start: 0.9211 (mm) cc_final: 0.8953 (tp) REVERT: b 472 LEU cc_start: 0.9061 (mt) cc_final: 0.8752 (mt) REVERT: B 107 GLU cc_start: 0.9384 (tt0) cc_final: 0.9149 (pp20) REVERT: B 155 HIS cc_start: 0.9376 (m90) cc_final: 0.9151 (m90) REVERT: B 196 ILE cc_start: 0.8607 (mm) cc_final: 0.8225 (mm) REVERT: B 315 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7882 (mm-30) REVERT: B 354 LEU cc_start: 0.4653 (mt) cc_final: 0.4047 (mt) REVERT: B 386 ASP cc_start: 0.8731 (m-30) cc_final: 0.7599 (t70) REVERT: B 406 CYS cc_start: 0.9452 (t) cc_final: 0.9005 (m) REVERT: B 409 MET cc_start: 0.9470 (tpp) cc_final: 0.9191 (ttm) REVERT: B 452 SER cc_start: 0.9308 (p) cc_final: 0.8837 (t) REVERT: B 472 LEU cc_start: 0.8905 (mt) cc_final: 0.8481 (mt) REVERT: d 31 VAL cc_start: 0.9320 (t) cc_final: 0.9097 (p) REVERT: d 166 TYR cc_start: 0.7143 (m-80) cc_final: 0.6791 (m-10) REVERT: d 209 MET cc_start: 0.3825 (mtm) cc_final: 0.3512 (ttp) REVERT: d 311 MET cc_start: 0.4363 (mmm) cc_final: 0.3501 (mmm) REVERT: d 315 ASP cc_start: 0.3704 (m-30) cc_final: 0.2569 (t70) REVERT: d 411 ILE cc_start: 0.9233 (pt) cc_final: 0.8784 (mp) REVERT: d 433 GLU cc_start: 0.8224 (pm20) cc_final: 0.7745 (tp30) REVERT: d 464 LYS cc_start: 0.9683 (mmmt) cc_final: 0.9018 (ptmm) REVERT: D 33 ASP cc_start: 0.9182 (m-30) cc_final: 0.8885 (m-30) REVERT: D 44 MET cc_start: 0.8310 (mpp) cc_final: 0.7784 (mpp) REVERT: D 108 GLU cc_start: 0.7932 (tt0) cc_final: 0.7630 (tt0) REVERT: D 110 LEU cc_start: 0.8623 (mt) cc_final: 0.8336 (mt) REVERT: D 209 MET cc_start: 0.5293 (mmt) cc_final: 0.4668 (mmt) REVERT: D 379 ILE cc_start: 0.8856 (mp) cc_final: 0.8621 (mp) REVERT: D 385 MET cc_start: 0.5690 (ppp) cc_final: 0.5396 (tmm) REVERT: D 470 ARG cc_start: 0.9151 (tpt90) cc_final: 0.8553 (tpt90) REVERT: D 509 THR cc_start: 0.9324 (t) cc_final: 0.9019 (t) REVERT: D 513 GLU cc_start: 0.9637 (mm-30) cc_final: 0.9147 (mp0) REVERT: e 50 HIS cc_start: 0.8562 (m-70) cc_final: 0.8337 (m-70) REVERT: e 83 ILE cc_start: 0.9032 (mt) cc_final: 0.8666 (mp) REVERT: e 107 LEU cc_start: 0.9382 (tp) cc_final: 0.9172 (tp) REVERT: e 113 ASP cc_start: 0.8570 (m-30) cc_final: 0.7835 (p0) REVERT: e 146 ILE cc_start: 0.9740 (mm) cc_final: 0.8917 (mm) REVERT: e 150 PHE cc_start: 0.9251 (m-10) cc_final: 0.8766 (m-80) REVERT: e 203 MET cc_start: 0.5372 (tmm) cc_final: 0.4518 (ptt) REVERT: e 210 ASN cc_start: 0.8813 (m-40) cc_final: 0.8240 (t0) REVERT: e 254 MET cc_start: 0.4043 (mtt) cc_final: 0.3763 (mtt) REVERT: e 472 PHE cc_start: 0.9268 (t80) cc_final: 0.9066 (t80) REVERT: e 495 LEU cc_start: 0.9270 (tp) cc_final: 0.8625 (mt) REVERT: e 536 GLN cc_start: 0.9028 (mp10) cc_final: 0.8644 (mp10) REVERT: e 540 LEU cc_start: 0.9525 (mt) cc_final: 0.9315 (mt) REVERT: e 553 ASN cc_start: 0.8960 (m-40) cc_final: 0.8257 (m-40) REVERT: E 63 THR cc_start: 0.9516 (p) cc_final: 0.9284 (p) REVERT: E 70 LEU cc_start: 0.8462 (mp) cc_final: 0.8153 (mp) REVERT: E 94 MET cc_start: 0.8153 (ttp) cc_final: 0.7246 (tpp) REVERT: E 113 ASP cc_start: 0.9173 (m-30) cc_final: 0.8953 (t0) REVERT: E 162 GLU cc_start: 0.9312 (tp30) cc_final: 0.9074 (tp30) REVERT: E 163 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9110 (mp0) REVERT: E 203 MET cc_start: 0.6379 (ptp) cc_final: 0.5936 (mpp) REVERT: E 368 ASP cc_start: 0.5618 (m-30) cc_final: 0.4945 (t0) REVERT: E 379 ARG cc_start: 0.7005 (tpt170) cc_final: 0.6427 (ttt90) REVERT: E 381 TYR cc_start: 0.8547 (p90) cc_final: 0.8106 (p90) REVERT: E 414 MET cc_start: 0.8919 (tpt) cc_final: 0.8658 (tmm) REVERT: E 481 MET cc_start: 0.9381 (mmm) cc_final: 0.9105 (mmm) REVERT: E 526 PHE cc_start: 0.7279 (m-10) cc_final: 0.6916 (m-10) REVERT: E 553 ASN cc_start: 0.8660 (m-40) cc_final: 0.8404 (m-40) REVERT: g 29 LYS cc_start: 0.9243 (tppt) cc_final: 0.8958 (tppt) REVERT: g 38 CYS cc_start: 0.9433 (m) cc_final: 0.9205 (m) REVERT: g 39 LEU cc_start: 0.6795 (tp) cc_final: 0.6471 (tp) REVERT: g 47 MET cc_start: 0.7291 (mmm) cc_final: 0.5811 (mmm) REVERT: g 57 LEU cc_start: 0.7962 (pp) cc_final: 0.7483 (pp) REVERT: g 102 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8330 (mm-30) REVERT: g 117 HIS cc_start: 0.8782 (t-90) cc_final: 0.8497 (t-90) REVERT: g 134 GLU cc_start: 0.9314 (pt0) cc_final: 0.9091 (pt0) REVERT: g 148 ASP cc_start: 0.8925 (m-30) cc_final: 0.8554 (m-30) REVERT: g 163 TYR cc_start: 0.6921 (t80) cc_final: 0.6529 (t80) REVERT: g 440 MET cc_start: 0.5438 (pmm) cc_final: 0.5078 (pmm) REVERT: g 481 MET cc_start: 0.9049 (tpt) cc_final: 0.8385 (tpt) REVERT: g 509 MET cc_start: 0.9581 (mmp) cc_final: 0.9283 (tpp) REVERT: g 540 PHE cc_start: 0.7860 (p90) cc_final: 0.6894 (p90) REVERT: G 45 LEU cc_start: 0.9132 (tp) cc_final: 0.8764 (tp) REVERT: G 81 LEU cc_start: 0.9260 (mt) cc_final: 0.9013 (mt) REVERT: G 117 HIS cc_start: 0.9097 (t-90) cc_final: 0.8855 (t-90) REVERT: G 234 MET cc_start: 0.3671 (ttm) cc_final: 0.0774 (ptm) REVERT: G 487 LEU cc_start: 0.9393 (mt) cc_final: 0.9149 (mt) REVERT: G 514 ARG cc_start: 0.8951 (ttm110) cc_final: 0.8704 (ttp-110) REVERT: G 531 LEU cc_start: 0.9388 (tp) cc_final: 0.9158 (tp) REVERT: G 563 GLU cc_start: 0.8291 (pm20) cc_final: 0.7706 (pm20) REVERT: G 567 GLN cc_start: 0.9245 (mt0) cc_final: 0.8158 (mt0) REVERT: G 568 GLN cc_start: 0.9488 (mp10) cc_final: 0.8892 (pm20) REVERT: G 571 LYS cc_start: 0.9437 (mttp) cc_final: 0.9074 (mttt) REVERT: G 585 ASP cc_start: 0.8498 (p0) cc_final: 0.8187 (p0) REVERT: h 52 LEU cc_start: 0.9288 (tp) cc_final: 0.9008 (tt) REVERT: h 69 ILE cc_start: 0.9006 (mt) cc_final: 0.8723 (mt) REVERT: h 70 LEU cc_start: 0.9207 (tp) cc_final: 0.8933 (tp) REVERT: h 104 LEU cc_start: 0.9500 (mm) cc_final: 0.9160 (mm) REVERT: h 107 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8848 (tm-30) REVERT: h 108 LEU cc_start: 0.9651 (mt) cc_final: 0.9430 (mt) REVERT: h 166 MET cc_start: 0.8027 (mmp) cc_final: 0.7820 (mmm) REVERT: h 355 MET cc_start: 0.6220 (ptt) cc_final: 0.5784 (pmm) REVERT: h 362 TYR cc_start: 0.7524 (m-10) cc_final: 0.7299 (m-80) REVERT: h 436 GLN cc_start: 0.9502 (tm-30) cc_final: 0.9108 (tp40) REVERT: h 440 ASN cc_start: 0.9509 (t0) cc_final: 0.9290 (t0) REVERT: h 455 GLU cc_start: 0.9514 (tp30) cc_final: 0.9312 (tp30) REVERT: h 460 ASP cc_start: 0.8345 (p0) cc_final: 0.8085 (p0) REVERT: h 465 LEU cc_start: 0.9569 (mp) cc_final: 0.9263 (mt) REVERT: h 466 ASN cc_start: 0.9431 (t0) cc_final: 0.9202 (p0) REVERT: H 44 LEU cc_start: 0.9509 (tp) cc_final: 0.9291 (tp) REVERT: H 85 ASP cc_start: 0.9565 (m-30) cc_final: 0.9136 (t70) REVERT: H 110 LYS cc_start: 0.8792 (pttm) cc_final: 0.8431 (ptpt) REVERT: H 126 MET cc_start: 0.9130 (tpp) cc_final: 0.8606 (tpp) REVERT: H 166 MET cc_start: 0.5330 (mmp) cc_final: 0.4978 (mmp) REVERT: H 362 TYR cc_start: 0.6142 (m-10) cc_final: 0.5871 (m-80) REVERT: H 398 MET cc_start: 0.9167 (mtm) cc_final: 0.8691 (mpp) REVERT: H 418 MET cc_start: 0.8982 (ttt) cc_final: 0.8432 (ptm) REVERT: H 440 ASN cc_start: 0.9169 (m-40) cc_final: 0.8949 (m110) REVERT: H 449 ILE cc_start: 0.9519 (mp) cc_final: 0.9270 (mp) REVERT: H 470 LEU cc_start: 0.9001 (mm) cc_final: 0.8685 (pp) REVERT: H 494 LYS cc_start: 0.9207 (mmmt) cc_final: 0.8685 (mptt) REVERT: q 39 HIS cc_start: 0.9187 (t-170) cc_final: 0.8800 (t-170) REVERT: q 41 MET cc_start: 0.8644 (tmm) cc_final: 0.8415 (tmm) REVERT: q 49 CYS cc_start: 0.8705 (m) cc_final: 0.7944 (m) REVERT: q 52 ASN cc_start: 0.8597 (m-40) cc_final: 0.8153 (m-40) REVERT: q 91 GLN cc_start: 0.9265 (tt0) cc_final: 0.8696 (tp-100) REVERT: q 94 ILE cc_start: 0.8356 (mm) cc_final: 0.8005 (mm) REVERT: q 96 MET cc_start: 0.8701 (ptm) cc_final: 0.7129 (pmm) REVERT: q 98 ASP cc_start: 0.4471 (t70) cc_final: 0.4116 (t70) REVERT: q 115 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8461 (tm-30) REVERT: q 126 GLU cc_start: 0.9250 (mp0) cc_final: 0.8997 (mp0) REVERT: q 145 MET cc_start: 0.8095 (ptp) cc_final: 0.7408 (ptp) REVERT: q 213 MET cc_start: 0.3587 (mmp) cc_final: 0.3140 (mmm) REVERT: q 361 MET cc_start: 0.8139 (mtt) cc_final: 0.7834 (ttt) REVERT: q 430 LEU cc_start: 0.9662 (mt) cc_final: 0.9238 (mt) REVERT: q 473 GLU cc_start: 0.9333 (tt0) cc_final: 0.9013 (tt0) REVERT: q 533 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9063 (tm-30) REVERT: q 542 ASP cc_start: 0.9048 (p0) cc_final: 0.8819 (p0) REVERT: q 543 GLN cc_start: 0.8703 (pt0) cc_final: 0.8346 (pp30) REVERT: Q 46 MET cc_start: 0.1618 (tpt) cc_final: 0.1089 (tpt) REVERT: Q 49 CYS cc_start: 0.8899 (m) cc_final: 0.8420 (m) REVERT: Q 53 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8710 (mmtm) REVERT: Q 109 GLU cc_start: 0.9240 (tp30) cc_final: 0.8994 (tp30) REVERT: Q 161 LYS cc_start: 0.9373 (mttt) cc_final: 0.8852 (mtmm) REVERT: Q 162 MET cc_start: 0.9075 (tmm) cc_final: 0.8703 (tmm) REVERT: Q 175 GLU cc_start: 0.8104 (pm20) cc_final: 0.7552 (mp0) REVERT: Q 202 PHE cc_start: 0.8051 (t80) cc_final: 0.7844 (t80) REVERT: Q 230 ARG cc_start: 0.1620 (ttt180) cc_final: -0.0084 (mmp-170) REVERT: Q 361 MET cc_start: 0.8071 (ppp) cc_final: 0.7307 (mtm) REVERT: Q 374 GLU cc_start: 0.5508 (mt-10) cc_final: 0.4655 (pm20) REVERT: Q 437 TYR cc_start: 0.8116 (m-80) cc_final: 0.7874 (m-80) REVERT: Q 470 ASP cc_start: 0.9209 (t0) cc_final: 0.8607 (t70) REVERT: Q 472 ASN cc_start: 0.8801 (m-40) cc_final: 0.8333 (t0) REVERT: Q 473 GLU cc_start: 0.9315 (pt0) cc_final: 0.8645 (pt0) REVERT: Q 533 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8697 (tm-30) REVERT: z 40 LYS cc_start: 0.9430 (mmpt) cc_final: 0.9162 (mmmt) REVERT: z 83 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8752 (tm-30) REVERT: z 107 ARG cc_start: 0.9011 (tmm-80) cc_final: 0.8710 (tmm-80) REVERT: z 122 PHE cc_start: 0.9334 (m-10) cc_final: 0.9099 (m-80) REVERT: z 197 MET cc_start: 0.8295 (ppp) cc_final: 0.8016 (ppp) REVERT: z 215 LEU cc_start: 0.8243 (tp) cc_final: 0.8010 (tp) REVERT: z 246 GLU cc_start: 0.5444 (tt0) cc_final: 0.5176 (mp0) REVERT: z 392 LYS cc_start: 0.9544 (ptmm) cc_final: 0.9236 (ptmm) REVERT: z 419 TYR cc_start: 0.9330 (m-10) cc_final: 0.8896 (m-10) REVERT: z 445 GLU cc_start: 0.9225 (mp0) cc_final: 0.8764 (mm-30) REVERT: z 525 SER cc_start: 0.9510 (m) cc_final: 0.9090 (p) REVERT: z 526 ASN cc_start: 0.9550 (m110) cc_final: 0.9250 (m-40) REVERT: z 527 LEU cc_start: 0.9685 (mt) cc_final: 0.9251 (mt) REVERT: Z 22 ASN cc_start: 0.8677 (m110) cc_final: 0.8416 (m110) REVERT: Z 37 LEU cc_start: 0.8623 (tp) cc_final: 0.8267 (tp) REVERT: Z 114 HIS cc_start: 0.8813 (t-90) cc_final: 0.8587 (t-90) REVERT: Z 118 ILE cc_start: 0.9058 (mt) cc_final: 0.8737 (mm) REVERT: Z 128 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8917 (tp30) REVERT: Z 168 GLU cc_start: 0.9592 (mp0) cc_final: 0.9330 (mp0) REVERT: Z 176 ASP cc_start: 0.8958 (m-30) cc_final: 0.8654 (m-30) REVERT: Z 189 LEU cc_start: 0.8638 (tp) cc_final: 0.8300 (tp) REVERT: Z 193 MET cc_start: 0.7335 (mtm) cc_final: 0.7115 (ttt) REVERT: Z 366 TYR cc_start: 0.7431 (m-10) cc_final: 0.7060 (m-10) REVERT: Z 376 CYS cc_start: 0.9295 (p) cc_final: 0.9073 (p) REVERT: Z 378 ILE cc_start: 0.9233 (mm) cc_final: 0.8990 (mm) REVERT: Z 451 LEU cc_start: 0.9567 (mt) cc_final: 0.9355 (tp) REVERT: Z 482 ASP cc_start: 0.8940 (m-30) cc_final: 0.8629 (m-30) REVERT: Z 504 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8759 (mm-30) outliers start: 2 outliers final: 0 residues processed: 1353 average time/residue: 0.5601 time to fit residues: 1313.2578 Evaluate side-chains 1070 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1070 time to evaluate : 5.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 474 optimal weight: 3.9990 chunk 763 optimal weight: 0.8980 chunk 466 optimal weight: 7.9990 chunk 362 optimal weight: 0.0970 chunk 530 optimal weight: 3.9990 chunk 800 optimal weight: 5.9990 chunk 737 optimal weight: 1.9990 chunk 637 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 492 optimal weight: 6.9990 chunk 391 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 89 GLN ** a 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 220 ASN b 375 GLN B 192 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS D 112 ASN ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 519 ASN g 530 GLN ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 373 GLN q 529 ASN q 543 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 430 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.8359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 62618 Z= 0.197 Angle : 0.636 13.412 84459 Z= 0.327 Chirality : 0.045 0.229 10166 Planarity : 0.003 0.062 10848 Dihedral : 4.200 21.401 8568 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 0.03 % Allowed : 0.29 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.09), residues: 8065 helix: 0.33 (0.08), residues: 3928 sheet: -0.57 (0.20), residues: 653 loop : -0.75 (0.10), residues: 3484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 500 HIS 0.014 0.001 HIS d 473 PHE 0.030 0.001 PHE H 495 TYR 0.021 0.001 TYR Z 355 ARG 0.011 0.001 ARG q 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1337 time to evaluate : 5.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 34 MET cc_start: 0.9237 (tmm) cc_final: 0.8941 (tmm) REVERT: a 44 LEU cc_start: 0.9395 (tp) cc_final: 0.9072 (tp) REVERT: a 49 LEU cc_start: 0.9363 (mm) cc_final: 0.8896 (mm) REVERT: a 85 GLU cc_start: 0.9416 (pp20) cc_final: 0.8913 (pp20) REVERT: a 89 GLN cc_start: 0.9101 (pt0) cc_final: 0.8794 (pt0) REVERT: a 119 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8756 (tppt) REVERT: a 135 GLU cc_start: 0.8625 (tp30) cc_final: 0.7759 (tp30) REVERT: a 175 PHE cc_start: 0.8000 (t80) cc_final: 0.7513 (t80) REVERT: a 179 MET cc_start: 0.7699 (mtp) cc_final: 0.7206 (mmm) REVERT: a 193 LYS cc_start: 0.7841 (mttt) cc_final: 0.7532 (mtmm) REVERT: a 258 MET cc_start: 0.2194 (mmm) cc_final: 0.1597 (mpp) REVERT: a 359 ASP cc_start: 0.7495 (m-30) cc_final: 0.7136 (p0) REVERT: a 398 MET cc_start: 0.6045 (ttt) cc_final: 0.5141 (mmt) REVERT: a 399 GLU cc_start: 0.7219 (tt0) cc_final: 0.6722 (pp20) REVERT: a 432 TYR cc_start: 0.8162 (t80) cc_final: 0.6200 (t80) REVERT: a 448 ILE cc_start: 0.9243 (mm) cc_final: 0.8712 (tp) REVERT: a 450 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8986 (tp30) REVERT: a 451 PHE cc_start: 0.9502 (t80) cc_final: 0.9149 (t80) REVERT: a 460 LYS cc_start: 0.9140 (tptt) cc_final: 0.8894 (tptt) REVERT: a 502 LEU cc_start: 0.8087 (mt) cc_final: 0.7506 (mt) REVERT: a 532 LEU cc_start: 0.9514 (mm) cc_final: 0.8997 (tt) REVERT: A 30 VAL cc_start: 0.9339 (p) cc_final: 0.9094 (m) REVERT: A 52 MET cc_start: 0.7975 (tpt) cc_final: 0.7398 (tpp) REVERT: A 108 LEU cc_start: 0.9406 (mt) cc_final: 0.9185 (mt) REVERT: A 111 ARG cc_start: 0.9028 (mmm-85) cc_final: 0.8635 (mmm-85) REVERT: A 121 HIS cc_start: 0.8676 (t-90) cc_final: 0.8365 (t-90) REVERT: A 233 MET cc_start: 0.4558 (ptt) cc_final: 0.4251 (ptt) REVERT: A 320 ARG cc_start: 0.7165 (mtt90) cc_final: 0.6831 (ptp90) REVERT: A 444 GLU cc_start: 0.9546 (pm20) cc_final: 0.9341 (pm20) REVERT: A 477 LEU cc_start: 0.9385 (mt) cc_final: 0.9013 (mt) REVERT: A 512 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8663 (mm-30) REVERT: A 533 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8689 (mm-30) REVERT: b 59 ASP cc_start: 0.8952 (t0) cc_final: 0.8692 (t0) REVERT: b 62 THR cc_start: 0.9271 (t) cc_final: 0.9031 (t) REVERT: b 78 VAL cc_start: 0.9360 (t) cc_final: 0.9090 (t) REVERT: b 144 HIS cc_start: 0.8347 (p90) cc_final: 0.8073 (p90) REVERT: b 148 MET cc_start: 0.8559 (ppp) cc_final: 0.8189 (ppp) REVERT: b 426 LYS cc_start: 0.9342 (mppt) cc_final: 0.8511 (mmtm) REVERT: b 439 GLN cc_start: 0.9175 (mm110) cc_final: 0.8945 (mp10) REVERT: b 443 ILE cc_start: 0.9168 (mm) cc_final: 0.8711 (tp) REVERT: b 472 LEU cc_start: 0.9103 (mt) cc_final: 0.8855 (mt) REVERT: B 107 GLU cc_start: 0.9377 (tt0) cc_final: 0.9074 (pp20) REVERT: B 109 LEU cc_start: 0.9447 (mt) cc_final: 0.9085 (mt) REVERT: B 155 HIS cc_start: 0.9348 (m90) cc_final: 0.9105 (m90) REVERT: B 196 ILE cc_start: 0.8722 (mm) cc_final: 0.8343 (mm) REVERT: B 315 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 354 LEU cc_start: 0.4692 (mt) cc_final: 0.3025 (tp) REVERT: B 386 ASP cc_start: 0.8653 (m-30) cc_final: 0.7532 (t70) REVERT: B 406 CYS cc_start: 0.9327 (t) cc_final: 0.9077 (m) REVERT: B 409 MET cc_start: 0.9404 (tpp) cc_final: 0.9113 (ttm) REVERT: B 452 SER cc_start: 0.9200 (p) cc_final: 0.8837 (t) REVERT: B 472 LEU cc_start: 0.8793 (mt) cc_final: 0.8412 (mt) REVERT: d 91 ASP cc_start: 0.6222 (t0) cc_final: 0.5839 (m-30) REVERT: d 133 ASP cc_start: 0.9362 (m-30) cc_final: 0.8980 (t70) REVERT: d 166 TYR cc_start: 0.7051 (m-80) cc_final: 0.6691 (m-80) REVERT: d 209 MET cc_start: 0.3986 (mtm) cc_final: 0.3786 (ttp) REVERT: d 311 MET cc_start: 0.3486 (mmm) cc_final: 0.2821 (mmm) REVERT: d 343 ARG cc_start: 0.1462 (mtt180) cc_final: 0.0810 (ttm170) REVERT: d 411 ILE cc_start: 0.9214 (pt) cc_final: 0.8770 (mp) REVERT: d 433 GLU cc_start: 0.8113 (pm20) cc_final: 0.7723 (tp30) REVERT: d 464 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9022 (ptmm) REVERT: D 33 ASP cc_start: 0.9210 (m-30) cc_final: 0.8953 (m-30) REVERT: D 44 MET cc_start: 0.8269 (mpp) cc_final: 0.7608 (mpp) REVERT: D 108 GLU cc_start: 0.8173 (tt0) cc_final: 0.7847 (tt0) REVERT: D 110 LEU cc_start: 0.8660 (mt) cc_final: 0.8354 (mt) REVERT: D 209 MET cc_start: 0.5409 (mmt) cc_final: 0.4865 (mmt) REVERT: D 311 MET cc_start: 0.1008 (tmm) cc_final: 0.0100 (tmm) REVERT: D 385 MET cc_start: 0.6096 (ppp) cc_final: 0.5793 (tmm) REVERT: D 470 ARG cc_start: 0.9122 (tpt90) cc_final: 0.8585 (tpt90) REVERT: D 509 THR cc_start: 0.9330 (t) cc_final: 0.9017 (t) REVERT: D 513 GLU cc_start: 0.9631 (mm-30) cc_final: 0.9148 (mp0) REVERT: e 50 HIS cc_start: 0.8546 (m-70) cc_final: 0.8309 (m-70) REVERT: e 107 LEU cc_start: 0.9390 (tp) cc_final: 0.9162 (tp) REVERT: e 113 ASP cc_start: 0.8459 (m-30) cc_final: 0.7773 (p0) REVERT: e 146 ILE cc_start: 0.9733 (mm) cc_final: 0.8868 (mm) REVERT: e 150 PHE cc_start: 0.9224 (m-10) cc_final: 0.8720 (m-80) REVERT: e 203 MET cc_start: 0.5410 (tmm) cc_final: 0.4562 (ptt) REVERT: e 210 ASN cc_start: 0.8793 (m-40) cc_final: 0.8220 (t0) REVERT: e 254 MET cc_start: 0.4166 (mtt) cc_final: 0.3954 (mtt) REVERT: e 467 TYR cc_start: 0.9249 (m-80) cc_final: 0.8912 (m-80) REVERT: e 492 ILE cc_start: 0.9238 (mt) cc_final: 0.8870 (mm) REVERT: e 495 LEU cc_start: 0.9256 (tp) cc_final: 0.8558 (mt) REVERT: e 536 GLN cc_start: 0.9007 (mp10) cc_final: 0.8655 (mp10) REVERT: E 94 MET cc_start: 0.8211 (ttp) cc_final: 0.7295 (tpp) REVERT: E 142 HIS cc_start: 0.8991 (t70) cc_final: 0.8786 (t-90) REVERT: E 162 GLU cc_start: 0.9268 (tp30) cc_final: 0.9009 (tp30) REVERT: E 163 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9091 (mp0) REVERT: E 203 MET cc_start: 0.6540 (ptp) cc_final: 0.6131 (mpp) REVERT: E 368 ASP cc_start: 0.5639 (m-30) cc_final: 0.4986 (t0) REVERT: E 379 ARG cc_start: 0.6881 (tpp-160) cc_final: 0.6454 (ttt90) REVERT: E 381 TYR cc_start: 0.8530 (p90) cc_final: 0.7972 (p90) REVERT: E 414 MET cc_start: 0.8846 (tpt) cc_final: 0.8624 (tmm) REVERT: E 522 MET cc_start: 0.7888 (ttm) cc_final: 0.7567 (ttt) REVERT: E 526 PHE cc_start: 0.6944 (m-10) cc_final: 0.6680 (m-10) REVERT: E 542 THR cc_start: 0.9354 (m) cc_final: 0.9089 (t) REVERT: E 553 ASN cc_start: 0.8608 (m-40) cc_final: 0.8066 (m-40) REVERT: g 29 LYS cc_start: 0.9305 (tppt) cc_final: 0.8921 (tppt) REVERT: g 38 CYS cc_start: 0.9377 (m) cc_final: 0.9136 (m) REVERT: g 39 LEU cc_start: 0.6992 (tp) cc_final: 0.6729 (tp) REVERT: g 47 MET cc_start: 0.7062 (mmm) cc_final: 0.5600 (mmm) REVERT: g 78 MET cc_start: 0.9292 (mmm) cc_final: 0.9064 (mmp) REVERT: g 117 HIS cc_start: 0.8664 (t-90) cc_final: 0.8404 (t-90) REVERT: g 134 GLU cc_start: 0.9294 (pt0) cc_final: 0.8825 (pp20) REVERT: g 148 ASP cc_start: 0.9101 (m-30) cc_final: 0.8714 (m-30) REVERT: g 151 MET cc_start: 0.8185 (mpp) cc_final: 0.7458 (mpp) REVERT: g 163 TYR cc_start: 0.6884 (t80) cc_final: 0.6631 (t80) REVERT: g 481 MET cc_start: 0.8795 (tpt) cc_final: 0.8074 (tpt) REVERT: g 509 MET cc_start: 0.9610 (mmp) cc_final: 0.9193 (tpp) REVERT: g 540 PHE cc_start: 0.7838 (p90) cc_final: 0.6853 (p90) REVERT: g 585 ASP cc_start: 0.8655 (m-30) cc_final: 0.8286 (m-30) REVERT: G 45 LEU cc_start: 0.9223 (tp) cc_final: 0.8846 (tp) REVERT: G 52 MET cc_start: 0.8689 (tmm) cc_final: 0.8393 (tmm) REVERT: G 104 LEU cc_start: 0.9703 (mt) cc_final: 0.9491 (mt) REVERT: G 117 HIS cc_start: 0.9063 (t-90) cc_final: 0.8845 (t-90) REVERT: G 127 LYS cc_start: 0.9083 (tmtt) cc_final: 0.8579 (tmtt) REVERT: G 203 TYR cc_start: 0.6507 (m-10) cc_final: 0.6297 (m-10) REVERT: G 234 MET cc_start: 0.3859 (ttm) cc_final: 0.0836 (ptm) REVERT: G 327 ARG cc_start: 0.4060 (mtp85) cc_final: 0.3693 (mmt90) REVERT: G 440 MET cc_start: 0.8680 (ppp) cc_final: 0.8477 (ppp) REVERT: G 487 LEU cc_start: 0.9380 (mt) cc_final: 0.9176 (mt) REVERT: G 502 TYR cc_start: 0.8616 (t80) cc_final: 0.8096 (t80) REVERT: G 507 ASP cc_start: 0.9407 (m-30) cc_final: 0.9004 (m-30) REVERT: G 531 LEU cc_start: 0.9393 (tp) cc_final: 0.9136 (tp) REVERT: G 563 GLU cc_start: 0.8443 (pm20) cc_final: 0.7963 (pm20) REVERT: G 567 GLN cc_start: 0.9224 (mt0) cc_final: 0.7974 (mt0) REVERT: G 568 GLN cc_start: 0.9464 (mp10) cc_final: 0.8778 (mp10) REVERT: G 571 LYS cc_start: 0.9424 (mttp) cc_final: 0.9068 (mttt) REVERT: G 585 ASP cc_start: 0.8554 (p0) cc_final: 0.8285 (p0) REVERT: h 70 LEU cc_start: 0.9175 (tp) cc_final: 0.8892 (tp) REVERT: h 104 LEU cc_start: 0.9439 (mm) cc_final: 0.9148 (mm) REVERT: h 107 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8907 (tm-30) REVERT: h 166 MET cc_start: 0.7991 (mmp) cc_final: 0.7612 (mmm) REVERT: h 355 MET cc_start: 0.6632 (ptt) cc_final: 0.6364 (ptt) REVERT: h 418 MET cc_start: 0.8493 (ppp) cc_final: 0.7716 (ppp) REVERT: h 436 GLN cc_start: 0.9374 (tm-30) cc_final: 0.9072 (tp40) REVERT: h 440 ASN cc_start: 0.9522 (t0) cc_final: 0.9304 (t0) REVERT: h 462 ILE cc_start: 0.9429 (mp) cc_final: 0.8944 (mp) REVERT: h 465 LEU cc_start: 0.9541 (mp) cc_final: 0.9259 (mt) REVERT: H 37 GLN cc_start: 0.9061 (tt0) cc_final: 0.8728 (tp-100) REVERT: H 85 ASP cc_start: 0.9549 (m-30) cc_final: 0.9116 (t70) REVERT: H 110 LYS cc_start: 0.8563 (pttm) cc_final: 0.8303 (ptpt) REVERT: H 126 MET cc_start: 0.9087 (tpp) cc_final: 0.8513 (tpp) REVERT: H 202 LYS cc_start: 0.8319 (mmpt) cc_final: 0.7834 (mmtm) REVERT: H 362 TYR cc_start: 0.6000 (m-10) cc_final: 0.5686 (m-80) REVERT: H 398 MET cc_start: 0.9143 (mtm) cc_final: 0.8661 (mpp) REVERT: H 418 MET cc_start: 0.9004 (ttt) cc_final: 0.8505 (ptm) REVERT: H 419 GLU cc_start: 0.8899 (tp30) cc_final: 0.8414 (tp30) REVERT: H 437 MET cc_start: 0.9548 (ttp) cc_final: 0.9259 (ttp) REVERT: H 440 ASN cc_start: 0.9166 (m-40) cc_final: 0.8941 (m110) REVERT: H 449 ILE cc_start: 0.9477 (mp) cc_final: 0.9253 (mp) REVERT: q 39 HIS cc_start: 0.9160 (t-170) cc_final: 0.8827 (t-170) REVERT: q 49 CYS cc_start: 0.8745 (m) cc_final: 0.8131 (m) REVERT: q 91 GLN cc_start: 0.9234 (tt0) cc_final: 0.8734 (tp40) REVERT: q 94 ILE cc_start: 0.8158 (mm) cc_final: 0.7861 (mm) REVERT: q 96 MET cc_start: 0.8598 (ptm) cc_final: 0.7399 (pmm) REVERT: q 98 ASP cc_start: 0.3910 (t70) cc_final: 0.3568 (t70) REVERT: q 115 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8488 (tm-30) REVERT: q 133 MET cc_start: 0.9313 (tpp) cc_final: 0.9088 (tpt) REVERT: q 140 LYS cc_start: 0.9304 (mmtm) cc_final: 0.8966 (mttt) REVERT: q 213 MET cc_start: 0.3470 (mmp) cc_final: 0.3026 (mmm) REVERT: q 226 MET cc_start: 0.4231 (mmp) cc_final: 0.1853 (tpt) REVERT: q 361 MET cc_start: 0.8250 (mtt) cc_final: 0.7998 (ttt) REVERT: q 430 LEU cc_start: 0.9652 (mt) cc_final: 0.9400 (mt) REVERT: q 518 TYR cc_start: 0.7632 (p90) cc_final: 0.6370 (p90) REVERT: q 519 ASP cc_start: 0.7775 (t0) cc_final: 0.7369 (t0) REVERT: q 533 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9054 (tm-30) REVERT: q 543 GLN cc_start: 0.8781 (pt0) cc_final: 0.8328 (pp30) REVERT: Q 30 LYS cc_start: 0.8551 (pttm) cc_final: 0.7913 (mttp) REVERT: Q 38 LEU cc_start: 0.9490 (tp) cc_final: 0.9174 (tp) REVERT: Q 42 CYS cc_start: 0.8998 (m) cc_final: 0.8466 (p) REVERT: Q 43 LEU cc_start: 0.9045 (pp) cc_final: 0.8644 (mt) REVERT: Q 46 MET cc_start: 0.1380 (tpt) cc_final: 0.0781 (tpt) REVERT: Q 49 CYS cc_start: 0.8796 (m) cc_final: 0.8309 (m) REVERT: Q 109 GLU cc_start: 0.9242 (tp30) cc_final: 0.8980 (tp30) REVERT: Q 161 LYS cc_start: 0.9358 (mttt) cc_final: 0.8790 (mtmm) REVERT: Q 162 MET cc_start: 0.9114 (tmm) cc_final: 0.8727 (tmm) REVERT: Q 175 GLU cc_start: 0.8082 (pm20) cc_final: 0.7570 (mp0) REVERT: Q 202 PHE cc_start: 0.8104 (t80) cc_final: 0.7537 (t80) REVERT: Q 230 ARG cc_start: 0.1431 (ttt180) cc_final: -0.0174 (mmp-170) REVERT: Q 374 GLU cc_start: 0.5571 (mt-10) cc_final: 0.4725 (pm20) REVERT: Q 387 ARG cc_start: 0.9004 (mtt90) cc_final: 0.8774 (mtt90) REVERT: Q 470 ASP cc_start: 0.9169 (t0) cc_final: 0.8622 (t70) REVERT: Q 472 ASN cc_start: 0.8830 (m-40) cc_final: 0.8322 (t0) REVERT: Q 473 GLU cc_start: 0.9319 (pt0) cc_final: 0.8730 (pt0) REVERT: z 36 ASN cc_start: 0.9298 (p0) cc_final: 0.8971 (p0) REVERT: z 37 LEU cc_start: 0.9448 (tp) cc_final: 0.9072 (mt) REVERT: z 40 LYS cc_start: 0.9391 (mmpt) cc_final: 0.9065 (mmmt) REVERT: z 66 MET cc_start: 0.4667 (tmm) cc_final: 0.4381 (tmm) REVERT: z 74 VAL cc_start: 0.9248 (t) cc_final: 0.8618 (t) REVERT: z 83 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8619 (tm-30) REVERT: z 197 MET cc_start: 0.8215 (ppp) cc_final: 0.7937 (ppp) REVERT: z 215 LEU cc_start: 0.8293 (tp) cc_final: 0.7995 (tp) REVERT: z 246 GLU cc_start: 0.5485 (tt0) cc_final: 0.5216 (mp0) REVERT: z 392 LYS cc_start: 0.9528 (ptmm) cc_final: 0.9256 (ptmm) REVERT: z 419 TYR cc_start: 0.9273 (m-10) cc_final: 0.8733 (m-10) REVERT: z 445 GLU cc_start: 0.9116 (mp0) cc_final: 0.8797 (mm-30) REVERT: z 526 ASN cc_start: 0.9574 (m110) cc_final: 0.9260 (m-40) REVERT: z 529 LEU cc_start: 0.9411 (mm) cc_final: 0.9075 (mm) REVERT: Z 22 ASN cc_start: 0.8629 (m110) cc_final: 0.8392 (m110) REVERT: Z 118 ILE cc_start: 0.9070 (mt) cc_final: 0.8763 (mm) REVERT: Z 119 THR cc_start: 0.9805 (p) cc_final: 0.9558 (p) REVERT: Z 128 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8752 (tp30) REVERT: Z 168 GLU cc_start: 0.9577 (mp0) cc_final: 0.9317 (mp0) REVERT: Z 176 ASP cc_start: 0.8940 (m-30) cc_final: 0.8698 (m-30) REVERT: Z 180 SER cc_start: 0.8964 (m) cc_final: 0.8753 (p) REVERT: Z 189 LEU cc_start: 0.8586 (tp) cc_final: 0.8327 (tp) REVERT: Z 205 LYS cc_start: 0.9051 (mttt) cc_final: 0.8633 (ptmt) REVERT: Z 366 TYR cc_start: 0.7501 (m-10) cc_final: 0.7139 (m-80) REVERT: Z 369 GLU cc_start: 0.8342 (tt0) cc_final: 0.8096 (tt0) REVERT: Z 425 TYR cc_start: 0.9186 (t80) cc_final: 0.8844 (t80) REVERT: Z 431 MET cc_start: 0.7101 (mmm) cc_final: 0.6808 (tmm) REVERT: Z 482 ASP cc_start: 0.8927 (m-30) cc_final: 0.8617 (m-30) REVERT: Z 504 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8725 (mm-30) outliers start: 2 outliers final: 1 residues processed: 1338 average time/residue: 0.5664 time to fit residues: 1309.1057 Evaluate side-chains 1085 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1084 time to evaluate : 5.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 506 optimal weight: 5.9990 chunk 679 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 588 optimal weight: 0.0970 chunk 94 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 638 optimal weight: 2.9990 chunk 267 optimal weight: 0.4980 chunk 655 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 89 GLN ** a 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 375 GLN ** b 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 259 GLN d 303 HIS D 112 ASN ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN e 138 GLN ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 519 ASN ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 373 GLN q 543 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 298 GLN ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.132858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.107771 restraints weight = 288125.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.110148 restraints weight = 208417.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.111264 restraints weight = 159824.319| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.8532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 62618 Z= 0.175 Angle : 0.620 9.582 84459 Z= 0.318 Chirality : 0.045 0.271 10166 Planarity : 0.003 0.050 10848 Dihedral : 4.089 21.879 8568 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 0.01 % Allowed : 0.25 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.09), residues: 8065 helix: 0.43 (0.08), residues: 3943 sheet: -0.58 (0.20), residues: 660 loop : -0.72 (0.10), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 440 HIS 0.010 0.001 HIS d 303 PHE 0.023 0.001 PHE e 472 TYR 0.019 0.001 TYR a 432 ARG 0.008 0.001 ARG Q 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20111.35 seconds wall clock time: 346 minutes 59.81 seconds (20819.81 seconds total)