Starting phenix.real_space_refine on Tue Mar 12 05:55:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/03_2024/6ks8_0760.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/03_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_0760/03_2024/6ks8_0760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/03_2024/6ks8_0760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/03_2024/6ks8_0760.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/03_2024/6ks8_0760.pdb" } 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 Residue "Z ARG 14": "NH1" <-> "NH2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 26.34, per 1000 atoms: 0.43 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 - 3.50 Amino acid : False - 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: 17.27 Conformation dependent library (CDL) restraints added in 8.7 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: 6.22 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: 22.74 Time building geometry restraints manager: 19.11 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: 100.26 - 107.01: 1249 107.01 - 113.77: 36756 113.77 - 120.52: 24724 120.52 - 127.27: 21344 127.27 - 134.02: 386 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 2.520 nonbonded pdb=" OH TYR Z 182 " pdb=" O GLN Z 185 " model vdw 2.229 2.440 nonbonded pdb=" O LEU B 317 " pdb=" OG1 THR B 321 " model vdw 2.241 2.440 nonbonded pdb=" O MET d 432 " pdb=" OG SER E 500 " model vdw 2.242 2.440 nonbonded pdb=" O LEU h 198 " pdb=" OG1 THR h 373 " model vdw 2.246 2.440 ... (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 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: 0.760 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: 0.040 Extract box with map and model: 6.250 Check model and map are aligned: 0.710 Set scattering table: 0.440 Process input model: 127.260 Find NCS groups from input model: 5.770 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.000 ------------------------------------------------------------------------------- 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 : 5.411 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: 0.6163 time to fit residues: 2515.8819 Evaluate side-chains 1302 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1302 time to evaluate : 5.426 ------------------------------------------------------------------------------- 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: 0.0060 chunk 609 optimal weight: 0.0040 chunk 338 optimal weight: 7.9990 chunk 208 optimal weight: 0.7980 chunk 411 optimal weight: 8.9990 chunk 325 optimal weight: 20.0000 chunk 630 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 chunk 383 optimal weight: 6.9990 chunk 469 optimal weight: 10.0000 chunk 730 optimal weight: 0.1980 overall best weight: 1.6010 ------------------------------------------------------------------------------- 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 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 375 GLN ** b 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN B 112 GLN B 192 HIS B 420 GLN d 85 GLN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 GLN ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 289 GLN d 461 ASN ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN ** e 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 397 GLN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 461 GLN ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS E 432 ASN E 466 GLN E 509 ASN E 543 GLN g 188 GLN g 286 GLN g 519 ASN g 530 GLN ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN G 465 ASN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 HIS h 172 HIS 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 406 ASN H 436 GLN q 66 ASN q 482 HIS Q 27 GLN Q 66 ASN ** 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 230 ASN z 237 ASN ** z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 356 GLN Z 22 ASN Z 104 GLN Z 430 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.4302 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= 0.196 Angle : 0.612 9.285 84459 Z= 0.321 Chirality : 0.044 0.263 10166 Planarity : 0.004 0.088 10848 Dihedral : 3.481 28.435 8568 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.00 % Rotamer: Outliers : 0.12 % Allowed : 2.51 % Favored : 97.37 % 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: -1.52 (0.08), residues: 8065 helix: -1.03 (0.07), residues: 3846 sheet: -0.64 (0.18), residues: 637 loop : -0.86 (0.09), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP h 478 HIS 0.014 0.001 HIS e 50 PHE 0.069 0.002 PHE h 492 TYR 0.037 0.002 TYR e 381 ARG 0.011 0.001 ARG d 29 *********************** 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 1612 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1604 time to evaluate : 6.299 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: a 44 LEU cc_start: 0.9335 (tp) cc_final: 0.9115 (tp) REVERT: a 73 LEU cc_start: 0.8908 (mt) cc_final: 0.8282 (mt) REVERT: a 81 LYS cc_start: 0.9577 (mttt) cc_final: 0.9290 (mttp) REVERT: a 125 ILE cc_start: 0.9622 (mt) cc_final: 0.9149 (tp) REVERT: a 129 PHE cc_start: 0.9370 (m-10) cc_final: 0.9158 (m-80) REVERT: a 135 GLU cc_start: 0.8290 (tp30) cc_final: 0.7484 (tp30) REVERT: a 142 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8771 (tm-30) REVERT: a 179 MET cc_start: 0.7513 (mtp) cc_final: 0.7151 (ptt) REVERT: a 316 MET cc_start: 0.4296 (tmm) cc_final: 0.3419 (tpt) REVERT: a 399 GLU cc_start: 0.6759 (tt0) cc_final: 0.6420 (pp20) REVERT: a 432 TYR cc_start: 0.7874 (t80) cc_final: 0.7628 (t80) REVERT: a 433 LEU cc_start: 0.9613 (mt) cc_final: 0.9292 (mp) REVERT: a 448 ILE cc_start: 0.9230 (mt) cc_final: 0.8874 (tp) REVERT: a 460 LYS cc_start: 0.8679 (tptt) cc_final: 0.8387 (tptt) REVERT: a 497 TYR cc_start: 0.7858 (m-80) cc_final: 0.7621 (m-80) REVERT: a 530 SER cc_start: 0.9575 (m) cc_final: 0.9213 (p) REVERT: a 532 LEU cc_start: 0.9402 (mm) cc_final: 0.8870 (tt) REVERT: A 20 ILE cc_start: 0.8193 (mm) cc_final: 0.7968 (tp) REVERT: A 25 ILE cc_start: 0.8298 (tp) cc_final: 0.8068 (tp) REVERT: A 88 GLN cc_start: 0.8822 (tp-100) cc_final: 0.8450 (mp10) REVERT: A 131 VAL cc_start: 0.9472 (t) cc_final: 0.9153 (p) REVERT: A 135 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8397 (mm-30) REVERT: A 204 ASN cc_start: 0.7779 (t0) cc_final: 0.7506 (m110) REVERT: A 233 MET cc_start: 0.1350 (mtm) cc_final: 0.0054 (ptm) REVERT: A 320 ARG cc_start: 0.8776 (mtt180) cc_final: 0.8514 (mtt90) REVERT: A 471 SER cc_start: 0.9401 (m) cc_final: 0.8738 (t) REVERT: A 533 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8907 (mm-30) REVERT: b 45 LEU cc_start: 0.9093 (tp) cc_final: 0.8427 (pp) REVERT: b 55 MET cc_start: 0.6170 (ttp) cc_final: 0.5834 (ttp) REVERT: b 59 ASP cc_start: 0.8849 (t0) cc_final: 0.8476 (t0) REVERT: b 62 THR cc_start: 0.9196 (t) cc_final: 0.8955 (t) REVERT: b 135 LEU cc_start: 0.9592 (mt) cc_final: 0.9331 (mt) REVERT: b 148 MET cc_start: 0.8506 (ppp) cc_final: 0.8194 (ppp) REVERT: b 158 LYS cc_start: 0.9477 (mttt) cc_final: 0.9239 (mmmt) REVERT: b 181 ILE cc_start: 0.8379 (mm) cc_final: 0.8172 (pt) REVERT: b 267 GLU cc_start: 0.6987 (tt0) cc_final: 0.6779 (tm-30) REVERT: b 347 MET cc_start: 0.7250 (mmm) cc_final: 0.6408 (tmm) REVERT: b 409 MET cc_start: 0.9118 (tpp) cc_final: 0.8896 (ttm) REVERT: b 439 GLN cc_start: 0.8900 (mm110) cc_final: 0.8635 (mp10) REVERT: B 75 LYS cc_start: 0.8549 (mttt) cc_final: 0.7910 (tttt) REVERT: B 79 ASN cc_start: 0.9077 (m-40) cc_final: 0.8773 (m-40) REVERT: B 233 ILE cc_start: 0.7521 (mt) cc_final: 0.7288 (mt) REVERT: B 354 LEU cc_start: 0.4104 (mt) cc_final: 0.3015 (tp) REVERT: B 409 MET cc_start: 0.9300 (tpp) cc_final: 0.9005 (ttm) REVERT: B 423 ASP cc_start: 0.7198 (m-30) cc_final: 0.6235 (m-30) REVERT: B 435 ARG cc_start: 0.9084 (mtm180) cc_final: 0.8747 (ptm160) REVERT: B 452 SER cc_start: 0.8379 (p) cc_final: 0.7751 (t) REVERT: B 472 LEU cc_start: 0.8817 (mt) cc_final: 0.8557 (mt) REVERT: d 67 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8557 (mm110) REVERT: d 209 MET cc_start: 0.3023 (mtm) cc_final: 0.2578 (ttp) REVERT: d 315 ASP cc_start: 0.2773 (m-30) cc_final: 0.2214 (t70) REVERT: d 442 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7977 (mp0) REVERT: d 513 GLU cc_start: 0.9554 (mm-30) cc_final: 0.8700 (mm-30) REVERT: d 516 LYS cc_start: 0.9316 (mtpp) cc_final: 0.8952 (mttm) REVERT: D 24 ASN cc_start: 0.8257 (m-40) cc_final: 0.7752 (m-40) REVERT: D 44 MET cc_start: 0.8562 (mpp) cc_final: 0.7956 (mpp) REVERT: D 56 ILE cc_start: 0.6937 (pt) cc_final: 0.6540 (pt) REVERT: D 138 MET cc_start: 0.7108 (ptp) cc_final: 0.6888 (tpp) REVERT: D 209 MET cc_start: 0.3282 (mmt) cc_final: 0.2969 (mmt) REVERT: D 447 LEU cc_start: 0.9647 (mt) cc_final: 0.9432 (mt) REVERT: D 470 ARG cc_start: 0.8830 (tpt90) cc_final: 0.7970 (ptt90) REVERT: D 513 GLU cc_start: 0.9044 (mp0) cc_final: 0.8817 (mp0) REVERT: e 94 MET cc_start: 0.6746 (tpt) cc_final: 0.6398 (tpt) REVERT: e 113 ASP cc_start: 0.8634 (m-30) cc_final: 0.7600 (p0) REVERT: e 131 ASP cc_start: 0.9093 (t70) cc_final: 0.8653 (m-30) REVERT: e 146 ILE cc_start: 0.9661 (mm) cc_final: 0.8605 (mm) REVERT: e 150 PHE cc_start: 0.8996 (m-10) cc_final: 0.8556 (m-80) REVERT: e 182 ARG cc_start: 0.9244 (mtt180) cc_final: 0.8920 (tpt90) REVERT: e 203 MET cc_start: 0.3621 (tmm) cc_final: 0.2622 (ptt) REVERT: e 210 ASN cc_start: 0.8731 (m-40) cc_final: 0.8194 (t0) REVERT: e 447 GLU cc_start: 0.8415 (mp0) cc_final: 0.8181 (mp0) REVERT: e 464 ILE cc_start: 0.8772 (mt) cc_final: 0.8530 (mt) REVERT: e 472 PHE cc_start: 0.9098 (t80) cc_final: 0.8852 (t80) REVERT: e 492 ILE cc_start: 0.8803 (mt) cc_final: 0.8525 (mm) REVERT: e 495 LEU cc_start: 0.9051 (tp) cc_final: 0.8398 (mt) REVERT: E 74 LEU cc_start: 0.7933 (mm) cc_final: 0.7706 (mt) REVERT: E 103 LEU cc_start: 0.9320 (mp) cc_final: 0.8993 (mp) REVERT: E 254 MET cc_start: 0.0696 (mtt) cc_final: -0.1530 (ttt) REVERT: E 379 ARG cc_start: 0.6998 (mmt-90) cc_final: 0.6716 (mmt-90) REVERT: E 547 MET cc_start: 0.9321 (mtp) cc_final: 0.9034 (tmm) REVERT: E 553 ASN cc_start: 0.8381 (t0) cc_final: 0.7800 (t0) REVERT: E 555 ILE cc_start: 0.8715 (mm) cc_final: 0.8233 (mm) REVERT: g 24 ASN cc_start: 0.9266 (m-40) cc_final: 0.8819 (t0) REVERT: g 44 MET cc_start: 0.9081 (mpp) cc_final: 0.8403 (mmm) REVERT: g 104 LEU cc_start: 0.9399 (tp) cc_final: 0.8971 (tp) REVERT: g 117 HIS cc_start: 0.7990 (t-90) cc_final: 0.7224 (t-90) REVERT: g 119 VAL cc_start: 0.9487 (t) cc_final: 0.9168 (p) REVERT: g 134 GLU cc_start: 0.9267 (pt0) cc_final: 0.8834 (pp20) REVERT: g 163 TYR cc_start: 0.6597 (t80) cc_final: 0.6307 (t80) REVERT: g 173 GLU cc_start: 0.8940 (tt0) cc_final: 0.8635 (mm-30) REVERT: g 440 MET cc_start: 0.5163 (pmm) cc_final: 0.3942 (pmm) REVERT: g 460 MET cc_start: 0.8981 (ptp) cc_final: 0.8757 (ptt) REVERT: g 487 LEU cc_start: 0.9254 (mt) cc_final: 0.8997 (mt) REVERT: g 509 MET cc_start: 0.8989 (mmm) cc_final: 0.8634 (mmt) REVERT: g 510 GLU cc_start: 0.8698 (pp20) cc_final: 0.8353 (tm-30) REVERT: g 514 ARG cc_start: 0.9094 (tpp80) cc_final: 0.8881 (tpp80) REVERT: g 528 LEU cc_start: 0.9360 (mm) cc_final: 0.9058 (mm) REVERT: g 540 PHE cc_start: 0.7885 (p90) cc_final: 0.7102 (p90) REVERT: g 564 VAL cc_start: 0.9350 (t) cc_final: 0.9100 (t) REVERT: g 567 GLN cc_start: 0.9127 (mt0) cc_final: 0.8267 (pt0) REVERT: g 571 LYS cc_start: 0.9394 (mttt) cc_final: 0.9157 (ptpt) REVERT: g 575 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8544 (pt0) REVERT: g 580 LEU cc_start: 0.9249 (mt) cc_final: 0.9016 (mt) REVERT: G 115 ASN cc_start: 0.8799 (t0) cc_final: 0.8556 (t0) REVERT: G 123 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8609 (tp-100) REVERT: G 130 THR cc_start: 0.9376 (m) cc_final: 0.9117 (p) REVERT: G 173 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8716 (mm-30) REVERT: G 176 LEU cc_start: 0.9407 (mm) cc_final: 0.8965 (pp) REVERT: G 234 MET cc_start: 0.2899 (ttm) cc_final: -0.0294 (ptm) REVERT: G 357 VAL cc_start: 0.5017 (m) cc_final: 0.4641 (p) REVERT: G 481 MET cc_start: 0.9048 (ttm) cc_final: 0.8819 (ttm) REVERT: G 497 ILE cc_start: 0.9027 (tp) cc_final: 0.8756 (tp) REVERT: G 507 ASP cc_start: 0.9347 (m-30) cc_final: 0.8634 (m-30) REVERT: G 510 GLU cc_start: 0.8595 (pp20) cc_final: 0.8018 (pp20) REVERT: G 512 ILE cc_start: 0.9307 (mm) cc_final: 0.8909 (mm) REVERT: G 519 ASN cc_start: 0.8813 (m-40) cc_final: 0.8536 (t0) REVERT: G 571 LYS cc_start: 0.9456 (tttm) cc_final: 0.8966 (mtmm) REVERT: G 585 ASP cc_start: 0.8084 (t0) cc_final: 0.7560 (p0) REVERT: h 70 LEU cc_start: 0.9180 (tp) cc_final: 0.8938 (tp) REVERT: h 87 SER cc_start: 0.8945 (t) cc_final: 0.8650 (p) REVERT: h 143 LEU cc_start: 0.9115 (mt) cc_final: 0.8766 (mt) REVERT: h 146 ASP cc_start: 0.7348 (t0) cc_final: 0.7065 (t0) REVERT: h 166 MET cc_start: 0.7241 (mtt) cc_final: 0.6545 (mtp) REVERT: h 447 GLU cc_start: 0.9060 (pp20) cc_final: 0.8734 (tm-30) REVERT: h 451 ARG cc_start: 0.9588 (tpp80) cc_final: 0.9181 (tpp80) REVERT: H 44 LEU cc_start: 0.9522 (tp) cc_final: 0.9292 (tp) REVERT: H 98 THR cc_start: 0.9469 (p) cc_final: 0.8372 (p) REVERT: H 116 LEU cc_start: 0.8220 (tp) cc_final: 0.7885 (tp) REVERT: H 125 ILE cc_start: 0.9381 (mt) cc_final: 0.9055 (tp) REVERT: H 135 LEU cc_start: 0.8688 (mt) cc_final: 0.8002 (mp) REVERT: H 138 GLU cc_start: 0.9375 (tt0) cc_final: 0.9018 (pt0) REVERT: H 166 MET cc_start: 0.5523 (mmp) cc_final: 0.4917 (mmp) REVERT: H 306 PHE cc_start: 0.8411 (t80) cc_final: 0.7830 (m-80) REVERT: H 444 LYS cc_start: 0.9134 (tttt) cc_final: 0.8834 (tptt) REVERT: H 449 ILE cc_start: 0.9237 (mp) cc_final: 0.8988 (mp) REVERT: H 501 LEU cc_start: 0.9338 (mt) cc_final: 0.9121 (tt) REVERT: q 39 HIS cc_start: 0.9122 (t-170) cc_final: 0.8537 (t70) REVERT: q 41 MET cc_start: 0.7960 (tmm) cc_final: 0.7682 (tmm) REVERT: q 49 CYS cc_start: 0.8229 (m) cc_final: 0.7283 (m) REVERT: q 52 ASN cc_start: 0.9016 (m-40) cc_final: 0.8068 (t0) REVERT: q 87 MET cc_start: 0.9097 (mtm) cc_final: 0.8864 (mmt) REVERT: q 91 GLN cc_start: 0.9183 (tt0) cc_final: 0.8399 (tm-30) REVERT: q 94 ILE cc_start: 0.8797 (pt) cc_final: 0.8460 (pt) REVERT: q 96 MET cc_start: 0.8590 (ptp) cc_final: 0.7931 (ptp) REVERT: q 114 SER cc_start: 0.9002 (m) cc_final: 0.8716 (p) REVERT: q 115 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7907 (tm-30) REVERT: q 128 ILE cc_start: 0.9495 (mt) cc_final: 0.9160 (mt) REVERT: q 144 GLU cc_start: 0.8627 (pp20) cc_final: 0.8051 (mp0) REVERT: q 174 SER cc_start: 0.8812 (m) cc_final: 0.8386 (t) REVERT: q 226 MET cc_start: 0.4973 (mmp) cc_final: 0.4754 (mmp) REVERT: q 361 MET cc_start: 0.7696 (mtt) cc_final: 0.7301 (ttt) REVERT: q 456 PHE cc_start: 0.9129 (m-10) cc_final: 0.8751 (m-80) REVERT: q 520 MET cc_start: 0.7047 (tpp) cc_final: 0.6778 (tpp) REVERT: q 521 LEU cc_start: 0.8863 (tt) cc_final: 0.8561 (tp) REVERT: q 533 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8857 (tm-30) REVERT: q 539 LEU cc_start: 0.9634 (mt) cc_final: 0.9208 (pp) REVERT: Q 27 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6293 (pp30) REVERT: Q 36 ARG cc_start: 0.9446 (ttt180) cc_final: 0.9220 (ttp80) REVERT: Q 109 GLU cc_start: 0.9407 (tp30) cc_final: 0.9116 (tp30) REVERT: Q 133 MET cc_start: 0.9593 (tpp) cc_final: 0.9243 (tpt) REVERT: Q 155 ASP cc_start: 0.8696 (t70) cc_final: 0.8460 (t70) REVERT: Q 230 ARG cc_start: 0.1547 (mtp85) cc_final: 0.0875 (mmp-170) REVERT: Q 437 TYR cc_start: 0.7563 (m-80) cc_final: 0.6559 (m-80) REVERT: Q 470 ASP cc_start: 0.8764 (t0) cc_final: 0.8353 (t70) REVERT: Q 473 GLU cc_start: 0.9128 (pt0) cc_final: 0.8341 (pt0) REVERT: Q 533 GLU cc_start: 0.9426 (mm-30) cc_final: 0.8859 (tm-30) REVERT: z 36 ASN cc_start: 0.9142 (p0) cc_final: 0.8741 (p0) REVERT: z 40 LYS cc_start: 0.9201 (mmpt) cc_final: 0.8902 (mmmt) REVERT: z 83 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8024 (tm-30) REVERT: z 92 THR cc_start: 0.7331 (p) cc_final: 0.7044 (p) REVERT: z 104 GLN cc_start: 0.9311 (tp40) cc_final: 0.9073 (tm-30) REVERT: z 130 MET cc_start: 0.9399 (mmp) cc_final: 0.9006 (mmm) REVERT: z 152 GLN cc_start: 0.8635 (mt0) cc_final: 0.8201 (mm-40) REVERT: z 201 HIS cc_start: 0.9112 (m-70) cc_final: 0.8819 (m90) REVERT: z 215 LEU cc_start: 0.8128 (tp) cc_final: 0.7693 (tp) REVERT: z 390 GLN cc_start: 0.9015 (tt0) cc_final: 0.8500 (tm-30) REVERT: z 412 ILE cc_start: 0.9487 (mm) cc_final: 0.9235 (mm) REVERT: z 472 MET cc_start: 0.8693 (ttp) cc_final: 0.8341 (tmm) REVERT: z 526 ASN cc_start: 0.9424 (m-40) cc_final: 0.9128 (m-40) REVERT: Z 37 LEU cc_start: 0.8088 (tp) cc_final: 0.6753 (tp) REVERT: Z 43 LEU cc_start: 0.7830 (tp) cc_final: 0.7447 (tp) REVERT: Z 106 HIS cc_start: 0.8380 (t70) cc_final: 0.8150 (t-90) REVERT: Z 118 ILE cc_start: 0.8493 (mt) cc_final: 0.8005 (mt) REVERT: Z 128 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8723 (tp30) REVERT: Z 136 PHE cc_start: 0.8370 (t80) cc_final: 0.7747 (t80) REVERT: Z 168 GLU cc_start: 0.9619 (mp0) cc_final: 0.9292 (pm20) REVERT: Z 176 ASP cc_start: 0.8625 (m-30) cc_final: 0.8319 (m-30) REVERT: Z 193 MET cc_start: 0.8015 (mtt) cc_final: 0.7332 (mtm) REVERT: Z 282 ASN cc_start: 0.8436 (m-40) cc_final: 0.8199 (p0) REVERT: Z 366 TYR cc_start: 0.6836 (m-10) cc_final: 0.6370 (m-80) REVERT: Z 393 ASP cc_start: 0.9547 (m-30) cc_final: 0.8841 (m-30) REVERT: Z 404 ASN cc_start: 0.9579 (m-40) cc_final: 0.9279 (m110) REVERT: Z 418 PHE cc_start: 0.9244 (t80) cc_final: 0.9032 (t80) REVERT: Z 431 MET cc_start: 0.6874 (tpt) cc_final: 0.6611 (tmm) REVERT: Z 468 ASP cc_start: 0.9263 (t0) cc_final: 0.8600 (p0) REVERT: Z 482 ASP cc_start: 0.8686 (m-30) cc_final: 0.8482 (m-30) REVERT: Z 504 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8470 (mm-30) REVERT: Z 515 ASN cc_start: 0.9559 (m-40) cc_final: 0.9339 (t0) REVERT: Z 523 ILE cc_start: 0.9685 (mm) cc_final: 0.9444 (mm) REVERT: Z 533 LEU cc_start: 0.9010 (mm) cc_final: 0.8745 (mt) outliers start: 8 outliers final: 2 residues processed: 1611 average time/residue: 0.5745 time to fit residues: 1580.7756 Evaluate side-chains 1164 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1161 time to evaluate : 5.574 ------------------------------------------------------------------------------- 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: 0.8980 chunk 226 optimal weight: 0.6980 chunk 607 optimal weight: 5.9990 chunk 497 optimal weight: 7.9990 chunk 201 optimal weight: 0.7980 chunk 731 optimal weight: 9.9990 chunk 790 optimal weight: 0.9990 chunk 651 optimal weight: 4.9990 chunk 725 optimal weight: 1.9990 chunk 249 optimal weight: 0.0050 chunk 586 optimal weight: 0.0370 overall best weight: 0.4872 ------------------------------------------------------------------------------- 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** b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 HIS d 303 HIS ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN D 284 ASN e 106 GLN e 111 GLN e 132 GLN e 251 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 HIS g 519 ASN g 530 GLN ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN G 465 ASN G 503 GLN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 394 HIS h 406 ASN ** 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 452 GLN q 66 ASN ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 482 HIS ** q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 298 GLN ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 GLN Z 106 HIS Z 142 ASN ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 62618 Z= 0.162 Angle : 0.543 9.974 84459 Z= 0.279 Chirality : 0.043 0.318 10166 Planarity : 0.003 0.060 10848 Dihedral : 3.439 29.130 8568 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.76 % Rotamer: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.90 % 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: -0.73 (0.09), residues: 8065 helix: -0.15 (0.08), residues: 3876 sheet: -0.43 (0.19), residues: 636 loop : -0.73 (0.10), residues: 3553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 440 HIS 0.010 0.001 HIS e 50 PHE 0.023 0.001 PHE b 433 TYR 0.019 0.001 TYR e 381 ARG 0.007 0.000 ARG E 199 *********************** 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 1487 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1482 time to evaluate : 5.500 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: 0.9140 (ptpp) cc_final: 0.8856 (pttm) REVERT: a 49 LEU cc_start: 0.9157 (mt) cc_final: 0.8570 (mm) REVERT: a 73 LEU cc_start: 0.8840 (mt) cc_final: 0.8125 (mt) REVERT: a 81 LYS cc_start: 0.9602 (mttt) cc_final: 0.9366 (mttp) REVERT: a 109 LEU cc_start: 0.9298 (mm) cc_final: 0.9032 (mm) REVERT: a 135 GLU cc_start: 0.8269 (tp30) cc_final: 0.7051 (tp30) REVERT: a 179 MET cc_start: 0.7604 (mtp) cc_final: 0.7084 (ptt) REVERT: a 233 MET cc_start: 0.4923 (mtm) cc_final: 0.4531 (mtt) REVERT: a 359 ASP cc_start: 0.7677 (m-30) cc_final: 0.7373 (p0) REVERT: a 399 GLU cc_start: 0.6663 (tt0) cc_final: 0.6228 (pp20) REVERT: a 433 LEU cc_start: 0.9530 (mt) cc_final: 0.9310 (mp) REVERT: a 448 ILE cc_start: 0.9203 (mt) cc_final: 0.8846 (tt) REVERT: a 450 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8931 (mm-30) REVERT: a 460 LYS cc_start: 0.8676 (tptt) cc_final: 0.8319 (tptt) REVERT: a 497 TYR cc_start: 0.7941 (m-80) cc_final: 0.7661 (m-80) REVERT: a 532 LEU cc_start: 0.9422 (mm) cc_final: 0.8876 (tt) REVERT: A 52 MET cc_start: 0.6146 (tpp) cc_final: 0.5645 (tpp) REVERT: A 70 LEU cc_start: 0.9544 (tp) cc_final: 0.9308 (pp) REVERT: A 88 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8491 (mp10) REVERT: A 119 LYS cc_start: 0.9375 (mppt) cc_final: 0.9114 (mppt) REVERT: A 131 VAL cc_start: 0.9467 (t) cc_final: 0.9037 (p) REVERT: A 179 MET cc_start: 0.4025 (ptt) cc_final: 0.3799 (ptp) REVERT: A 204 ASN cc_start: 0.7777 (t0) cc_final: 0.7476 (m110) REVERT: A 233 MET cc_start: 0.1011 (mtm) cc_final: -0.0195 (ptt) REVERT: A 307 LEU cc_start: 0.4521 (mt) cc_final: 0.4229 (pp) REVERT: A 320 ARG cc_start: 0.8769 (mtt180) cc_final: 0.8511 (mtt90) REVERT: A 533 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8885 (mm-30) REVERT: b 45 LEU cc_start: 0.9049 (tp) cc_final: 0.8405 (pp) REVERT: b 46 LEU cc_start: 0.9000 (mm) cc_final: 0.8726 (mm) REVERT: b 59 ASP cc_start: 0.8777 (t0) cc_final: 0.8397 (t0) REVERT: b 62 THR cc_start: 0.9108 (t) cc_final: 0.8895 (t) REVERT: b 148 MET cc_start: 0.8528 (ppp) cc_final: 0.7943 (ppp) REVERT: b 158 LYS cc_start: 0.9489 (mttt) cc_final: 0.9257 (mmmt) REVERT: b 347 MET cc_start: 0.7126 (mmm) cc_final: 0.6489 (tmm) REVERT: b 384 LEU cc_start: 0.9489 (tp) cc_final: 0.9173 (mt) REVERT: b 409 MET cc_start: 0.9257 (tpp) cc_final: 0.9000 (ttm) REVERT: b 439 GLN cc_start: 0.9071 (mm110) cc_final: 0.8558 (mp10) REVERT: b 489 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9122 (mm-30) REVERT: B 75 LYS cc_start: 0.8692 (mttt) cc_final: 0.8330 (mmtm) REVERT: B 79 ASN cc_start: 0.9088 (m-40) cc_final: 0.8879 (m-40) REVERT: B 155 HIS cc_start: 0.9153 (m90) cc_final: 0.8842 (m90) REVERT: B 161 LEU cc_start: 0.8864 (tt) cc_final: 0.8561 (tt) REVERT: B 170 LYS cc_start: 0.9166 (ttpp) cc_final: 0.8962 (tppt) REVERT: B 354 LEU cc_start: 0.4282 (mt) cc_final: 0.3555 (mt) REVERT: B 409 MET cc_start: 0.9372 (tpp) cc_final: 0.9102 (ttm) REVERT: B 423 ASP cc_start: 0.7184 (m-30) cc_final: 0.6550 (t70) REVERT: B 435 ARG cc_start: 0.9190 (mtm180) cc_final: 0.8947 (ptm160) REVERT: B 452 SER cc_start: 0.8681 (p) cc_final: 0.8152 (t) REVERT: B 472 LEU cc_start: 0.8752 (mt) cc_final: 0.8445 (mt) REVERT: d 39 LEU cc_start: 0.8588 (tp) cc_final: 0.8362 (tp) REVERT: d 110 LEU cc_start: 0.9391 (mt) cc_final: 0.9143 (mt) REVERT: d 209 MET cc_start: 0.3316 (mtm) cc_final: 0.3022 (ttp) REVERT: d 315 ASP cc_start: 0.2736 (m-30) cc_final: 0.2214 (t70) REVERT: d 442 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8155 (mp0) REVERT: d 513 GLU cc_start: 0.9528 (mm-30) cc_final: 0.8629 (mm-30) REVERT: d 516 LYS cc_start: 0.9297 (mtpp) cc_final: 0.8904 (mttm) REVERT: D 24 ASN cc_start: 0.8216 (m-40) cc_final: 0.7939 (m110) REVERT: D 209 MET cc_start: 0.3104 (mmt) cc_final: 0.2800 (mmt) REVERT: D 304 PHE cc_start: 0.7092 (m-10) cc_final: 0.6173 (t80) REVERT: D 385 MET cc_start: 0.6228 (ppp) cc_final: 0.5355 (ttm) REVERT: D 470 ARG cc_start: 0.8455 (tpt90) cc_final: 0.7952 (ptt180) REVERT: D 513 GLU cc_start: 0.9066 (mp0) cc_final: 0.8684 (mp0) REVERT: e 94 MET cc_start: 0.6821 (tpt) cc_final: 0.6459 (tpt) REVERT: e 107 LEU cc_start: 0.9486 (tp) cc_final: 0.9262 (tp) REVERT: e 113 ASP cc_start: 0.8643 (m-30) cc_final: 0.7688 (p0) REVERT: e 129 LEU cc_start: 0.9672 (mm) cc_final: 0.9449 (mm) REVERT: e 142 HIS cc_start: 0.9010 (m170) cc_final: 0.8753 (m170) REVERT: e 151 ASP cc_start: 0.9345 (t0) cc_final: 0.8906 (m-30) REVERT: e 182 ARG cc_start: 0.9171 (mtt180) cc_final: 0.8932 (tpt90) REVERT: e 202 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7985 (tp30) REVERT: e 203 MET cc_start: 0.3228 (tmm) cc_final: 0.2109 (ptt) REVERT: e 210 ASN cc_start: 0.8746 (m-40) cc_final: 0.8184 (t0) REVERT: e 492 ILE cc_start: 0.8747 (mt) cc_final: 0.8483 (mm) REVERT: e 495 LEU cc_start: 0.8918 (tp) cc_final: 0.8417 (mt) REVERT: e 553 ASN cc_start: 0.8533 (m-40) cc_final: 0.8040 (m-40) REVERT: E 74 LEU cc_start: 0.7878 (mm) cc_final: 0.7564 (mm) REVERT: E 226 MET cc_start: 0.5837 (pmm) cc_final: 0.5628 (pmm) REVERT: E 254 MET cc_start: 0.0767 (mtt) cc_final: -0.1436 (ttt) REVERT: E 379 ARG cc_start: 0.7056 (mmt-90) cc_final: 0.6752 (mmt-90) REVERT: E 481 MET cc_start: 0.9297 (mmm) cc_final: 0.8894 (mmt) REVERT: E 495 LEU cc_start: 0.9489 (pp) cc_final: 0.9188 (pp) REVERT: E 499 LYS cc_start: 0.9204 (ptpp) cc_final: 0.8805 (ptpp) REVERT: E 526 PHE cc_start: 0.6653 (m-10) cc_final: 0.6379 (m-10) REVERT: E 547 MET cc_start: 0.9363 (mtp) cc_final: 0.9125 (tmm) REVERT: E 548 ILE cc_start: 0.9312 (tp) cc_final: 0.8966 (tt) REVERT: E 553 ASN cc_start: 0.8406 (t0) cc_final: 0.8127 (m110) REVERT: g 24 ASN cc_start: 0.9324 (m-40) cc_final: 0.8947 (t0) REVERT: g 33 ASP cc_start: 0.9241 (t0) cc_final: 0.8967 (p0) REVERT: g 44 MET cc_start: 0.9101 (mpp) cc_final: 0.8145 (mmm) REVERT: g 98 ILE cc_start: 0.9602 (mm) cc_final: 0.9078 (mm) REVERT: g 102 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8493 (mm-30) REVERT: g 110 TYR cc_start: 0.8548 (m-80) cc_final: 0.8262 (m-80) REVERT: g 113 GLU cc_start: 0.9118 (pp20) cc_final: 0.8900 (pp20) REVERT: g 117 HIS cc_start: 0.7887 (t-90) cc_final: 0.7321 (t-90) REVERT: g 120 ILE cc_start: 0.9654 (mm) cc_final: 0.9449 (mm) REVERT: g 122 ILE cc_start: 0.9511 (mm) cc_final: 0.9228 (mm) REVERT: g 126 LYS cc_start: 0.9451 (mmpt) cc_final: 0.9078 (mmmt) REVERT: g 134 GLU cc_start: 0.9331 (pt0) cc_final: 0.8862 (pp20) REVERT: g 163 TYR cc_start: 0.6589 (t80) cc_final: 0.6323 (t80) REVERT: g 173 GLU cc_start: 0.9053 (tt0) cc_final: 0.8773 (mm-30) REVERT: g 440 MET cc_start: 0.4372 (pmm) cc_final: 0.4164 (pmm) REVERT: g 481 MET cc_start: 0.8424 (tpt) cc_final: 0.8127 (tpt) REVERT: g 487 LEU cc_start: 0.9220 (mt) cc_final: 0.8965 (mt) REVERT: g 492 LYS cc_start: 0.8331 (mmtm) cc_final: 0.8110 (mmtm) REVERT: g 497 ILE cc_start: 0.8899 (tp) cc_final: 0.8335 (tp) REVERT: g 509 MET cc_start: 0.9022 (mmm) cc_final: 0.8497 (tpp) REVERT: g 510 GLU cc_start: 0.8674 (pp20) cc_final: 0.8240 (tm-30) REVERT: g 514 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8848 (tpp80) REVERT: g 528 LEU cc_start: 0.9440 (mm) cc_final: 0.9166 (mm) REVERT: g 540 PHE cc_start: 0.7827 (p90) cc_final: 0.7101 (p90) REVERT: g 564 VAL cc_start: 0.9381 (t) cc_final: 0.8561 (t) REVERT: g 567 GLN cc_start: 0.9074 (mt0) cc_final: 0.7726 (pt0) REVERT: g 568 GLN cc_start: 0.9493 (mm-40) cc_final: 0.8676 (mm110) REVERT: g 571 LYS cc_start: 0.9437 (mttt) cc_final: 0.9203 (ptpt) REVERT: g 575 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8524 (pt0) REVERT: G 48 LEU cc_start: 0.7273 (tp) cc_final: 0.6808 (tp) REVERT: G 123 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8509 (tp-100) REVERT: G 173 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8493 (mm-30) REVERT: G 234 MET cc_start: 0.2503 (ttm) cc_final: -0.0114 (ptm) REVERT: G 512 ILE cc_start: 0.9059 (mm) cc_final: 0.8767 (mm) REVERT: G 567 GLN cc_start: 0.9273 (mt0) cc_final: 0.8531 (mm-40) REVERT: G 584 ASP cc_start: 0.8300 (p0) cc_final: 0.7835 (p0) REVERT: h 70 LEU cc_start: 0.9248 (tp) cc_final: 0.8762 (pp) REVERT: h 143 LEU cc_start: 0.9001 (mt) cc_final: 0.8718 (mt) REVERT: h 166 MET cc_start: 0.7122 (mtt) cc_final: 0.6677 (mtp) REVERT: h 171 ILE cc_start: 0.5111 (pt) cc_final: 0.4812 (pt) REVERT: h 355 MET cc_start: 0.3754 (ptt) cc_final: 0.3499 (ptp) REVERT: h 362 TYR cc_start: 0.7388 (m-10) cc_final: 0.7086 (m-10) REVERT: h 440 ASN cc_start: 0.9606 (t0) cc_final: 0.9359 (t0) REVERT: h 451 ARG cc_start: 0.9599 (tpp80) cc_final: 0.9251 (tpp80) REVERT: H 44 LEU cc_start: 0.9442 (tp) cc_final: 0.9196 (tp) REVERT: H 47 LEU cc_start: 0.8656 (tp) cc_final: 0.8353 (tp) REVERT: H 84 VAL cc_start: 0.9256 (t) cc_final: 0.8934 (p) REVERT: H 109 MET cc_start: 0.9601 (mmp) cc_final: 0.9367 (mmp) REVERT: H 135 LEU cc_start: 0.8769 (mt) cc_final: 0.8156 (mp) REVERT: H 166 MET cc_start: 0.5427 (mmp) cc_final: 0.4790 (mmp) REVERT: H 202 LYS cc_start: 0.7923 (mmpt) cc_final: 0.7419 (mmtm) REVERT: H 402 ARG cc_start: 0.9351 (mpt180) cc_final: 0.8878 (mmt90) REVERT: H 418 MET cc_start: 0.8485 (ttt) cc_final: 0.7937 (ptm) REVERT: H 449 ILE cc_start: 0.9305 (mp) cc_final: 0.9052 (mp) REVERT: H 477 LYS cc_start: 0.7970 (pttm) cc_final: 0.7703 (pptt) REVERT: H 508 ASN cc_start: 0.9155 (m-40) cc_final: 0.8536 (m110) REVERT: q 39 HIS cc_start: 0.8867 (t-170) cc_final: 0.8482 (t-170) REVERT: q 41 MET cc_start: 0.8106 (tmm) cc_final: 0.7667 (tmm) REVERT: q 49 CYS cc_start: 0.7792 (m) cc_final: 0.7069 (m) REVERT: q 52 ASN cc_start: 0.8962 (m-40) cc_final: 0.7979 (t0) REVERT: q 87 MET cc_start: 0.9166 (mtm) cc_final: 0.8806 (mmt) REVERT: q 96 MET cc_start: 0.8423 (ptp) cc_final: 0.7280 (ttm) REVERT: q 115 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7795 (tm-30) REVERT: q 144 GLU cc_start: 0.8497 (pp20) cc_final: 0.8208 (mp0) REVERT: q 155 ASP cc_start: 0.8717 (t0) cc_final: 0.8384 (t0) REVERT: q 174 SER cc_start: 0.8852 (m) cc_final: 0.8382 (t) REVERT: q 226 MET cc_start: 0.4383 (mmp) cc_final: 0.0869 (tpt) REVERT: q 361 MET cc_start: 0.7672 (mtt) cc_final: 0.7288 (ttt) REVERT: q 452 PHE cc_start: 0.9054 (t80) cc_final: 0.8774 (t80) REVERT: q 456 PHE cc_start: 0.9157 (m-10) cc_final: 0.8666 (m-80) REVERT: q 525 LYS cc_start: 0.9310 (ptpt) cc_final: 0.9016 (mtmm) REVERT: q 533 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8996 (tm-30) REVERT: q 542 ASP cc_start: 0.8789 (p0) cc_final: 0.8517 (p0) REVERT: q 546 MET cc_start: 0.7518 (mmp) cc_final: 0.6995 (mmp) REVERT: Q 30 LYS cc_start: 0.8610 (pttm) cc_final: 0.8238 (ptpt) REVERT: Q 38 LEU cc_start: 0.9584 (tp) cc_final: 0.9380 (tp) REVERT: Q 41 MET cc_start: 0.8543 (tmm) cc_final: 0.8106 (tmm) REVERT: Q 86 VAL cc_start: 0.9228 (t) cc_final: 0.8566 (t) REVERT: Q 89 THR cc_start: 0.9674 (m) cc_final: 0.9338 (p) REVERT: Q 109 GLU cc_start: 0.9387 (tp30) cc_final: 0.9170 (tp30) REVERT: Q 113 VAL cc_start: 0.9476 (p) cc_final: 0.9240 (p) REVERT: Q 122 LEU cc_start: 0.7346 (tp) cc_final: 0.7095 (tp) REVERT: Q 133 MET cc_start: 0.9511 (tpp) cc_final: 0.9178 (tpt) REVERT: Q 361 MET cc_start: 0.7699 (ppp) cc_final: 0.7440 (ptt) REVERT: Q 387 ARG cc_start: 0.8907 (mtt90) cc_final: 0.8660 (mtt90) REVERT: Q 420 LEU cc_start: 0.9483 (mp) cc_final: 0.9275 (mp) REVERT: Q 457 GLU cc_start: 0.9091 (mp0) cc_final: 0.8823 (mp0) REVERT: Q 472 ASN cc_start: 0.8394 (m-40) cc_final: 0.8186 (m-40) REVERT: Q 533 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8913 (tm-30) REVERT: z 36 ASN cc_start: 0.9202 (p0) cc_final: 0.8848 (p0) REVERT: z 40 LYS cc_start: 0.9174 (mmpt) cc_final: 0.8840 (mmmt) REVERT: z 83 GLN cc_start: 0.8909 (mm-40) cc_final: 0.7961 (tm-30) REVERT: z 92 THR cc_start: 0.7099 (p) cc_final: 0.6758 (p) REVERT: z 128 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8312 (mt-10) REVERT: z 130 MET cc_start: 0.9435 (mmp) cc_final: 0.9223 (mmm) REVERT: z 152 GLN cc_start: 0.8635 (mt0) cc_final: 0.8233 (mm-40) REVERT: z 215 LEU cc_start: 0.8108 (tp) cc_final: 0.7674 (tp) REVERT: z 330 LEU cc_start: 0.8875 (tp) cc_final: 0.8500 (mp) REVERT: z 355 TYR cc_start: 0.8521 (p90) cc_final: 0.8115 (p90) REVERT: z 386 TYR cc_start: 0.8194 (p90) cc_final: 0.7683 (p90) REVERT: z 412 ILE cc_start: 0.9491 (mm) cc_final: 0.9161 (mm) REVERT: z 523 ILE cc_start: 0.9432 (tp) cc_final: 0.9204 (tp) REVERT: z 526 ASN cc_start: 0.9344 (m-40) cc_final: 0.9039 (m-40) REVERT: z 527 LEU cc_start: 0.9251 (mt) cc_final: 0.8943 (mt) REVERT: Z 37 LEU cc_start: 0.8297 (tp) cc_final: 0.8090 (tp) REVERT: Z 106 HIS cc_start: 0.8637 (t-90) cc_final: 0.8433 (t-90) REVERT: Z 118 ILE cc_start: 0.8690 (mt) cc_final: 0.8415 (mm) REVERT: Z 119 THR cc_start: 0.9514 (t) cc_final: 0.9205 (p) REVERT: Z 128 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8587 (tp30) REVERT: Z 136 PHE cc_start: 0.8458 (t80) cc_final: 0.7558 (t80) REVERT: Z 168 GLU cc_start: 0.9603 (mp0) cc_final: 0.9257 (pm20) REVERT: Z 176 ASP cc_start: 0.8527 (m-30) cc_final: 0.8320 (m-30) REVERT: Z 189 LEU cc_start: 0.8191 (tp) cc_final: 0.7897 (tp) REVERT: Z 282 ASN cc_start: 0.8345 (m-40) cc_final: 0.7973 (p0) REVERT: Z 366 TYR cc_start: 0.6803 (m-10) cc_final: 0.6465 (m-10) REVERT: Z 418 PHE cc_start: 0.9188 (t80) cc_final: 0.8793 (t80) REVERT: Z 431 MET cc_start: 0.7093 (tpt) cc_final: 0.6774 (tpt) REVERT: Z 465 ASP cc_start: 0.9319 (t0) cc_final: 0.8722 (t0) REVERT: Z 468 ASP cc_start: 0.9256 (t0) cc_final: 0.8739 (p0) REVERT: Z 478 ASP cc_start: 0.8821 (t70) cc_final: 0.8603 (m-30) REVERT: Z 504 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8488 (mm-30) REVERT: Z 523 ILE cc_start: 0.9645 (mm) cc_final: 0.9373 (mm) REVERT: Z 533 LEU cc_start: 0.8812 (mm) cc_final: 0.8585 (mt) outliers start: 5 outliers final: 2 residues processed: 1486 average time/residue: 0.5546 time to fit residues: 1417.0407 Evaluate side-chains 1121 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1119 time to evaluate : 5.487 ------------------------------------------------------------------------------- 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: 9.9990 chunk 549 optimal weight: 10.0000 chunk 379 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 349 optimal weight: 8.9990 chunk 491 optimal weight: 10.0000 chunk 734 optimal weight: 0.6980 chunk 777 optimal weight: 10.0000 chunk 383 optimal weight: 0.8980 chunk 695 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- 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 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 ASN b 228 ASN b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 GLN d 140 HIS D 59 ASN D 112 ASN ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 50 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 432 ASN ** e 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS g 85 GLN ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 HIS g 455 ASN g 465 ASN g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 HIS ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 174 ASN ** 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 58 GLN ** 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 66 ASN q 188 HIS q 451 GLN Q 66 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 22 ASN z 329 GLN ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN ** Z 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.6431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 62618 Z= 0.288 Angle : 0.712 13.344 84459 Z= 0.369 Chirality : 0.046 0.231 10166 Planarity : 0.005 0.071 10848 Dihedral : 4.124 24.517 8568 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.03 % 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: -0.55 (0.09), residues: 8065 helix: 0.14 (0.08), residues: 3921 sheet: -0.41 (0.19), residues: 682 loop : -0.83 (0.10), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP g 560 HIS 0.013 0.002 HIS E 353 PHE 0.028 0.002 PHE Z 309 TYR 0.020 0.002 TYR A 432 ARG 0.015 0.001 ARG E 470 *********************** 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 1430 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1425 time to evaluate : 5.526 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: a 44 LEU cc_start: 0.9409 (tp) cc_final: 0.9192 (tp) REVERT: a 49 LEU cc_start: 0.9185 (mt) cc_final: 0.8533 (mm) REVERT: a 73 LEU cc_start: 0.8997 (mt) cc_final: 0.8264 (mt) REVERT: a 109 LEU cc_start: 0.9345 (mm) cc_final: 0.9065 (mm) REVERT: a 125 ILE cc_start: 0.9571 (tp) cc_final: 0.8956 (tp) REVERT: a 135 GLU cc_start: 0.8381 (tp30) cc_final: 0.7643 (tp30) REVERT: a 258 MET cc_start: 0.2030 (mmm) cc_final: 0.1027 (mmt) REVERT: a 359 ASP cc_start: 0.7522 (m-30) cc_final: 0.7241 (p0) REVERT: a 399 GLU cc_start: 0.6894 (tt0) cc_final: 0.6386 (pp20) REVERT: a 448 ILE cc_start: 0.9325 (mt) cc_final: 0.9057 (tt) REVERT: a 450 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8844 (mm-30) REVERT: a 451 PHE cc_start: 0.9575 (t80) cc_final: 0.9173 (t80) REVERT: a 460 LYS cc_start: 0.8870 (tptt) cc_final: 0.8668 (tptt) REVERT: a 497 TYR cc_start: 0.8098 (m-80) cc_final: 0.7712 (m-80) REVERT: a 526 LYS cc_start: 0.9303 (mmtt) cc_final: 0.9020 (mmmt) REVERT: a 532 LEU cc_start: 0.9516 (mm) cc_final: 0.8937 (tt) REVERT: a 542 ASP cc_start: 0.8799 (m-30) cc_final: 0.8329 (t70) REVERT: A 52 MET cc_start: 0.7383 (tpp) cc_final: 0.6813 (tpp) REVERT: A 179 MET cc_start: 0.3678 (ptt) cc_final: 0.3170 (ptt) REVERT: A 204 ASN cc_start: 0.7709 (t0) cc_final: 0.7321 (m110) REVERT: A 233 MET cc_start: 0.2479 (mtm) cc_final: 0.1190 (ptm) REVERT: A 398 MET cc_start: 0.7058 (ttt) cc_final: 0.6365 (ptm) REVERT: A 448 ILE cc_start: 0.9156 (mm) cc_final: 0.8943 (mt) REVERT: A 460 LYS cc_start: 0.9376 (tppt) cc_final: 0.9102 (tppt) REVERT: A 533 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8739 (mm-30) REVERT: b 59 ASP cc_start: 0.8987 (t0) cc_final: 0.8580 (t0) REVERT: b 121 ILE cc_start: 0.9114 (mt) cc_final: 0.8681 (mt) REVERT: b 148 MET cc_start: 0.8530 (ppp) cc_final: 0.8042 (ppp) REVERT: b 409 MET cc_start: 0.9367 (tpp) cc_final: 0.9112 (ttm) REVERT: b 418 GLU cc_start: 0.9184 (mp0) cc_final: 0.8975 (mp0) REVERT: b 431 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9150 (mm-30) REVERT: b 439 GLN cc_start: 0.9240 (mm110) cc_final: 0.8892 (mp10) REVERT: b 489 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9183 (mm-30) REVERT: B 155 HIS cc_start: 0.9200 (m90) cc_final: 0.8878 (m90) REVERT: B 354 LEU cc_start: 0.4474 (mt) cc_final: 0.3094 (tp) REVERT: B 386 ASP cc_start: 0.8708 (m-30) cc_final: 0.7443 (t70) REVERT: B 409 MET cc_start: 0.9435 (tpp) cc_final: 0.9221 (ttm) REVERT: B 452 SER cc_start: 0.9218 (p) cc_final: 0.8829 (t) REVERT: B 472 LEU cc_start: 0.8738 (mt) cc_final: 0.8501 (mt) REVERT: d 209 MET cc_start: 0.3100 (mtm) cc_final: 0.2305 (ttm) REVERT: d 315 ASP cc_start: 0.3092 (m-30) cc_final: 0.2164 (t70) REVERT: d 411 ILE cc_start: 0.8582 (mp) cc_final: 0.8094 (mm) REVERT: d 432 MET cc_start: 0.7382 (mmp) cc_final: 0.6929 (mmp) REVERT: d 433 GLU cc_start: 0.8575 (pm20) cc_final: 0.7856 (tp30) REVERT: d 513 GLU cc_start: 0.9568 (mm-30) cc_final: 0.8524 (mm-30) REVERT: d 516 LYS cc_start: 0.9488 (mtpp) cc_final: 0.8970 (mttm) REVERT: d 518 ILE cc_start: 0.8997 (mm) cc_final: 0.8772 (mm) REVERT: D 29 ARG cc_start: 0.9000 (mtp85) cc_final: 0.8587 (mtp85) REVERT: D 33 ASP cc_start: 0.9044 (m-30) cc_final: 0.8819 (m-30) REVERT: D 44 MET cc_start: 0.7965 (mpp) cc_final: 0.7650 (mpp) REVERT: D 67 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7859 (pp30) REVERT: D 104 LEU cc_start: 0.9385 (mt) cc_final: 0.8862 (mt) REVERT: D 108 GLU cc_start: 0.8077 (tt0) cc_final: 0.7733 (pt0) REVERT: D 133 ASP cc_start: 0.9392 (m-30) cc_final: 0.9096 (t0) REVERT: D 138 MET cc_start: 0.4947 (mmt) cc_final: 0.4626 (mmt) REVERT: D 209 MET cc_start: 0.4416 (mmt) cc_final: 0.3897 (mmt) REVERT: D 379 ILE cc_start: 0.8855 (mp) cc_final: 0.8653 (mp) REVERT: D 385 MET cc_start: 0.6298 (ppp) cc_final: 0.5463 (tpp) REVERT: D 513 GLU cc_start: 0.9233 (mp0) cc_final: 0.8909 (mp0) REVERT: e 102 LYS cc_start: 0.9195 (mppt) cc_final: 0.8966 (mmtp) REVERT: e 109 LYS cc_start: 0.9486 (mmpt) cc_final: 0.9235 (mmmt) REVERT: e 113 ASP cc_start: 0.8642 (m-30) cc_final: 0.7784 (p0) REVERT: e 135 GLU cc_start: 0.8363 (pp20) cc_final: 0.8147 (pm20) REVERT: e 146 ILE cc_start: 0.9666 (mm) cc_final: 0.8870 (mm) REVERT: e 150 PHE cc_start: 0.9126 (m-10) cc_final: 0.8721 (m-80) REVERT: e 210 ASN cc_start: 0.8782 (m-40) cc_final: 0.8235 (t0) REVERT: e 492 ILE cc_start: 0.8939 (mt) cc_final: 0.8700 (mm) REVERT: e 495 LEU cc_start: 0.9143 (tp) cc_final: 0.8488 (mt) REVERT: E 63 THR cc_start: 0.9505 (p) cc_final: 0.9246 (t) REVERT: E 113 ASP cc_start: 0.9157 (m-30) cc_final: 0.8792 (t0) REVERT: E 163 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9061 (mp0) REVERT: E 224 ILE cc_start: 0.6148 (mm) cc_final: 0.5938 (mm) REVERT: E 226 MET cc_start: 0.6419 (pmm) cc_final: 0.5928 (pmm) REVERT: E 447 GLU cc_start: 0.9291 (mp0) cc_final: 0.8801 (mp0) REVERT: E 481 MET cc_start: 0.9329 (mmm) cc_final: 0.8655 (tpt) REVERT: E 526 PHE cc_start: 0.7239 (m-10) cc_final: 0.6952 (m-10) REVERT: g 24 ASN cc_start: 0.9436 (m-40) cc_final: 0.9230 (t0) REVERT: g 102 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8565 (mm-30) REVERT: g 116 ILE cc_start: 0.9097 (mp) cc_final: 0.8869 (mp) REVERT: g 117 HIS cc_start: 0.8640 (t-90) cc_final: 0.8113 (t-90) REVERT: g 134 GLU cc_start: 0.9303 (pt0) cc_final: 0.8872 (pp20) REVERT: g 163 TYR cc_start: 0.6924 (t80) cc_final: 0.6560 (t80) REVERT: g 173 GLU cc_start: 0.9183 (tt0) cc_final: 0.8934 (mm-30) REVERT: g 440 MET cc_start: 0.4813 (pmm) cc_final: 0.4283 (pmm) REVERT: g 481 MET cc_start: 0.8717 (tpt) cc_final: 0.8508 (tpt) REVERT: g 509 MET cc_start: 0.9334 (mmm) cc_final: 0.8616 (tpp) REVERT: g 510 GLU cc_start: 0.8976 (pp20) cc_final: 0.8635 (tm-30) REVERT: g 512 ILE cc_start: 0.9675 (mp) cc_final: 0.9347 (mp) REVERT: g 528 LEU cc_start: 0.9401 (mm) cc_final: 0.9105 (mm) REVERT: g 540 PHE cc_start: 0.8118 (p90) cc_final: 0.7269 (p90) REVERT: g 575 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8751 (pt0) REVERT: G 117 HIS cc_start: 0.9167 (t-90) cc_final: 0.8948 (t-90) REVERT: G 234 MET cc_start: 0.3478 (ttm) cc_final: 0.0429 (ptm) REVERT: G 507 ASP cc_start: 0.9359 (m-30) cc_final: 0.8821 (m-30) REVERT: G 571 LYS cc_start: 0.9525 (mttp) cc_final: 0.8962 (ptpt) REVERT: G 575 GLU cc_start: 0.9388 (pm20) cc_final: 0.9107 (pm20) REVERT: G 578 CYS cc_start: 0.9485 (p) cc_final: 0.9233 (p) REVERT: G 585 ASP cc_start: 0.8161 (p0) cc_final: 0.7786 (p0) REVERT: h 70 LEU cc_start: 0.9213 (tp) cc_final: 0.8959 (pp) REVERT: h 116 LEU cc_start: 0.9364 (mt) cc_final: 0.9118 (pp) REVERT: h 138 GLU cc_start: 0.9575 (pp20) cc_final: 0.9325 (pm20) REVERT: h 146 ASP cc_start: 0.7440 (t0) cc_final: 0.7181 (t0) REVERT: h 160 ARG cc_start: 0.8749 (mtt180) cc_final: 0.8530 (mtp180) REVERT: h 376 LEU cc_start: 0.8632 (tt) cc_final: 0.8339 (mp) REVERT: h 436 GLN cc_start: 0.9592 (tm-30) cc_final: 0.9340 (tp40) REVERT: h 440 ASN cc_start: 0.9501 (t0) cc_final: 0.9297 (t0) REVERT: h 447 GLU cc_start: 0.9364 (pp20) cc_final: 0.8960 (tm-30) REVERT: h 451 ARG cc_start: 0.9517 (tpp80) cc_final: 0.8868 (tpp80) REVERT: h 460 ASP cc_start: 0.8787 (p0) cc_final: 0.8270 (p0) REVERT: h 465 LEU cc_start: 0.9754 (mp) cc_final: 0.9318 (mt) REVERT: h 503 LYS cc_start: 0.9321 (mmtt) cc_final: 0.9085 (mmtp) REVERT: h 524 ILE cc_start: 0.8086 (mt) cc_final: 0.7861 (mm) REVERT: H 44 LEU cc_start: 0.9504 (tp) cc_final: 0.9222 (tp) REVERT: H 110 LYS cc_start: 0.9139 (ptpp) cc_final: 0.8775 (pttt) REVERT: H 116 LEU cc_start: 0.8266 (tp) cc_final: 0.7956 (tp) REVERT: H 166 MET cc_start: 0.5444 (mmp) cc_final: 0.5118 (mmp) REVERT: H 398 MET cc_start: 0.8866 (mtm) cc_final: 0.8414 (mpp) REVERT: H 418 MET cc_start: 0.8809 (ttt) cc_final: 0.8212 (ptm) REVERT: H 449 ILE cc_start: 0.9418 (mp) cc_final: 0.9151 (mp) REVERT: H 453 LEU cc_start: 0.9389 (mt) cc_final: 0.9168 (mt) REVERT: H 494 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8644 (mptt) REVERT: q 41 MET cc_start: 0.8281 (tmm) cc_final: 0.7808 (tmm) REVERT: q 49 CYS cc_start: 0.8377 (m) cc_final: 0.7432 (m) REVERT: q 52 ASN cc_start: 0.9063 (m-40) cc_final: 0.8843 (m-40) REVERT: q 87 MET cc_start: 0.9185 (mtm) cc_final: 0.8976 (mmt) REVERT: q 91 GLN cc_start: 0.9181 (tt0) cc_final: 0.8522 (tp40) REVERT: q 104 MET cc_start: 0.8925 (mmm) cc_final: 0.8666 (mmm) REVERT: q 106 LEU cc_start: 0.9568 (mm) cc_final: 0.9278 (mm) REVERT: q 144 GLU cc_start: 0.8544 (pp20) cc_final: 0.8291 (mp0) REVERT: q 361 MET cc_start: 0.7971 (mtt) cc_final: 0.7539 (ttt) REVERT: q 452 PHE cc_start: 0.9248 (t80) cc_final: 0.8737 (t80) REVERT: q 456 PHE cc_start: 0.9184 (m-10) cc_final: 0.8797 (m-80) REVERT: q 470 ASP cc_start: 0.9174 (t0) cc_final: 0.8958 (t0) REVERT: q 473 GLU cc_start: 0.9081 (tt0) cc_final: 0.8759 (tt0) REVERT: q 520 MET cc_start: 0.7862 (tpp) cc_final: 0.7522 (tpp) REVERT: q 533 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8941 (tm-30) REVERT: q 542 ASP cc_start: 0.9219 (p0) cc_final: 0.8965 (p0) REVERT: Q 39 HIS cc_start: 0.9420 (t70) cc_final: 0.9212 (t70) REVERT: Q 41 MET cc_start: 0.8652 (tmm) cc_final: 0.8283 (tmm) REVERT: Q 49 CYS cc_start: 0.8685 (m) cc_final: 0.8164 (m) REVERT: Q 115 GLU cc_start: 0.8941 (pp20) cc_final: 0.8719 (tm-30) REVERT: Q 126 GLU cc_start: 0.9523 (tm-30) cc_final: 0.9300 (tm-30) REVERT: Q 129 GLN cc_start: 0.9694 (tm-30) cc_final: 0.9437 (pp30) REVERT: Q 133 MET cc_start: 0.9507 (tpp) cc_final: 0.9251 (tpt) REVERT: Q 155 ASP cc_start: 0.8674 (t70) cc_final: 0.8439 (t70) REVERT: Q 161 LYS cc_start: 0.9431 (mttt) cc_final: 0.9009 (mtmm) REVERT: Q 162 MET cc_start: 0.8945 (tmm) cc_final: 0.8621 (tmm) REVERT: Q 202 PHE cc_start: 0.7753 (t80) cc_final: 0.7439 (t80) REVERT: Q 213 MET cc_start: 0.2778 (mmp) cc_final: 0.2050 (mmp) REVERT: Q 374 GLU cc_start: 0.5680 (mt-10) cc_final: 0.4811 (pm20) REVERT: Q 387 ARG cc_start: 0.8864 (mtt90) cc_final: 0.8571 (mtt90) REVERT: Q 457 GLU cc_start: 0.9211 (mp0) cc_final: 0.8443 (mp0) REVERT: Q 461 ARG cc_start: 0.9487 (ptp-170) cc_final: 0.8880 (ptp90) REVERT: Q 470 ASP cc_start: 0.9116 (t70) cc_final: 0.8446 (t70) REVERT: Q 472 ASN cc_start: 0.8784 (m-40) cc_final: 0.8189 (m-40) REVERT: Q 473 GLU cc_start: 0.9223 (pt0) cc_final: 0.8322 (pt0) REVERT: Q 525 LYS cc_start: 0.9404 (tttt) cc_final: 0.8993 (ptmm) REVERT: Q 533 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8925 (tm-30) REVERT: z 36 ASN cc_start: 0.9051 (p0) cc_final: 0.8770 (p0) REVERT: z 40 LYS cc_start: 0.9442 (mmpt) cc_final: 0.9235 (mmmt) REVERT: z 83 GLN cc_start: 0.8947 (mm-40) cc_final: 0.7869 (tm-30) REVERT: z 128 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8285 (mt-10) REVERT: z 152 GLN cc_start: 0.8833 (mt0) cc_final: 0.8310 (mm-40) REVERT: z 158 LEU cc_start: 0.9100 (mt) cc_final: 0.8866 (mt) REVERT: z 185 GLN cc_start: 0.8763 (tt0) cc_final: 0.8490 (pm20) REVERT: z 215 LEU cc_start: 0.8285 (tp) cc_final: 0.7790 (tp) REVERT: z 364 PHE cc_start: 0.8566 (m-10) cc_final: 0.8266 (m-10) REVERT: z 392 LYS cc_start: 0.9541 (ptmm) cc_final: 0.9305 (ptmm) REVERT: z 418 PHE cc_start: 0.9290 (t80) cc_final: 0.9003 (t80) REVERT: z 419 TYR cc_start: 0.9129 (m-10) cc_final: 0.8763 (m-10) REVERT: z 527 LEU cc_start: 0.9398 (mt) cc_final: 0.9088 (mt) REVERT: z 529 LEU cc_start: 0.9027 (mt) cc_final: 0.8711 (mt) REVERT: z 531 ASP cc_start: 0.7069 (m-30) cc_final: 0.6709 (m-30) REVERT: Z 22 ASN cc_start: 0.8730 (m110) cc_final: 0.8472 (m110) REVERT: Z 106 HIS cc_start: 0.8667 (t-90) cc_final: 0.7867 (t-90) REVERT: Z 118 ILE cc_start: 0.9005 (mt) cc_final: 0.8724 (mm) REVERT: Z 128 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8754 (tp30) REVERT: Z 176 ASP cc_start: 0.8762 (m-30) cc_final: 0.8537 (m-30) REVERT: Z 224 MET cc_start: 0.2707 (mmm) cc_final: 0.2498 (mmm) REVERT: Z 366 TYR cc_start: 0.6636 (m-10) cc_final: 0.6019 (m-10) REVERT: Z 376 CYS cc_start: 0.8445 (m) cc_final: 0.8048 (m) REVERT: Z 431 MET cc_start: 0.7227 (tpt) cc_final: 0.6905 (tpt) REVERT: Z 434 LEU cc_start: 0.6093 (mm) cc_final: 0.5757 (mm) REVERT: Z 437 LYS cc_start: 0.8386 (tmmt) cc_final: 0.8060 (ttpp) REVERT: Z 451 LEU cc_start: 0.9553 (mt) cc_final: 0.8983 (tp) REVERT: Z 460 LYS cc_start: 0.9413 (mmmm) cc_final: 0.9153 (tppp) REVERT: Z 465 ASP cc_start: 0.9375 (t0) cc_final: 0.8909 (t0) REVERT: Z 468 ASP cc_start: 0.9510 (t0) cc_final: 0.9064 (p0) REVERT: Z 478 ASP cc_start: 0.8927 (t70) cc_final: 0.8692 (m-30) REVERT: Z 482 ASP cc_start: 0.8429 (m-30) cc_final: 0.8226 (m-30) REVERT: Z 504 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8738 (mm-30) REVERT: Z 526 ASN cc_start: 0.9293 (m-40) cc_final: 0.8649 (t0) outliers start: 5 outliers final: 0 residues processed: 1426 average time/residue: 0.5511 time to fit residues: 1355.6164 Evaluate side-chains 1084 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1084 time to evaluate : 5.424 ------------------------------------------------------------------------------- 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: 3.9990 chunk 441 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 578 optimal weight: 20.0000 chunk 320 optimal weight: 6.9990 chunk 663 optimal weight: 4.9990 chunk 537 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 396 optimal weight: 0.9980 chunk 697 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 89 GLN a 90 GLN ** a 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 ASN b 172 HIS b 375 GLN ** b 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 HIS D 59 ASN D 112 ASN D 436 GLN ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 474 GLN ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN E 353 HIS ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 465 ASN g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 216 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 276 GLN H 436 GLN q 235 HIS ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN Q 92 GLN Q 451 GLN ** z 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 329 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 62618 Z= 0.221 Angle : 0.612 11.163 84459 Z= 0.316 Chirality : 0.044 0.253 10166 Planarity : 0.004 0.093 10848 Dihedral : 4.059 25.621 8568 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % 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: 0.40 (0.08), residues: 3905 sheet: -0.52 (0.18), residues: 748 loop : -0.76 (0.10), residues: 3412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP z 507 HIS 0.012 0.001 HIS d 303 PHE 0.022 0.002 PHE Q 137 TYR 0.027 0.002 TYR Q 496 ARG 0.017 0.001 ARG q 387 *********************** 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 1407 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1404 time to evaluate : 5.523 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: a 41 LYS cc_start: 0.9398 (ptpp) cc_final: 0.9064 (pttt) REVERT: a 44 LEU cc_start: 0.9342 (tp) cc_final: 0.9139 (tp) REVERT: a 73 LEU cc_start: 0.9116 (mt) cc_final: 0.8448 (mt) REVERT: a 109 LEU cc_start: 0.9242 (mm) cc_final: 0.8981 (mm) REVERT: a 125 ILE cc_start: 0.9545 (tp) cc_final: 0.9286 (tp) REVERT: a 175 PHE cc_start: 0.8050 (t80) cc_final: 0.7803 (t80) REVERT: a 258 MET cc_start: 0.1871 (mmm) cc_final: 0.1253 (mmm) REVERT: a 399 GLU cc_start: 0.6736 (tt0) cc_final: 0.6208 (pp20) REVERT: a 448 ILE cc_start: 0.9363 (mt) cc_final: 0.9060 (tp) REVERT: a 450 GLU cc_start: 0.9269 (mm-30) cc_final: 0.9042 (mm-30) REVERT: a 460 LYS cc_start: 0.8998 (tptt) cc_final: 0.8756 (tptt) REVERT: a 497 TYR cc_start: 0.7981 (m-80) cc_final: 0.7519 (m-80) REVERT: a 502 LEU cc_start: 0.7880 (mt) cc_final: 0.7565 (mt) REVERT: a 526 LYS cc_start: 0.9317 (mmtt) cc_final: 0.8985 (mmtt) REVERT: a 532 LEU cc_start: 0.9488 (mm) cc_final: 0.8927 (tt) REVERT: A 30 VAL cc_start: 0.9456 (t) cc_final: 0.9250 (t) REVERT: A 52 MET cc_start: 0.8031 (tpp) cc_final: 0.7568 (tpp) REVERT: A 108 LEU cc_start: 0.9428 (mt) cc_final: 0.9134 (mt) REVERT: A 179 MET cc_start: 0.4877 (ptt) cc_final: 0.4184 (ptp) REVERT: A 204 ASN cc_start: 0.7868 (t0) cc_final: 0.7548 (m110) REVERT: A 393 TYR cc_start: 0.8413 (m-80) cc_final: 0.8205 (m-80) REVERT: A 398 MET cc_start: 0.6874 (ttt) cc_final: 0.6137 (ptm) REVERT: A 444 GLU cc_start: 0.9468 (pm20) cc_final: 0.9006 (pm20) REVERT: A 460 LYS cc_start: 0.9197 (tppt) cc_final: 0.8903 (tppt) REVERT: A 533 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8762 (mm-30) REVERT: b 45 LEU cc_start: 0.9507 (tp) cc_final: 0.9286 (tp) REVERT: b 59 ASP cc_start: 0.8978 (t0) cc_final: 0.8708 (t0) REVERT: b 78 VAL cc_start: 0.9325 (t) cc_final: 0.8997 (t) REVERT: b 82 LYS cc_start: 0.9486 (mmtm) cc_final: 0.9268 (mmmm) REVERT: b 115 ILE cc_start: 0.8140 (mm) cc_final: 0.7809 (mm) REVERT: b 121 ILE cc_start: 0.9178 (mt) cc_final: 0.8974 (mt) REVERT: b 148 MET cc_start: 0.8496 (ppp) cc_final: 0.8026 (ppp) REVERT: b 384 LEU cc_start: 0.9456 (tp) cc_final: 0.9157 (mt) REVERT: b 425 LYS cc_start: 0.8820 (pptt) cc_final: 0.8573 (pttp) REVERT: b 431 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9127 (mm-30) REVERT: b 439 GLN cc_start: 0.9351 (mm110) cc_final: 0.8998 (mp10) REVERT: b 472 LEU cc_start: 0.9068 (mt) cc_final: 0.8745 (mt) REVERT: b 489 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9189 (mm-30) REVERT: B 44 LYS cc_start: 0.8377 (tptt) cc_final: 0.7853 (mmmt) REVERT: B 102 LEU cc_start: 0.9522 (mt) cc_final: 0.9318 (mt) REVERT: B 109 LEU cc_start: 0.9469 (mt) cc_final: 0.9259 (mt) REVERT: B 155 HIS cc_start: 0.9284 (m90) cc_final: 0.9029 (m90) REVERT: B 315 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 354 LEU cc_start: 0.4753 (mt) cc_final: 0.3230 (tp) REVERT: B 409 MET cc_start: 0.9419 (tpp) cc_final: 0.9162 (ttm) REVERT: B 452 SER cc_start: 0.9051 (p) cc_final: 0.8596 (t) REVERT: B 472 LEU cc_start: 0.8679 (mt) cc_final: 0.8453 (mt) REVERT: d 44 MET cc_start: 0.8167 (tmm) cc_final: 0.7545 (tmm) REVERT: d 80 GLU cc_start: 0.8680 (pp20) cc_final: 0.8379 (pm20) REVERT: d 166 TYR cc_start: 0.6490 (m-10) cc_final: 0.6274 (m-10) REVERT: d 209 MET cc_start: 0.3106 (mtm) cc_final: 0.2849 (ttp) REVERT: d 311 MET cc_start: 0.4148 (mmm) cc_final: 0.3571 (mmm) REVERT: d 315 ASP cc_start: 0.3142 (m-30) cc_final: 0.1996 (t70) REVERT: d 411 ILE cc_start: 0.8676 (mp) cc_final: 0.8139 (mm) REVERT: d 432 MET cc_start: 0.7697 (mmp) cc_final: 0.7190 (mmp) REVERT: d 433 GLU cc_start: 0.8701 (pm20) cc_final: 0.8032 (tp30) REVERT: d 513 GLU cc_start: 0.9581 (mm-30) cc_final: 0.8632 (mm-30) REVERT: d 516 LYS cc_start: 0.9508 (mtpp) cc_final: 0.8913 (mttm) REVERT: D 33 ASP cc_start: 0.9241 (m-30) cc_final: 0.8995 (m-30) REVERT: D 44 MET cc_start: 0.8517 (mpp) cc_final: 0.8222 (mpp) REVERT: D 47 MET cc_start: 0.6704 (tpt) cc_final: 0.6179 (tpt) REVERT: D 62 HIS cc_start: 0.8246 (t-90) cc_final: 0.7915 (t-90) REVERT: D 108 GLU cc_start: 0.8312 (tt0) cc_final: 0.8014 (tt0) REVERT: D 110 LEU cc_start: 0.8506 (mt) cc_final: 0.8299 (mt) REVERT: D 133 ASP cc_start: 0.9393 (m-30) cc_final: 0.9071 (t0) REVERT: D 199 LYS cc_start: 0.6298 (mmtt) cc_final: 0.5884 (pttp) REVERT: D 209 MET cc_start: 0.4697 (mmt) cc_final: 0.4195 (mmt) REVERT: D 380 ARG cc_start: 0.7857 (mpp80) cc_final: 0.7618 (mpt-90) REVERT: D 385 MET cc_start: 0.5993 (ppp) cc_final: 0.5126 (ttm) REVERT: D 509 THR cc_start: 0.9283 (t) cc_final: 0.9031 (t) REVERT: D 513 GLU cc_start: 0.9287 (mp0) cc_final: 0.8944 (mp0) REVERT: e 94 MET cc_start: 0.7624 (tpt) cc_final: 0.7362 (tpt) REVERT: e 109 LYS cc_start: 0.9517 (mmpt) cc_final: 0.9314 (mmmt) REVERT: e 113 ASP cc_start: 0.8609 (m-30) cc_final: 0.7827 (p0) REVERT: e 134 LEU cc_start: 0.9195 (tp) cc_final: 0.8980 (tp) REVERT: e 146 ILE cc_start: 0.9756 (mm) cc_final: 0.8736 (mm) REVERT: e 150 PHE cc_start: 0.9110 (m-10) cc_final: 0.8564 (m-80) REVERT: e 203 MET cc_start: 0.4364 (tmm) cc_final: 0.3499 (ptt) REVERT: e 210 ASN cc_start: 0.8808 (m-40) cc_final: 0.8201 (t0) REVERT: e 254 MET cc_start: 0.3914 (mtt) cc_final: 0.3589 (mtt) REVERT: e 472 PHE cc_start: 0.9276 (t80) cc_final: 0.9010 (t80) REVERT: e 495 LEU cc_start: 0.9155 (tp) cc_final: 0.8483 (mt) REVERT: e 553 ASN cc_start: 0.8982 (m-40) cc_final: 0.8444 (m-40) REVERT: e 554 VAL cc_start: 0.7964 (p) cc_final: 0.7429 (p) REVERT: E 63 THR cc_start: 0.9593 (p) cc_final: 0.9366 (t) REVERT: E 113 ASP cc_start: 0.9219 (m-30) cc_final: 0.8923 (t0) REVERT: E 162 GLU cc_start: 0.9260 (tp30) cc_final: 0.8989 (tp30) REVERT: E 163 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9112 (mp0) REVERT: E 226 MET cc_start: 0.6290 (pmm) cc_final: 0.5878 (pmm) REVERT: E 447 GLU cc_start: 0.9281 (mp0) cc_final: 0.8799 (mp0) REVERT: E 481 MET cc_start: 0.9185 (mmm) cc_final: 0.8751 (tpt) REVERT: E 526 PHE cc_start: 0.6871 (m-10) cc_final: 0.6550 (m-10) REVERT: E 550 LYS cc_start: 0.9409 (tppt) cc_final: 0.8920 (tppt) REVERT: g 24 ASN cc_start: 0.9441 (m-40) cc_final: 0.9208 (t0) REVERT: g 38 CYS cc_start: 0.9432 (m) cc_final: 0.9216 (m) REVERT: g 102 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8462 (mm-30) REVERT: g 117 HIS cc_start: 0.8687 (t-90) cc_final: 0.8475 (t-90) REVERT: g 134 GLU cc_start: 0.9312 (pt0) cc_final: 0.8905 (pp20) REVERT: g 163 TYR cc_start: 0.6896 (t80) cc_final: 0.6658 (t80) REVERT: g 171 MET cc_start: 0.8646 (mmm) cc_final: 0.7989 (tpt) REVERT: g 465 ASN cc_start: 0.8887 (m110) cc_final: 0.8631 (m-40) REVERT: g 509 MET cc_start: 0.9425 (mmm) cc_final: 0.8551 (tpp) REVERT: g 510 GLU cc_start: 0.9002 (pp20) cc_final: 0.8552 (tm-30) REVERT: g 528 LEU cc_start: 0.9406 (mm) cc_final: 0.9126 (mm) REVERT: g 540 PHE cc_start: 0.8012 (p90) cc_final: 0.7120 (p90) REVERT: g 571 LYS cc_start: 0.9307 (ptpp) cc_final: 0.8922 (pttt) REVERT: g 575 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8841 (pt0) REVERT: g 579 LEU cc_start: 0.9311 (mt) cc_final: 0.8915 (pp) REVERT: g 585 ASP cc_start: 0.8626 (m-30) cc_final: 0.8338 (m-30) REVERT: G 44 MET cc_start: 0.8362 (tpp) cc_final: 0.7987 (tpt) REVERT: G 45 LEU cc_start: 0.9062 (tp) cc_final: 0.8773 (tp) REVERT: G 49 LEU cc_start: 0.9075 (mt) cc_final: 0.8751 (tt) REVERT: G 52 MET cc_start: 0.8084 (tmm) cc_final: 0.7842 (tmm) REVERT: G 234 MET cc_start: 0.3504 (ttm) cc_final: -0.0100 (ptm) REVERT: G 357 VAL cc_start: 0.5781 (m) cc_final: 0.5373 (t) REVERT: G 511 CYS cc_start: 0.9162 (m) cc_final: 0.8865 (m) REVERT: G 571 LYS cc_start: 0.9430 (mttp) cc_final: 0.9062 (mttp) REVERT: G 578 CYS cc_start: 0.9504 (p) cc_final: 0.9249 (p) REVERT: G 585 ASP cc_start: 0.8229 (p0) cc_final: 0.7879 (p0) REVERT: h 52 LEU cc_start: 0.9257 (tp) cc_final: 0.8800 (tt) REVERT: h 70 LEU cc_start: 0.9075 (tp) cc_final: 0.8811 (pp) REVERT: h 146 ASP cc_start: 0.7406 (t0) cc_final: 0.7062 (t0) REVERT: h 323 MET cc_start: 0.7385 (mtp) cc_final: 0.7079 (mmm) REVERT: h 376 LEU cc_start: 0.8636 (tt) cc_final: 0.8219 (mp) REVERT: h 436 GLN cc_start: 0.9569 (tm-30) cc_final: 0.9242 (tp40) REVERT: h 440 ASN cc_start: 0.9590 (t0) cc_final: 0.9366 (t0) REVERT: h 447 GLU cc_start: 0.9418 (pp20) cc_final: 0.8958 (pp20) REVERT: h 451 ARG cc_start: 0.9518 (tpp80) cc_final: 0.9116 (tpp80) REVERT: h 460 ASP cc_start: 0.8428 (p0) cc_final: 0.7978 (p0) REVERT: h 465 LEU cc_start: 0.9671 (mp) cc_final: 0.9351 (mp) REVERT: h 524 ILE cc_start: 0.8034 (mt) cc_final: 0.7833 (mm) REVERT: H 44 LEU cc_start: 0.9503 (tp) cc_final: 0.9234 (tp) REVERT: H 85 ASP cc_start: 0.9526 (m-30) cc_final: 0.9159 (t70) REVERT: H 362 TYR cc_start: 0.6011 (m-10) cc_final: 0.5789 (m-80) REVERT: H 398 MET cc_start: 0.8923 (mtm) cc_final: 0.8405 (mpp) REVERT: H 402 ARG cc_start: 0.9457 (mpt180) cc_final: 0.9032 (mmt-90) REVERT: H 418 MET cc_start: 0.8866 (ttt) cc_final: 0.8348 (ptm) REVERT: H 419 GLU cc_start: 0.8626 (tp30) cc_final: 0.8247 (tp30) REVERT: H 449 ILE cc_start: 0.9463 (mp) cc_final: 0.9228 (mp) REVERT: H 470 LEU cc_start: 0.8931 (mm) cc_final: 0.8710 (pp) REVERT: q 41 MET cc_start: 0.8300 (tmm) cc_final: 0.7818 (tmm) REVERT: q 49 CYS cc_start: 0.8275 (m) cc_final: 0.7812 (m) REVERT: q 87 MET cc_start: 0.9232 (mtm) cc_final: 0.9008 (mmt) REVERT: q 91 GLN cc_start: 0.9114 (tt0) cc_final: 0.8580 (tp40) REVERT: q 96 MET cc_start: 0.8628 (ptp) cc_final: 0.7972 (pmm) REVERT: q 106 LEU cc_start: 0.9546 (mm) cc_final: 0.9256 (mm) REVERT: q 144 GLU cc_start: 0.8590 (pp20) cc_final: 0.8342 (mp0) REVERT: q 361 MET cc_start: 0.7948 (mtt) cc_final: 0.7510 (ttt) REVERT: q 429 GLU cc_start: 0.9573 (pt0) cc_final: 0.9294 (pp20) REVERT: q 430 LEU cc_start: 0.9661 (mt) cc_final: 0.9252 (mt) REVERT: q 456 PHE cc_start: 0.9327 (m-10) cc_final: 0.8651 (m-80) REVERT: q 470 ASP cc_start: 0.9261 (t0) cc_final: 0.9039 (t0) REVERT: q 473 GLU cc_start: 0.9196 (tt0) cc_final: 0.8863 (tt0) REVERT: q 533 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8916 (tm-30) REVERT: q 541 ILE cc_start: 0.9502 (mp) cc_final: 0.9119 (tp) REVERT: Q 39 HIS cc_start: 0.9379 (t70) cc_final: 0.9151 (t70) REVERT: Q 41 MET cc_start: 0.8673 (tmm) cc_final: 0.8339 (tmm) REVERT: Q 49 CYS cc_start: 0.8900 (m) cc_final: 0.8439 (m) REVERT: Q 109 GLU cc_start: 0.9398 (tp30) cc_final: 0.9142 (tp30) REVERT: Q 113 VAL cc_start: 0.9630 (p) cc_final: 0.8806 (p) REVERT: Q 133 MET cc_start: 0.9538 (tpp) cc_final: 0.9324 (tpt) REVERT: Q 155 ASP cc_start: 0.8769 (t70) cc_final: 0.8544 (t70) REVERT: Q 161 LYS cc_start: 0.9447 (mttt) cc_final: 0.8973 (mtmm) REVERT: Q 162 MET cc_start: 0.8946 (tmm) cc_final: 0.8281 (tmm) REVERT: Q 213 MET cc_start: 0.3108 (mmp) cc_final: 0.2320 (mmp) REVERT: Q 374 GLU cc_start: 0.5690 (mt-10) cc_final: 0.4825 (pm20) REVERT: Q 456 PHE cc_start: 0.9122 (m-80) cc_final: 0.8902 (m-80) REVERT: Q 457 GLU cc_start: 0.9179 (mp0) cc_final: 0.8395 (mp0) REVERT: Q 461 ARG cc_start: 0.9495 (ptp-170) cc_final: 0.8835 (ptp90) REVERT: Q 470 ASP cc_start: 0.9073 (t70) cc_final: 0.8527 (t70) REVERT: Q 472 ASN cc_start: 0.8710 (m-40) cc_final: 0.8356 (m-40) REVERT: Q 473 GLU cc_start: 0.9255 (pt0) cc_final: 0.8555 (pt0) REVERT: Q 525 LYS cc_start: 0.9351 (tttt) cc_final: 0.8999 (ptmm) REVERT: z 36 ASN cc_start: 0.8960 (p0) cc_final: 0.8687 (p0) REVERT: z 37 LEU cc_start: 0.9523 (tp) cc_final: 0.9090 (mt) REVERT: z 40 LYS cc_start: 0.9394 (mmpt) cc_final: 0.9101 (mmmt) REVERT: z 74 VAL cc_start: 0.9190 (t) cc_final: 0.8708 (t) REVERT: z 83 GLN cc_start: 0.9034 (mm-40) cc_final: 0.7805 (tm-30) REVERT: z 128 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8227 (mt-10) REVERT: z 152 GLN cc_start: 0.8922 (mt0) cc_final: 0.8381 (mm110) REVERT: z 185 GLN cc_start: 0.8745 (tt0) cc_final: 0.8493 (pm20) REVERT: z 192 HIS cc_start: 0.8397 (m-70) cc_final: 0.8123 (m90) REVERT: z 197 MET cc_start: 0.8333 (ppp) cc_final: 0.8007 (ppp) REVERT: z 215 LEU cc_start: 0.8123 (tp) cc_final: 0.7745 (tp) REVERT: z 355 TYR cc_start: 0.8247 (p90) cc_final: 0.7731 (p90) REVERT: z 364 PHE cc_start: 0.8473 (m-10) cc_final: 0.8103 (m-10) REVERT: z 392 LYS cc_start: 0.9550 (ptmm) cc_final: 0.9235 (ptmm) REVERT: z 419 TYR cc_start: 0.9225 (m-10) cc_final: 0.8827 (m-10) REVERT: z 526 ASN cc_start: 0.9540 (m110) cc_final: 0.9290 (m-40) REVERT: z 527 LEU cc_start: 0.9402 (mt) cc_final: 0.9084 (mt) REVERT: z 529 LEU cc_start: 0.9029 (mt) cc_final: 0.8643 (mt) REVERT: z 531 ASP cc_start: 0.7116 (m-30) cc_final: 0.6603 (m-30) REVERT: Z 22 ASN cc_start: 0.8732 (m110) cc_final: 0.8470 (m110) REVERT: Z 106 HIS cc_start: 0.8747 (t-90) cc_final: 0.8078 (t-90) REVERT: Z 114 HIS cc_start: 0.8671 (t-90) cc_final: 0.8457 (t-90) REVERT: Z 128 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8779 (tp30) REVERT: Z 165 ASP cc_start: 0.9209 (p0) cc_final: 0.8704 (t0) REVERT: Z 168 GLU cc_start: 0.9582 (mp0) cc_final: 0.9337 (pm20) REVERT: Z 176 ASP cc_start: 0.8848 (m-30) cc_final: 0.8635 (m-30) REVERT: Z 192 HIS cc_start: 0.9074 (m90) cc_final: 0.8846 (m90) REVERT: Z 431 MET cc_start: 0.7234 (tpt) cc_final: 0.6888 (tpt) REVERT: Z 434 LEU cc_start: 0.6248 (mm) cc_final: 0.5927 (mm) REVERT: Z 451 LEU cc_start: 0.9575 (mt) cc_final: 0.9312 (pp) REVERT: Z 460 LYS cc_start: 0.9417 (mmmm) cc_final: 0.9165 (tppp) REVERT: Z 482 ASP cc_start: 0.8507 (m-30) cc_final: 0.8287 (m-30) REVERT: Z 504 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8714 (mm-30) outliers start: 3 outliers final: 0 residues processed: 1405 average time/residue: 0.5645 time to fit residues: 1378.4721 Evaluate side-chains 1116 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1116 time to evaluate : 5.461 ------------------------------------------------------------------------------- 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: 10.0000 chunk 699 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 456 optimal weight: 0.0870 chunk 191 optimal weight: 0.9980 chunk 777 optimal weight: 20.0000 chunk 645 optimal weight: 7.9990 chunk 360 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 408 optimal weight: 5.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 90 GLN ** a 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 465 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 174 ASN ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 491 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 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 69 GLN z 142 ASN ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 110 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.7299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 62618 Z= 0.159 Angle : 0.556 9.618 84459 Z= 0.283 Chirality : 0.043 0.234 10166 Planarity : 0.003 0.058 10848 Dihedral : 3.849 26.798 8568 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Rotamer: Outliers : 0.03 % Allowed : 1.30 % Favored : 98.67 % 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: -0.16 (0.09), residues: 8065 helix: 0.56 (0.08), residues: 3952 sheet: -0.40 (0.19), residues: 684 loop : -0.73 (0.10), residues: 3429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 440 HIS 0.009 0.001 HIS d 473 PHE 0.026 0.001 PHE a 436 TYR 0.016 0.001 TYR a 480 ARG 0.009 0.000 ARG Z 318 *********************** 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 1410 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1408 time to evaluate : 5.535 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: a 34 MET cc_start: 0.9419 (tpp) cc_final: 0.8783 (tmm) REVERT: a 38 ASN cc_start: 0.9441 (t0) cc_final: 0.9237 (t0) REVERT: a 44 LEU cc_start: 0.9346 (tp) cc_final: 0.9072 (tp) REVERT: a 49 LEU cc_start: 0.9281 (mm) cc_final: 0.8801 (mt) REVERT: a 51 LYS cc_start: 0.7927 (mmtp) cc_final: 0.7602 (mmtp) REVERT: a 73 LEU cc_start: 0.9138 (mt) cc_final: 0.8454 (mt) REVERT: a 109 LEU cc_start: 0.9252 (mm) cc_final: 0.8976 (mm) REVERT: a 117 LYS cc_start: 0.9039 (mppt) cc_final: 0.8618 (mptt) REVERT: a 129 PHE cc_start: 0.9359 (m-80) cc_final: 0.9140 (m-10) REVERT: a 135 GLU cc_start: 0.8612 (tm-30) cc_final: 0.7479 (tm-30) REVERT: a 164 MET cc_start: 0.6692 (mmp) cc_final: 0.6372 (mmp) REVERT: a 175 PHE cc_start: 0.7962 (t80) cc_final: 0.7482 (t80) REVERT: a 179 MET cc_start: 0.7645 (mtp) cc_final: 0.7165 (mmm) REVERT: a 258 MET cc_start: 0.1653 (mmm) cc_final: 0.1043 (mpp) REVERT: a 399 GLU cc_start: 0.6760 (tt0) cc_final: 0.6144 (pp20) REVERT: a 450 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8966 (mm-30) REVERT: a 451 PHE cc_start: 0.9454 (t80) cc_final: 0.9077 (t80) REVERT: a 526 LYS cc_start: 0.9322 (mmtt) cc_final: 0.8997 (mmtt) REVERT: A 108 LEU cc_start: 0.9415 (mt) cc_final: 0.9093 (mt) REVERT: A 179 MET cc_start: 0.5160 (ptt) cc_final: 0.4369 (ptp) REVERT: A 204 ASN cc_start: 0.7872 (t0) cc_final: 0.7642 (m110) REVERT: A 233 MET cc_start: 0.2411 (ptt) cc_final: 0.2194 (ptt) REVERT: A 307 LEU cc_start: 0.4522 (mt) cc_final: 0.4194 (pp) REVERT: A 320 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7053 (ptp90) REVERT: A 398 MET cc_start: 0.6824 (ttt) cc_final: 0.6071 (ptm) REVERT: A 460 LYS cc_start: 0.9191 (tppt) cc_final: 0.8804 (tppt) REVERT: A 533 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8633 (mm-30) REVERT: b 59 ASP cc_start: 0.8927 (t0) cc_final: 0.8638 (t0) REVERT: b 78 VAL cc_start: 0.9304 (t) cc_final: 0.8930 (t) REVERT: b 115 ILE cc_start: 0.8175 (mm) cc_final: 0.7910 (mm) REVERT: b 116 HIS cc_start: 0.6556 (t70) cc_final: 0.6153 (t-90) REVERT: b 121 ILE cc_start: 0.9200 (mt) cc_final: 0.8923 (mt) REVERT: b 148 MET cc_start: 0.8507 (ppp) cc_final: 0.8029 (ppp) REVERT: b 384 LEU cc_start: 0.9452 (tp) cc_final: 0.9164 (mt) REVERT: b 439 GLN cc_start: 0.9273 (mm110) cc_final: 0.8959 (mp10) REVERT: b 443 ILE cc_start: 0.9055 (mm) cc_final: 0.8811 (tt) REVERT: b 472 LEU cc_start: 0.9093 (mt) cc_final: 0.8843 (mt) REVERT: b 489 GLU cc_start: 0.9450 (mm-30) cc_final: 0.9154 (mm-30) REVERT: B 44 LYS cc_start: 0.8439 (tptt) cc_final: 0.7910 (mmmt) REVERT: B 102 LEU cc_start: 0.9514 (mt) cc_final: 0.9269 (mt) REVERT: B 103 LEU cc_start: 0.8826 (tp) cc_final: 0.8590 (tp) REVERT: B 155 HIS cc_start: 0.9286 (m90) cc_final: 0.9009 (m90) REVERT: B 315 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 354 LEU cc_start: 0.4737 (mt) cc_final: 0.3273 (tp) REVERT: B 409 MET cc_start: 0.9447 (tpp) cc_final: 0.9207 (ttm) REVERT: B 452 SER cc_start: 0.8999 (p) cc_final: 0.8514 (t) REVERT: B 472 LEU cc_start: 0.8635 (mt) cc_final: 0.8268 (mt) REVERT: d 19 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8557 (pm20) REVERT: d 29 ARG cc_start: 0.9242 (mtp85) cc_final: 0.8620 (mtp85) REVERT: d 80 GLU cc_start: 0.8716 (pp20) cc_final: 0.8463 (pm20) REVERT: d 133 ASP cc_start: 0.9411 (m-30) cc_final: 0.8973 (t0) REVERT: d 166 TYR cc_start: 0.6353 (m-10) cc_final: 0.6126 (m-10) REVERT: d 209 MET cc_start: 0.3355 (mtm) cc_final: 0.3018 (ttp) REVERT: d 311 MET cc_start: 0.3925 (mmm) cc_final: 0.3251 (mmm) REVERT: d 315 ASP cc_start: 0.3076 (m-30) cc_final: 0.2099 (t70) REVERT: d 411 ILE cc_start: 0.8602 (mp) cc_final: 0.8092 (mm) REVERT: d 433 GLU cc_start: 0.8608 (pm20) cc_final: 0.7432 (tp30) REVERT: D 33 ASP cc_start: 0.9196 (m-30) cc_final: 0.8957 (m-30) REVERT: D 47 MET cc_start: 0.6408 (tpt) cc_final: 0.6098 (mmm) REVERT: D 108 GLU cc_start: 0.8157 (tt0) cc_final: 0.7793 (tt0) REVERT: D 133 ASP cc_start: 0.9380 (m-30) cc_final: 0.9056 (t0) REVERT: D 199 LYS cc_start: 0.6270 (mmtt) cc_final: 0.5857 (pttp) REVERT: D 209 MET cc_start: 0.4656 (mmt) cc_final: 0.4097 (mmt) REVERT: D 311 MET cc_start: 0.0654 (tmm) cc_final: 0.0054 (ppp) REVERT: D 380 ARG cc_start: 0.7803 (mpp80) cc_final: 0.7509 (mpt-90) REVERT: D 385 MET cc_start: 0.5815 (ppp) cc_final: 0.4962 (ttm) REVERT: D 447 LEU cc_start: 0.9524 (mt) cc_final: 0.9235 (mt) REVERT: D 509 THR cc_start: 0.9291 (t) cc_final: 0.9009 (t) REVERT: D 513 GLU cc_start: 0.9237 (mp0) cc_final: 0.8822 (mp0) REVERT: e 50 HIS cc_start: 0.8618 (m-70) cc_final: 0.8266 (m-70) REVERT: e 107 LEU cc_start: 0.9460 (tp) cc_final: 0.9247 (tp) REVERT: e 113 ASP cc_start: 0.8514 (m-30) cc_final: 0.7759 (p0) REVERT: e 146 ILE cc_start: 0.9719 (mm) cc_final: 0.8807 (mm) REVERT: e 150 PHE cc_start: 0.9116 (m-10) cc_final: 0.8613 (m-80) REVERT: e 203 MET cc_start: 0.4577 (tmm) cc_final: 0.3390 (ptt) REVERT: e 210 ASN cc_start: 0.8783 (m-40) cc_final: 0.8186 (t0) REVERT: e 254 MET cc_start: 0.4065 (mtt) cc_final: 0.3730 (mtt) REVERT: e 492 ILE cc_start: 0.9148 (mt) cc_final: 0.8931 (mm) REVERT: e 495 LEU cc_start: 0.9147 (tp) cc_final: 0.8503 (mt) REVERT: e 553 ASN cc_start: 0.8931 (m-40) cc_final: 0.8476 (m-40) REVERT: e 554 VAL cc_start: 0.7923 (p) cc_final: 0.7429 (p) REVERT: E 113 ASP cc_start: 0.9146 (m-30) cc_final: 0.8860 (t0) REVERT: E 162 GLU cc_start: 0.9273 (tp30) cc_final: 0.9030 (tp30) REVERT: E 163 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9098 (mp0) REVERT: E 226 MET cc_start: 0.6208 (pmm) cc_final: 0.5867 (pmm) REVERT: E 379 ARG cc_start: 0.6492 (mpt180) cc_final: 0.5349 (ptp-170) REVERT: E 447 GLU cc_start: 0.9290 (mp0) cc_final: 0.9079 (mp0) REVERT: E 526 PHE cc_start: 0.6719 (m-10) cc_final: 0.6387 (m-10) REVERT: g 24 ASN cc_start: 0.9466 (m-40) cc_final: 0.9156 (t0) REVERT: g 38 CYS cc_start: 0.9453 (m) cc_final: 0.9145 (m) REVERT: g 47 MET cc_start: 0.6681 (mmm) cc_final: 0.6256 (mmm) REVERT: g 102 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8294 (mm-30) REVERT: g 117 HIS cc_start: 0.8501 (t-90) cc_final: 0.8301 (t-90) REVERT: g 134 GLU cc_start: 0.9261 (pt0) cc_final: 0.8941 (pp20) REVERT: g 163 TYR cc_start: 0.6718 (t80) cc_final: 0.6467 (t80) REVERT: g 481 MET cc_start: 0.8711 (tpt) cc_final: 0.8196 (tpt) REVERT: g 509 MET cc_start: 0.9376 (mmm) cc_final: 0.8692 (tpp) REVERT: g 528 LEU cc_start: 0.9393 (mm) cc_final: 0.9113 (mm) REVERT: g 540 PHE cc_start: 0.7832 (p90) cc_final: 0.6913 (p90) REVERT: g 575 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8772 (pt0) REVERT: g 579 LEU cc_start: 0.9262 (mt) cc_final: 0.8825 (pp) REVERT: g 585 ASP cc_start: 0.8494 (m-30) cc_final: 0.7926 (m-30) REVERT: G 44 MET cc_start: 0.8349 (tpp) cc_final: 0.7797 (tpt) REVERT: G 45 LEU cc_start: 0.9031 (tp) cc_final: 0.8688 (tp) REVERT: G 49 LEU cc_start: 0.9088 (mt) cc_final: 0.8768 (tt) REVERT: G 117 HIS cc_start: 0.9193 (t-90) cc_final: 0.8919 (t-90) REVERT: G 203 TYR cc_start: 0.7700 (m-80) cc_final: 0.7350 (m-80) REVERT: G 234 MET cc_start: 0.3822 (ttm) cc_final: 0.0983 (ptm) REVERT: G 357 VAL cc_start: 0.5878 (m) cc_final: 0.5662 (t) REVERT: G 507 ASP cc_start: 0.9144 (m-30) cc_final: 0.8672 (m-30) REVERT: G 512 ILE cc_start: 0.9160 (mm) cc_final: 0.8752 (mm) REVERT: G 567 GLN cc_start: 0.9083 (mt0) cc_final: 0.7959 (mt0) REVERT: G 568 GLN cc_start: 0.9340 (mp-120) cc_final: 0.8859 (mm-40) REVERT: G 571 LYS cc_start: 0.9417 (mttp) cc_final: 0.8941 (mttp) REVERT: G 574 ILE cc_start: 0.8292 (mp) cc_final: 0.8083 (mp) REVERT: G 578 CYS cc_start: 0.9502 (p) cc_final: 0.9224 (p) REVERT: G 584 ASP cc_start: 0.8611 (p0) cc_final: 0.8291 (p0) REVERT: G 585 ASP cc_start: 0.8142 (p0) cc_final: 0.7805 (p0) REVERT: h 52 LEU cc_start: 0.9222 (tp) cc_final: 0.8808 (tt) REVERT: h 70 LEU cc_start: 0.9049 (tp) cc_final: 0.8784 (pp) REVERT: h 166 MET cc_start: 0.8000 (mmp) cc_final: 0.7729 (mmm) REVERT: h 355 MET cc_start: 0.5316 (ptt) cc_final: 0.5002 (ptt) REVERT: h 376 LEU cc_start: 0.8633 (tt) cc_final: 0.8265 (mp) REVERT: h 447 GLU cc_start: 0.9363 (pp20) cc_final: 0.8905 (pp20) REVERT: h 451 ARG cc_start: 0.9492 (tpp80) cc_final: 0.8998 (tpp80) REVERT: h 460 ASP cc_start: 0.8288 (p0) cc_final: 0.8008 (p0) REVERT: h 465 LEU cc_start: 0.9643 (mp) cc_final: 0.9376 (mp) REVERT: H 44 LEU cc_start: 0.9466 (tp) cc_final: 0.9197 (tp) REVERT: H 85 ASP cc_start: 0.9525 (m-30) cc_final: 0.9156 (t70) REVERT: H 108 LEU cc_start: 0.9561 (mt) cc_final: 0.9257 (mt) REVERT: H 109 MET cc_start: 0.9652 (mmp) cc_final: 0.9445 (mmp) REVERT: H 110 LYS cc_start: 0.9221 (pttm) cc_final: 0.8884 (ptpp) REVERT: H 125 ILE cc_start: 0.9576 (mm) cc_final: 0.9342 (mm) REVERT: H 166 MET cc_start: 0.5504 (mmp) cc_final: 0.5252 (mmp) REVERT: H 362 TYR cc_start: 0.6072 (m-10) cc_final: 0.5754 (m-80) REVERT: H 402 ARG cc_start: 0.9473 (mpt180) cc_final: 0.8976 (mmt90) REVERT: H 418 MET cc_start: 0.8883 (ttt) cc_final: 0.8398 (ptm) REVERT: H 419 GLU cc_start: 0.8601 (tp30) cc_final: 0.8258 (tp30) REVERT: H 444 LYS cc_start: 0.9430 (tmtt) cc_final: 0.9163 (tptt) REVERT: H 449 ILE cc_start: 0.9408 (mp) cc_final: 0.9178 (mp) REVERT: H 470 LEU cc_start: 0.8822 (mm) cc_final: 0.8584 (pp) REVERT: H 494 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8618 (mptt) REVERT: q 41 MET cc_start: 0.8324 (tmm) cc_final: 0.7823 (tmm) REVERT: q 49 CYS cc_start: 0.8346 (m) cc_final: 0.7616 (m) REVERT: q 87 MET cc_start: 0.9221 (mtm) cc_final: 0.8985 (mmt) REVERT: q 89 THR cc_start: 0.9270 (m) cc_final: 0.9031 (m) REVERT: q 91 GLN cc_start: 0.9210 (tt0) cc_final: 0.8749 (tp40) REVERT: q 96 MET cc_start: 0.8523 (ptp) cc_final: 0.7950 (pmm) REVERT: q 126 GLU cc_start: 0.9315 (mp0) cc_final: 0.9108 (mp0) REVERT: q 144 GLU cc_start: 0.8556 (pp20) cc_final: 0.8318 (mp0) REVERT: q 226 MET cc_start: 0.4766 (mmp) cc_final: 0.4482 (mmp) REVERT: q 361 MET cc_start: 0.7910 (mtt) cc_final: 0.7462 (ttt) REVERT: q 429 GLU cc_start: 0.9631 (pt0) cc_final: 0.9348 (pp20) REVERT: q 430 LEU cc_start: 0.9623 (mt) cc_final: 0.9364 (mt) REVERT: q 451 GLN cc_start: 0.9237 (mt0) cc_final: 0.8958 (mt0) REVERT: q 456 PHE cc_start: 0.9285 (m-10) cc_final: 0.8529 (m-80) REVERT: q 470 ASP cc_start: 0.9254 (t0) cc_final: 0.9051 (t0) REVERT: q 473 GLU cc_start: 0.9187 (tt0) cc_final: 0.8865 (tt0) REVERT: q 533 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8939 (tm-30) REVERT: Q 39 HIS cc_start: 0.9330 (t70) cc_final: 0.9091 (t70) REVERT: Q 41 MET cc_start: 0.8716 (tmm) cc_final: 0.8369 (tmm) REVERT: Q 49 CYS cc_start: 0.8792 (m) cc_final: 0.8352 (m) REVERT: Q 87 MET cc_start: 0.9595 (mpp) cc_final: 0.9359 (mmt) REVERT: Q 90 GLU cc_start: 0.9271 (mp0) cc_final: 0.9052 (mp0) REVERT: Q 92 GLN cc_start: 0.9352 (tp-100) cc_final: 0.9084 (tp40) REVERT: Q 103 VAL cc_start: 0.9611 (p) cc_final: 0.9336 (m) REVERT: Q 109 GLU cc_start: 0.9406 (tp30) cc_final: 0.9100 (tp30) REVERT: Q 113 VAL cc_start: 0.9590 (p) cc_final: 0.8955 (p) REVERT: Q 129 GLN cc_start: 0.9481 (pp30) cc_final: 0.9249 (pp30) REVERT: Q 155 ASP cc_start: 0.8632 (t70) cc_final: 0.8396 (t70) REVERT: Q 161 LYS cc_start: 0.9426 (mttt) cc_final: 0.8916 (mtmm) REVERT: Q 162 MET cc_start: 0.9021 (tmm) cc_final: 0.8377 (tmm) REVERT: Q 175 GLU cc_start: 0.7884 (mp0) cc_final: 0.7673 (mp0) REVERT: Q 213 MET cc_start: 0.3421 (mmp) cc_final: 0.2671 (mmp) REVERT: Q 230 ARG cc_start: 0.1760 (ttt180) cc_final: -0.0081 (mmp-170) REVERT: Q 374 GLU cc_start: 0.5663 (mt-10) cc_final: 0.4795 (pm20) REVERT: Q 451 GLN cc_start: 0.9256 (tp-100) cc_final: 0.9014 (tp-100) REVERT: Q 457 GLU cc_start: 0.9042 (mp0) cc_final: 0.8815 (mp0) REVERT: Q 470 ASP cc_start: 0.9045 (t70) cc_final: 0.8504 (t70) REVERT: Q 472 ASN cc_start: 0.8679 (m-40) cc_final: 0.8351 (m-40) REVERT: Q 473 GLU cc_start: 0.9238 (pt0) cc_final: 0.8579 (pt0) REVERT: Q 496 TYR cc_start: 0.8170 (m-80) cc_final: 0.7948 (m-80) REVERT: Q 525 LYS cc_start: 0.9308 (tttt) cc_final: 0.8967 (ptmm) REVERT: z 24 THR cc_start: 0.9011 (m) cc_final: 0.8764 (m) REVERT: z 37 LEU cc_start: 0.9515 (tp) cc_final: 0.9140 (mt) REVERT: z 40 LYS cc_start: 0.9350 (mmpt) cc_final: 0.9047 (mmmt) REVERT: z 74 VAL cc_start: 0.9258 (t) cc_final: 0.8300 (t) REVERT: z 83 GLN cc_start: 0.9053 (mm-40) cc_final: 0.7821 (tm-30) REVERT: z 128 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8196 (mt-10) REVERT: z 185 GLN cc_start: 0.8735 (tt0) cc_final: 0.8505 (pm20) REVERT: z 215 LEU cc_start: 0.8080 (tp) cc_final: 0.7754 (tp) REVERT: z 246 GLU cc_start: 0.5379 (tt0) cc_final: 0.5107 (mp0) REVERT: z 364 PHE cc_start: 0.8469 (m-10) cc_final: 0.8197 (m-10) REVERT: z 392 LYS cc_start: 0.9545 (ptmm) cc_final: 0.9266 (ptmm) REVERT: z 419 TYR cc_start: 0.9204 (m-10) cc_final: 0.8887 (m-10) REVERT: z 452 LEU cc_start: 0.9552 (mp) cc_final: 0.9192 (mp) REVERT: z 456 LYS cc_start: 0.9677 (mtmm) cc_final: 0.9377 (mttp) REVERT: z 525 SER cc_start: 0.9468 (m) cc_final: 0.8954 (p) REVERT: z 526 ASN cc_start: 0.9564 (m110) cc_final: 0.9316 (m-40) REVERT: z 527 LEU cc_start: 0.9389 (mt) cc_final: 0.9046 (mt) REVERT: z 529 LEU cc_start: 0.9028 (mt) cc_final: 0.8616 (mt) REVERT: Z 22 ASN cc_start: 0.8662 (m110) cc_final: 0.8393 (m110) REVERT: Z 106 HIS cc_start: 0.8672 (t-90) cc_final: 0.7981 (t-90) REVERT: Z 128 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8799 (tp30) REVERT: Z 165 ASP cc_start: 0.9189 (p0) cc_final: 0.8683 (t0) REVERT: Z 168 GLU cc_start: 0.9610 (mp0) cc_final: 0.9344 (pm20) REVERT: Z 176 ASP cc_start: 0.8847 (m-30) cc_final: 0.8632 (m-30) REVERT: Z 189 LEU cc_start: 0.8767 (mp) cc_final: 0.8261 (tp) REVERT: Z 199 MET cc_start: 0.8157 (ppp) cc_final: 0.7926 (ppp) REVERT: Z 224 MET cc_start: 0.3802 (mmm) cc_final: 0.3585 (mmm) REVERT: Z 366 TYR cc_start: 0.6791 (m-80) cc_final: 0.6175 (m-80) REVERT: Z 431 MET cc_start: 0.7219 (tpt) cc_final: 0.6823 (tpp) REVERT: Z 451 LEU cc_start: 0.9594 (mt) cc_final: 0.9351 (mt) REVERT: Z 460 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9184 (tppp) REVERT: Z 465 ASP cc_start: 0.9358 (t70) cc_final: 0.9133 (t0) REVERT: Z 482 ASP cc_start: 0.8693 (m-30) cc_final: 0.8366 (m-30) REVERT: Z 504 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8679 (mm-30) REVERT: Z 523 ILE cc_start: 0.9680 (mm) cc_final: 0.9438 (mm) outliers start: 2 outliers final: 1 residues processed: 1410 average time/residue: 0.5530 time to fit residues: 1348.0909 Evaluate side-chains 1126 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1125 time to evaluate : 5.473 ------------------------------------------------------------------------------- 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: 1.9990 chunk 87 optimal weight: 7.9990 chunk 443 optimal weight: 6.9990 chunk 568 optimal weight: 7.9990 chunk 440 optimal weight: 0.9990 chunk 654 optimal weight: 5.9990 chunk 434 optimal weight: 4.9990 chunk 774 optimal weight: 20.0000 chunk 484 optimal weight: 4.9990 chunk 472 optimal weight: 30.0000 chunk 357 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 ASN ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 HIS D 112 ASN e 50 HIS e 251 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS E 383 GLN ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 HIS ** g 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 HIS ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 436 GLN ** 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 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 22 ASN z 298 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.7992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 62618 Z= 0.212 Angle : 0.619 11.474 84459 Z= 0.319 Chirality : 0.044 0.215 10166 Planarity : 0.004 0.067 10848 Dihedral : 4.090 27.161 8568 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 0.01 % Allowed : 1.15 % Favored : 98.83 % 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: 0.55 (0.08), residues: 3939 sheet: -0.55 (0.19), residues: 683 loop : -0.74 (0.10), residues: 3443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP d 440 HIS 0.010 0.001 HIS d 303 PHE 0.034 0.002 PHE Q 137 TYR 0.027 0.002 TYR Q 437 ARG 0.014 0.001 ARG a 111 *********************** 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 1369 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1368 time to evaluate : 5.578 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: a 34 MET cc_start: 0.9489 (tpp) cc_final: 0.9010 (tmm) REVERT: a 41 LYS cc_start: 0.9348 (ptpp) cc_final: 0.9027 (mtmt) REVERT: a 44 LEU cc_start: 0.9341 (tp) cc_final: 0.9056 (tp) REVERT: a 49 LEU cc_start: 0.9342 (mm) cc_final: 0.8876 (mm) REVERT: a 51 LYS cc_start: 0.8086 (mmtp) cc_final: 0.7687 (mmtp) REVERT: a 73 LEU cc_start: 0.9119 (mt) cc_final: 0.8371 (mt) REVERT: a 109 LEU cc_start: 0.9318 (mm) cc_final: 0.9092 (mm) REVERT: a 117 LYS cc_start: 0.9166 (mppt) cc_final: 0.8863 (mptt) REVERT: a 129 PHE cc_start: 0.9479 (m-80) cc_final: 0.9234 (m-10) REVERT: a 135 GLU cc_start: 0.8830 (tm-30) cc_final: 0.7042 (tm-30) REVERT: a 164 MET cc_start: 0.6752 (mmp) cc_final: 0.6391 (mmm) REVERT: a 175 PHE cc_start: 0.8004 (t80) cc_final: 0.7543 (t80) REVERT: a 179 MET cc_start: 0.7730 (mtp) cc_final: 0.7262 (mmm) REVERT: a 258 MET cc_start: 0.2204 (mmm) cc_final: 0.1534 (mpp) REVERT: a 399 GLU cc_start: 0.6534 (tt0) cc_final: 0.5950 (pp20) REVERT: a 450 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8900 (mm-30) REVERT: a 451 PHE cc_start: 0.9428 (t80) cc_final: 0.9019 (t80) REVERT: a 460 LYS cc_start: 0.9170 (tptt) cc_final: 0.8897 (tptt) REVERT: a 469 ASP cc_start: 0.8847 (t0) cc_final: 0.7699 (t0) REVERT: a 472 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8510 (mm-30) REVERT: a 526 LYS cc_start: 0.9326 (mmtt) cc_final: 0.9115 (mmmt) REVERT: a 532 LEU cc_start: 0.9520 (mm) cc_final: 0.9055 (tt) REVERT: A 30 VAL cc_start: 0.9363 (p) cc_final: 0.9077 (m) REVERT: A 52 MET cc_start: 0.7651 (tpt) cc_final: 0.7450 (tpp) REVERT: A 108 LEU cc_start: 0.9462 (mt) cc_final: 0.9170 (mt) REVERT: A 181 VAL cc_start: 0.7161 (t) cc_final: 0.6959 (t) REVERT: A 204 ASN cc_start: 0.8102 (t0) cc_final: 0.7814 (m110) REVERT: A 233 MET cc_start: 0.3459 (ptt) cc_final: 0.3196 (ptt) REVERT: A 320 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7299 (ptp-170) REVERT: A 398 MET cc_start: 0.6988 (ttt) cc_final: 0.6294 (ptm) REVERT: A 444 GLU cc_start: 0.9514 (pm20) cc_final: 0.9274 (pm20) REVERT: A 533 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8664 (mm-30) REVERT: b 45 LEU cc_start: 0.9507 (tp) cc_final: 0.9260 (tp) REVERT: b 55 MET cc_start: 0.7501 (mtt) cc_final: 0.7197 (mtt) REVERT: b 59 ASP cc_start: 0.9042 (t0) cc_final: 0.8755 (t0) REVERT: b 62 THR cc_start: 0.9320 (t) cc_final: 0.9082 (t) REVERT: b 78 VAL cc_start: 0.9390 (t) cc_final: 0.9127 (t) REVERT: b 115 ILE cc_start: 0.8192 (mm) cc_final: 0.7852 (mm) REVERT: b 116 HIS cc_start: 0.6689 (t70) cc_final: 0.6206 (t-90) REVERT: b 148 MET cc_start: 0.8596 (ppp) cc_final: 0.8184 (ppp) REVERT: b 181 ILE cc_start: 0.7948 (pt) cc_final: 0.7697 (pt) REVERT: b 384 LEU cc_start: 0.9447 (tp) cc_final: 0.9151 (mt) REVERT: b 388 LEU cc_start: 0.9670 (tp) cc_final: 0.9456 (tp) REVERT: b 425 LYS cc_start: 0.8863 (pptt) cc_final: 0.8607 (pttp) REVERT: b 439 GLN cc_start: 0.9416 (mm110) cc_final: 0.9073 (mp10) REVERT: b 443 ILE cc_start: 0.9098 (mm) cc_final: 0.8858 (tp) REVERT: b 472 LEU cc_start: 0.9081 (mt) cc_final: 0.8790 (mt) REVERT: B 155 HIS cc_start: 0.9265 (m90) cc_final: 0.8986 (m90) REVERT: B 269 MET cc_start: 0.0066 (mtm) cc_final: -0.0212 (mtm) REVERT: B 315 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7600 (mm-30) REVERT: B 354 LEU cc_start: 0.5504 (mt) cc_final: 0.3993 (tp) REVERT: B 386 ASP cc_start: 0.8453 (m-30) cc_final: 0.7300 (t70) REVERT: B 409 MET cc_start: 0.9486 (tpp) cc_final: 0.9227 (ttm) REVERT: B 452 SER cc_start: 0.9144 (p) cc_final: 0.8658 (t) REVERT: B 472 LEU cc_start: 0.8611 (mt) cc_final: 0.8168 (mt) REVERT: d 19 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8627 (pm20) REVERT: d 29 ARG cc_start: 0.9090 (mtp85) cc_final: 0.8862 (mtp-110) REVERT: d 108 GLU cc_start: 0.9237 (tt0) cc_final: 0.8999 (tt0) REVERT: d 209 MET cc_start: 0.3179 (mtm) cc_final: 0.2797 (ttp) REVERT: d 311 MET cc_start: 0.4070 (mmm) cc_final: 0.3442 (mmm) REVERT: d 315 ASP cc_start: 0.3626 (m-30) cc_final: 0.2474 (t70) REVERT: d 411 ILE cc_start: 0.8637 (mp) cc_final: 0.8133 (mm) REVERT: d 432 MET cc_start: 0.7851 (mmm) cc_final: 0.7292 (mmp) REVERT: d 433 GLU cc_start: 0.8102 (pm20) cc_final: 0.7484 (tp30) REVERT: d 442 GLU cc_start: 0.9071 (mp0) cc_final: 0.8785 (mp0) REVERT: d 502 LEU cc_start: 0.8954 (mt) cc_final: 0.8724 (mt) REVERT: D 29 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8006 (mtp85) REVERT: D 33 ASP cc_start: 0.9163 (m-30) cc_final: 0.8862 (m-30) REVERT: D 44 MET cc_start: 0.8339 (mpp) cc_final: 0.7932 (mpp) REVERT: D 47 MET cc_start: 0.6943 (tpt) cc_final: 0.6700 (tpt) REVERT: D 104 LEU cc_start: 0.9281 (mt) cc_final: 0.8676 (mt) REVERT: D 108 GLU cc_start: 0.8290 (tt0) cc_final: 0.7846 (pt0) REVERT: D 209 MET cc_start: 0.4954 (mmt) cc_final: 0.4388 (mmt) REVERT: D 380 ARG cc_start: 0.7747 (mpp80) cc_final: 0.7513 (mpt-90) REVERT: D 385 MET cc_start: 0.5877 (ppp) cc_final: 0.4742 (ttm) REVERT: D 509 THR cc_start: 0.9448 (t) cc_final: 0.9088 (t) REVERT: D 513 GLU cc_start: 0.9574 (mm-30) cc_final: 0.9118 (mp0) REVERT: e 113 ASP cc_start: 0.8646 (m-30) cc_final: 0.7922 (p0) REVERT: e 136 LEU cc_start: 0.8763 (mt) cc_final: 0.8485 (mt) REVERT: e 146 ILE cc_start: 0.9740 (mm) cc_final: 0.8838 (mm) REVERT: e 150 PHE cc_start: 0.9229 (m-10) cc_final: 0.8603 (m-80) REVERT: e 203 MET cc_start: 0.5030 (tmm) cc_final: 0.4133 (ptt) REVERT: e 210 ASN cc_start: 0.8825 (m-40) cc_final: 0.8221 (t0) REVERT: e 396 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6404 (tm-30) REVERT: e 472 PHE cc_start: 0.9326 (t80) cc_final: 0.8909 (t80) REVERT: e 492 ILE cc_start: 0.9269 (mt) cc_final: 0.9027 (mm) REVERT: e 495 LEU cc_start: 0.9208 (tp) cc_final: 0.8616 (mt) REVERT: E 94 MET cc_start: 0.8184 (ttp) cc_final: 0.7575 (tmm) REVERT: E 113 ASP cc_start: 0.9152 (m-30) cc_final: 0.8950 (t0) REVERT: E 162 GLU cc_start: 0.9308 (tp30) cc_final: 0.9084 (tp30) REVERT: E 163 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9141 (mp0) REVERT: E 226 MET cc_start: 0.6505 (pmm) cc_final: 0.6021 (pmm) REVERT: E 414 MET cc_start: 0.8618 (tpt) cc_final: 0.8356 (tmm) REVERT: E 447 GLU cc_start: 0.9439 (mp0) cc_final: 0.8908 (mp0) REVERT: E 481 MET cc_start: 0.9140 (mmm) cc_final: 0.8908 (tpt) REVERT: E 522 MET cc_start: 0.7710 (tmm) cc_final: 0.7500 (tmm) REVERT: E 526 PHE cc_start: 0.6885 (m-10) cc_final: 0.6615 (m-10) REVERT: E 553 ASN cc_start: 0.9376 (t0) cc_final: 0.8970 (p0) REVERT: g 24 ASN cc_start: 0.9496 (m-40) cc_final: 0.9186 (t0) REVERT: g 38 CYS cc_start: 0.9377 (m) cc_final: 0.9155 (m) REVERT: g 39 LEU cc_start: 0.6914 (tp) cc_final: 0.6674 (tp) REVERT: g 47 MET cc_start: 0.6712 (mmm) cc_final: 0.5981 (mmm) REVERT: g 57 LEU cc_start: 0.7906 (pp) cc_final: 0.7687 (pp) REVERT: g 78 MET cc_start: 0.9331 (mmm) cc_final: 0.9098 (mmp) REVERT: g 102 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8382 (mm-30) REVERT: g 117 HIS cc_start: 0.8645 (t-90) cc_final: 0.8407 (t-90) REVERT: g 134 GLU cc_start: 0.9323 (pt0) cc_final: 0.9068 (pp20) REVERT: g 163 TYR cc_start: 0.6926 (t80) cc_final: 0.6552 (t80) REVERT: g 440 MET cc_start: 0.5632 (pmm) cc_final: 0.4909 (pmm) REVERT: g 467 MET cc_start: 0.9242 (mmp) cc_final: 0.9011 (tmm) REVERT: g 481 MET cc_start: 0.8760 (tpt) cc_final: 0.8320 (tpt) REVERT: g 509 MET cc_start: 0.9468 (mmm) cc_final: 0.8714 (tpp) REVERT: g 540 PHE cc_start: 0.7876 (p90) cc_final: 0.6919 (p90) REVERT: g 571 LYS cc_start: 0.9212 (ptpp) cc_final: 0.8815 (pttt) REVERT: g 575 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8797 (pt0) REVERT: g 579 LEU cc_start: 0.9336 (mt) cc_final: 0.8867 (pp) REVERT: g 585 ASP cc_start: 0.8650 (m-30) cc_final: 0.8004 (m-30) REVERT: G 44 MET cc_start: 0.8284 (tpp) cc_final: 0.7712 (tpt) REVERT: G 45 LEU cc_start: 0.9035 (tp) cc_final: 0.8718 (tp) REVERT: G 49 LEU cc_start: 0.9115 (mt) cc_final: 0.8825 (tt) REVERT: G 52 MET cc_start: 0.8373 (tmm) cc_final: 0.8082 (tmm) REVERT: G 117 HIS cc_start: 0.9148 (t-90) cc_final: 0.8920 (t-90) REVERT: G 151 MET cc_start: 0.8722 (mmt) cc_final: 0.8481 (mmm) REVERT: G 203 TYR cc_start: 0.7572 (m-80) cc_final: 0.7371 (m-80) REVERT: G 234 MET cc_start: 0.3812 (ttm) cc_final: 0.0301 (ptm) REVERT: G 507 ASP cc_start: 0.9252 (m-30) cc_final: 0.8866 (m-30) REVERT: G 512 ILE cc_start: 0.9005 (mm) cc_final: 0.8784 (mm) REVERT: G 514 ARG cc_start: 0.8892 (ttp-110) cc_final: 0.8670 (ttp-110) REVERT: G 531 LEU cc_start: 0.9508 (tp) cc_final: 0.9045 (tp) REVERT: G 568 GLN cc_start: 0.9368 (mp-120) cc_final: 0.9152 (mm-40) REVERT: G 574 ILE cc_start: 0.8471 (mp) cc_final: 0.8192 (mp) REVERT: G 578 CYS cc_start: 0.9516 (p) cc_final: 0.9232 (p) REVERT: G 584 ASP cc_start: 0.8718 (p0) cc_final: 0.8440 (p0) REVERT: G 585 ASP cc_start: 0.8423 (p0) cc_final: 0.8134 (p0) REVERT: h 166 MET cc_start: 0.7890 (mmp) cc_final: 0.7587 (mmm) REVERT: h 172 HIS cc_start: 0.5469 (t70) cc_final: 0.5264 (t-90) REVERT: h 355 MET cc_start: 0.5895 (ptt) cc_final: 0.5685 (ptt) REVERT: h 447 GLU cc_start: 0.9388 (pp20) cc_final: 0.9024 (pp20) REVERT: h 451 ARG cc_start: 0.9472 (tpp80) cc_final: 0.9181 (tpp80) REVERT: h 460 ASP cc_start: 0.8385 (p0) cc_final: 0.8080 (p0) REVERT: H 37 GLN cc_start: 0.8964 (tt0) cc_final: 0.8653 (tp-100) REVERT: H 44 LEU cc_start: 0.9487 (tp) cc_final: 0.9255 (tp) REVERT: H 85 ASP cc_start: 0.9527 (m-30) cc_final: 0.9220 (t70) REVERT: H 110 LYS cc_start: 0.8893 (pttm) cc_final: 0.8655 (ptpp) REVERT: H 166 MET cc_start: 0.5327 (mmp) cc_final: 0.4972 (mmp) REVERT: H 362 TYR cc_start: 0.6101 (m-10) cc_final: 0.5834 (m-80) REVERT: H 398 MET cc_start: 0.9169 (mtm) cc_final: 0.8612 (mpp) REVERT: H 402 ARG cc_start: 0.9485 (mpt180) cc_final: 0.9091 (mmt90) REVERT: H 418 MET cc_start: 0.8998 (ttt) cc_final: 0.8484 (ptm) REVERT: H 419 GLU cc_start: 0.8592 (tp30) cc_final: 0.8112 (tp30) REVERT: H 434 LYS cc_start: 0.9075 (mtpt) cc_final: 0.8735 (mttt) REVERT: H 437 MET cc_start: 0.9354 (mtm) cc_final: 0.9001 (ttp) REVERT: H 440 ASN cc_start: 0.9186 (m-40) cc_final: 0.8965 (m110) REVERT: H 449 ILE cc_start: 0.9519 (mp) cc_final: 0.9278 (mp) REVERT: H 494 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8682 (mptt) REVERT: q 41 MET cc_start: 0.8460 (tmm) cc_final: 0.8019 (tmm) REVERT: q 49 CYS cc_start: 0.8246 (m) cc_final: 0.7385 (m) REVERT: q 70 THR cc_start: 0.8861 (m) cc_final: 0.8600 (p) REVERT: q 87 MET cc_start: 0.9260 (mtm) cc_final: 0.8963 (mmt) REVERT: q 89 THR cc_start: 0.9258 (m) cc_final: 0.9031 (m) REVERT: q 91 GLN cc_start: 0.9203 (tt0) cc_final: 0.8781 (tp40) REVERT: q 110 LEU cc_start: 0.9277 (mm) cc_final: 0.8938 (mm) REVERT: q 126 GLU cc_start: 0.9294 (mp0) cc_final: 0.9060 (mp0) REVERT: q 145 MET cc_start: 0.7271 (ptp) cc_final: 0.6979 (ptp) REVERT: q 226 MET cc_start: 0.5418 (mmp) cc_final: 0.5060 (mmp) REVERT: q 361 MET cc_start: 0.8041 (mtt) cc_final: 0.7714 (ttt) REVERT: q 429 GLU cc_start: 0.9653 (pt0) cc_final: 0.9308 (pp20) REVERT: q 430 LEU cc_start: 0.9691 (mt) cc_final: 0.9285 (mt) REVERT: q 451 GLN cc_start: 0.9399 (mt0) cc_final: 0.9147 (mt0) REVERT: q 456 PHE cc_start: 0.9308 (m-10) cc_final: 0.8685 (m-80) REVERT: q 473 GLU cc_start: 0.9371 (tt0) cc_final: 0.9043 (tt0) REVERT: q 520 MET cc_start: 0.8073 (tpt) cc_final: 0.7707 (tpt) REVERT: q 533 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8929 (tm-30) REVERT: q 541 ILE cc_start: 0.9457 (mt) cc_final: 0.8754 (mt) REVERT: q 543 GLN cc_start: 0.8957 (pt0) cc_final: 0.8580 (pp30) REVERT: Q 38 LEU cc_start: 0.9607 (tp) cc_final: 0.9264 (tp) REVERT: Q 39 HIS cc_start: 0.9418 (t70) cc_final: 0.9036 (t70) REVERT: Q 42 CYS cc_start: 0.9441 (m) cc_final: 0.8944 (p) REVERT: Q 49 CYS cc_start: 0.8763 (m) cc_final: 0.8333 (m) REVERT: Q 92 GLN cc_start: 0.9354 (tp-100) cc_final: 0.9015 (tp40) REVERT: Q 103 VAL cc_start: 0.9533 (p) cc_final: 0.9177 (m) REVERT: Q 109 GLU cc_start: 0.9378 (tp30) cc_final: 0.9111 (tp30) REVERT: Q 129 GLN cc_start: 0.9593 (pp30) cc_final: 0.9239 (pp30) REVERT: Q 161 LYS cc_start: 0.9411 (mttt) cc_final: 0.8893 (mtmm) REVERT: Q 162 MET cc_start: 0.9147 (tmm) cc_final: 0.8526 (tmm) REVERT: Q 175 GLU cc_start: 0.8212 (mp0) cc_final: 0.7993 (mp0) REVERT: Q 213 MET cc_start: 0.3683 (mmp) cc_final: 0.2930 (mmp) REVERT: Q 230 ARG cc_start: 0.2008 (ttt180) cc_final: 0.0030 (mmp-170) REVERT: Q 374 GLU cc_start: 0.4963 (mt-10) cc_final: 0.4067 (pm20) REVERT: Q 470 ASP cc_start: 0.9132 (t70) cc_final: 0.8544 (t70) REVERT: Q 472 ASN cc_start: 0.8877 (m-40) cc_final: 0.8487 (m-40) REVERT: Q 473 GLU cc_start: 0.9253 (pt0) cc_final: 0.8678 (pt0) REVERT: Q 525 LYS cc_start: 0.9375 (tttt) cc_final: 0.9092 (ptmm) REVERT: z 37 LEU cc_start: 0.9554 (tp) cc_final: 0.9167 (mt) REVERT: z 40 LYS cc_start: 0.9407 (mmpt) cc_final: 0.9125 (mmmt) REVERT: z 60 LYS cc_start: 0.8576 (pptt) cc_final: 0.8304 (ttpp) REVERT: z 74 VAL cc_start: 0.9347 (t) cc_final: 0.8704 (t) REVERT: z 83 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8123 (tm-30) REVERT: z 128 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8343 (mt-10) REVERT: z 185 GLN cc_start: 0.8805 (tt0) cc_final: 0.8584 (pm20) REVERT: z 215 LEU cc_start: 0.8158 (tp) cc_final: 0.7804 (tp) REVERT: z 246 GLU cc_start: 0.5429 (tt0) cc_final: 0.5130 (mp0) REVERT: z 355 TYR cc_start: 0.7990 (p90) cc_final: 0.7709 (p90) REVERT: z 364 PHE cc_start: 0.8472 (m-10) cc_final: 0.8157 (m-10) REVERT: z 372 ASP cc_start: 0.7642 (m-30) cc_final: 0.7351 (m-30) REVERT: z 392 LYS cc_start: 0.9567 (ptmm) cc_final: 0.9318 (ptmm) REVERT: z 419 TYR cc_start: 0.9276 (m-10) cc_final: 0.8943 (m-10) REVERT: z 452 LEU cc_start: 0.9561 (mp) cc_final: 0.9125 (mp) REVERT: z 456 LYS cc_start: 0.9698 (mtmm) cc_final: 0.9412 (mttp) REVERT: z 481 GLN cc_start: 0.9049 (mp10) cc_final: 0.8845 (pm20) REVERT: z 525 SER cc_start: 0.9477 (m) cc_final: 0.9037 (p) REVERT: z 526 ASN cc_start: 0.9574 (m110) cc_final: 0.9284 (m-40) REVERT: z 527 LEU cc_start: 0.9423 (mt) cc_final: 0.9072 (mt) REVERT: Z 22 ASN cc_start: 0.8866 (m110) cc_final: 0.8510 (m110) REVERT: Z 106 HIS cc_start: 0.8746 (t-90) cc_final: 0.8043 (t-90) REVERT: Z 114 HIS cc_start: 0.8848 (t-90) cc_final: 0.8598 (t-90) REVERT: Z 120 ASP cc_start: 0.9753 (t70) cc_final: 0.9133 (t0) REVERT: Z 165 ASP cc_start: 0.9171 (p0) cc_final: 0.8742 (t0) REVERT: Z 366 TYR cc_start: 0.7397 (m-80) cc_final: 0.6808 (m-80) REVERT: Z 431 MET cc_start: 0.7336 (tpt) cc_final: 0.7120 (tpp) REVERT: Z 460 LYS cc_start: 0.9569 (mmmm) cc_final: 0.9285 (tppp) REVERT: Z 482 ASP cc_start: 0.8834 (m-30) cc_final: 0.8496 (m-30) REVERT: Z 504 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8712 (mm-30) outliers start: 1 outliers final: 0 residues processed: 1369 average time/residue: 0.5871 time to fit residues: 1401.9876 Evaluate side-chains 1103 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1103 time to evaluate : 5.497 ------------------------------------------------------------------------------- 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: 5.9990 chunk 309 optimal weight: 6.9990 chunk 462 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 492 optimal weight: 6.9990 chunk 527 optimal weight: 0.0060 chunk 383 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 609 optimal weight: 0.5980 overall best weight: 1.5202 ------------------------------------------------------------------------------- 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 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 393 GLN ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 251 HIS e 285 HIS ** e 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 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 106 GLN ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 466 ASN ** 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 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 451 GLN ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.8153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 62618 Z= 0.166 Angle : 0.578 14.229 84459 Z= 0.294 Chirality : 0.044 0.361 10166 Planarity : 0.003 0.051 10848 Dihedral : 3.947 25.728 8568 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 0.01 % Allowed : 0.76 % Favored : 99.23 % 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: 0.66 (0.08), residues: 3956 sheet: -0.51 (0.20), residues: 672 loop : -0.73 (0.10), residues: 3437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP d 440 HIS 0.009 0.001 HIS d 473 PHE 0.040 0.001 PHE Q 137 TYR 0.021 0.001 TYR z 355 ARG 0.009 0.000 ARG D 130 *********************** 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 1371 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1370 time to evaluate : 5.544 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 28 GLN cc_start: 0.8850 (tp40) cc_final: 0.8618 (tp40) REVERT: a 34 MET cc_start: 0.9439 (tpp) cc_final: 0.8812 (tmm) REVERT: a 41 LYS cc_start: 0.9261 (ptpp) cc_final: 0.8946 (pttt) REVERT: a 44 LEU cc_start: 0.9344 (tp) cc_final: 0.9002 (tp) REVERT: a 49 LEU cc_start: 0.9351 (mm) cc_final: 0.8924 (mm) REVERT: a 51 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7538 (mmtp) REVERT: a 73 LEU cc_start: 0.9194 (mt) cc_final: 0.8473 (mt) REVERT: a 109 LEU cc_start: 0.9190 (mm) cc_final: 0.8973 (mm) REVERT: a 117 LYS cc_start: 0.9099 (mppt) cc_final: 0.8875 (mptt) REVERT: a 135 GLU cc_start: 0.8882 (tm-30) cc_final: 0.7167 (tm-30) REVERT: a 175 PHE cc_start: 0.8009 (t80) cc_final: 0.7542 (t80) REVERT: a 179 MET cc_start: 0.7690 (mtp) cc_final: 0.7261 (mmm) REVERT: a 258 MET cc_start: 0.2098 (mmm) cc_final: 0.1411 (mpp) REVERT: a 398 MET cc_start: 0.5777 (ttt) cc_final: 0.5195 (ttp) REVERT: a 399 GLU cc_start: 0.6702 (tt0) cc_final: 0.6003 (pp20) REVERT: a 450 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8913 (mm-30) REVERT: a 451 PHE cc_start: 0.9350 (t80) cc_final: 0.9023 (t80) REVERT: a 460 LYS cc_start: 0.9058 (tptt) cc_final: 0.8817 (tptt) REVERT: a 469 ASP cc_start: 0.8831 (t0) cc_final: 0.7716 (t0) REVERT: a 472 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8560 (mm-30) REVERT: a 526 LYS cc_start: 0.9331 (mmtt) cc_final: 0.9090 (mmmt) REVERT: A 30 VAL cc_start: 0.9378 (p) cc_final: 0.9126 (m) REVERT: A 52 MET cc_start: 0.7596 (tpt) cc_final: 0.7132 (tpt) REVERT: A 108 LEU cc_start: 0.9449 (mt) cc_final: 0.9155 (mt) REVERT: A 179 MET cc_start: 0.5818 (ptt) cc_final: 0.5094 (ptp) REVERT: A 233 MET cc_start: 0.3775 (ptt) cc_final: 0.3519 (ptt) REVERT: A 320 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7281 (ptp-170) REVERT: A 398 MET cc_start: 0.7000 (ttt) cc_final: 0.6250 (ptm) REVERT: A 444 GLU cc_start: 0.9435 (pm20) cc_final: 0.9189 (pm20) REVERT: A 533 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8678 (mm-30) REVERT: b 55 MET cc_start: 0.7387 (mtt) cc_final: 0.7072 (mtt) REVERT: b 59 ASP cc_start: 0.9010 (t0) cc_final: 0.8754 (t0) REVERT: b 62 THR cc_start: 0.9304 (t) cc_final: 0.9048 (t) REVERT: b 69 LEU cc_start: 0.8209 (mt) cc_final: 0.6905 (tp) REVERT: b 78 VAL cc_start: 0.9406 (t) cc_final: 0.9084 (t) REVERT: b 115 ILE cc_start: 0.8261 (mm) cc_final: 0.8041 (mm) REVERT: b 116 HIS cc_start: 0.6648 (t70) cc_final: 0.6130 (t-90) REVERT: b 148 MET cc_start: 0.8588 (ppp) cc_final: 0.8145 (ppp) REVERT: b 384 LEU cc_start: 0.9439 (tp) cc_final: 0.9164 (mt) REVERT: b 425 LYS cc_start: 0.8650 (pptt) cc_final: 0.8412 (pttp) REVERT: b 439 GLN cc_start: 0.9389 (mm110) cc_final: 0.9019 (mp10) REVERT: b 443 ILE cc_start: 0.9075 (mm) cc_final: 0.8629 (tp) REVERT: b 447 ASN cc_start: 0.8440 (m-40) cc_final: 0.8229 (m-40) REVERT: b 472 LEU cc_start: 0.9149 (mt) cc_final: 0.8868 (mt) REVERT: b 489 GLU cc_start: 0.9495 (mm-30) cc_final: 0.9169 (mm-30) REVERT: B 107 GLU cc_start: 0.8994 (pp20) cc_final: 0.8790 (pp20) REVERT: B 155 HIS cc_start: 0.9259 (m90) cc_final: 0.8993 (m90) REVERT: B 193 ILE cc_start: 0.5357 (mm) cc_final: 0.5140 (mm) REVERT: B 269 MET cc_start: 0.0096 (mtm) cc_final: -0.0226 (mtm) REVERT: B 315 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 354 LEU cc_start: 0.5106 (mt) cc_final: 0.3649 (tp) REVERT: B 386 ASP cc_start: 0.8417 (m-30) cc_final: 0.7316 (t70) REVERT: B 409 MET cc_start: 0.9435 (tpp) cc_final: 0.9192 (ttm) REVERT: B 452 SER cc_start: 0.8934 (p) cc_final: 0.8582 (t) REVERT: B 472 LEU cc_start: 0.8607 (mt) cc_final: 0.8125 (mt) REVERT: d 19 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8591 (pm20) REVERT: d 29 ARG cc_start: 0.9082 (mtp85) cc_final: 0.8868 (mtp85) REVERT: d 108 GLU cc_start: 0.9257 (tt0) cc_final: 0.9027 (tt0) REVERT: d 209 MET cc_start: 0.3545 (mtm) cc_final: 0.3136 (ttp) REVERT: d 311 MET cc_start: 0.4074 (mmm) cc_final: 0.3454 (mmm) REVERT: d 315 ASP cc_start: 0.3635 (m-30) cc_final: 0.2483 (t70) REVERT: d 411 ILE cc_start: 0.8618 (mp) cc_final: 0.8211 (mm) REVERT: d 433 GLU cc_start: 0.8171 (pm20) cc_final: 0.7548 (tp30) REVERT: d 464 LYS cc_start: 0.9669 (mmmt) cc_final: 0.9032 (ptmm) REVERT: d 502 LEU cc_start: 0.8893 (mt) cc_final: 0.8587 (mt) REVERT: D 29 ARG cc_start: 0.8898 (mtp85) cc_final: 0.8204 (mtp85) REVERT: D 33 ASP cc_start: 0.9206 (m-30) cc_final: 0.8970 (m-30) REVERT: D 44 MET cc_start: 0.8345 (mpp) cc_final: 0.8026 (mpp) REVERT: D 47 MET cc_start: 0.7161 (tpt) cc_final: 0.6796 (mmm) REVERT: D 104 LEU cc_start: 0.9342 (mt) cc_final: 0.9039 (mt) REVERT: D 108 GLU cc_start: 0.8126 (tt0) cc_final: 0.7656 (tt0) REVERT: D 133 ASP cc_start: 0.9449 (m-30) cc_final: 0.9180 (t0) REVERT: D 209 MET cc_start: 0.5073 (mmt) cc_final: 0.4465 (mmt) REVERT: D 379 ILE cc_start: 0.8955 (mp) cc_final: 0.8731 (mp) REVERT: D 385 MET cc_start: 0.5990 (ppp) cc_final: 0.4878 (ttm) REVERT: D 509 THR cc_start: 0.9412 (t) cc_final: 0.9034 (t) REVERT: D 513 GLU cc_start: 0.9570 (mm-30) cc_final: 0.9119 (mp0) REVERT: e 113 ASP cc_start: 0.8579 (m-30) cc_final: 0.7922 (p0) REVERT: e 146 ILE cc_start: 0.9747 (mm) cc_final: 0.8823 (mm) REVERT: e 150 PHE cc_start: 0.9235 (m-10) cc_final: 0.8630 (m-80) REVERT: e 203 MET cc_start: 0.5046 (tmm) cc_final: 0.4244 (ptt) REVERT: e 210 ASN cc_start: 0.8800 (m-40) cc_final: 0.8208 (t0) REVERT: e 396 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6427 (tm-30) REVERT: e 472 PHE cc_start: 0.9401 (t80) cc_final: 0.9130 (t80) REVERT: E 113 ASP cc_start: 0.9230 (m-30) cc_final: 0.9016 (t0) REVERT: E 142 HIS cc_start: 0.8914 (t70) cc_final: 0.8693 (t-90) REVERT: E 163 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9123 (mp0) REVERT: E 203 MET cc_start: 0.6255 (ptp) cc_final: 0.5841 (mpp) REVERT: E 226 MET cc_start: 0.6443 (pmm) cc_final: 0.6009 (pmm) REVERT: E 379 ARG cc_start: 0.7420 (mmt180) cc_final: 0.6465 (ptp-170) REVERT: E 414 MET cc_start: 0.8616 (tpt) cc_final: 0.8357 (tmm) REVERT: E 481 MET cc_start: 0.9118 (mmm) cc_final: 0.8815 (tpt) REVERT: E 522 MET cc_start: 0.7728 (tmm) cc_final: 0.7425 (tmm) REVERT: E 526 PHE cc_start: 0.6893 (m-10) cc_final: 0.6624 (m-10) REVERT: E 539 LEU cc_start: 0.9428 (tp) cc_final: 0.9165 (tp) REVERT: E 542 THR cc_start: 0.9317 (m) cc_final: 0.9069 (t) REVERT: E 553 ASN cc_start: 0.9411 (t0) cc_final: 0.8928 (p0) REVERT: g 24 ASN cc_start: 0.9507 (m-40) cc_final: 0.9189 (t0) REVERT: g 38 CYS cc_start: 0.9291 (m) cc_final: 0.8933 (m) REVERT: g 39 LEU cc_start: 0.6677 (tp) cc_final: 0.6458 (tp) REVERT: g 47 MET cc_start: 0.7210 (mmm) cc_final: 0.6947 (mmm) REVERT: g 78 MET cc_start: 0.9371 (mmm) cc_final: 0.9093 (mmp) REVERT: g 102 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8607 (mm-30) REVERT: g 117 HIS cc_start: 0.8549 (t-90) cc_final: 0.8327 (t-90) REVERT: g 134 GLU cc_start: 0.9305 (pt0) cc_final: 0.9025 (pp20) REVERT: g 163 TYR cc_start: 0.6926 (t80) cc_final: 0.6650 (t80) REVERT: g 440 MET cc_start: 0.5432 (pmm) cc_final: 0.4602 (pmm) REVERT: g 467 MET cc_start: 0.9224 (mmp) cc_final: 0.8811 (tpt) REVERT: g 481 MET cc_start: 0.8692 (tpt) cc_final: 0.8292 (tpt) REVERT: g 509 MET cc_start: 0.9434 (mmm) cc_final: 0.8681 (tpp) REVERT: g 540 PHE cc_start: 0.7850 (p90) cc_final: 0.6833 (p90) REVERT: g 575 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8666 (pt0) REVERT: g 585 ASP cc_start: 0.8627 (m-30) cc_final: 0.7987 (m-30) REVERT: G 44 MET cc_start: 0.8389 (tpp) cc_final: 0.8093 (tpt) REVERT: G 45 LEU cc_start: 0.9182 (tp) cc_final: 0.8895 (tp) REVERT: G 49 LEU cc_start: 0.9135 (mt) cc_final: 0.8853 (tt) REVERT: G 52 MET cc_start: 0.8193 (tmm) cc_final: 0.7952 (tmm) REVERT: G 103 ILE cc_start: 0.9428 (mt) cc_final: 0.9189 (mt) REVERT: G 117 HIS cc_start: 0.9063 (t-90) cc_final: 0.8789 (t-90) REVERT: G 234 MET cc_start: 0.3519 (ttm) cc_final: 0.0325 (ptm) REVERT: G 507 ASP cc_start: 0.9172 (m-30) cc_final: 0.8882 (m-30) REVERT: G 512 ILE cc_start: 0.9128 (mm) cc_final: 0.8912 (mm) REVERT: G 567 GLN cc_start: 0.9171 (mt0) cc_final: 0.8404 (mt0) REVERT: G 568 GLN cc_start: 0.9348 (mp-120) cc_final: 0.9084 (mm-40) REVERT: G 574 ILE cc_start: 0.8450 (mp) cc_final: 0.8178 (mp) REVERT: G 578 CYS cc_start: 0.9515 (p) cc_final: 0.9215 (p) REVERT: G 584 ASP cc_start: 0.8783 (p0) cc_final: 0.8493 (p0) REVERT: G 585 ASP cc_start: 0.8269 (p0) cc_final: 0.7990 (p0) REVERT: h 166 MET cc_start: 0.8400 (mmp) cc_final: 0.6851 (mtp) REVERT: h 172 HIS cc_start: 0.5664 (t70) cc_final: 0.5302 (t70) REVERT: h 447 GLU cc_start: 0.9388 (pp20) cc_final: 0.8972 (pp20) REVERT: h 451 ARG cc_start: 0.9488 (tpp80) cc_final: 0.9139 (tpp80) REVERT: h 460 ASP cc_start: 0.8240 (p0) cc_final: 0.8013 (p0) REVERT: H 37 GLN cc_start: 0.8848 (tt0) cc_final: 0.8567 (tp-100) REVERT: H 85 ASP cc_start: 0.9527 (m-30) cc_final: 0.9199 (t70) REVERT: H 126 MET cc_start: 0.9347 (mmm) cc_final: 0.8079 (mmt) REVERT: H 362 TYR cc_start: 0.6191 (m-10) cc_final: 0.5916 (m-80) REVERT: H 402 ARG cc_start: 0.9501 (mpt180) cc_final: 0.8994 (mmt90) REVERT: H 418 MET cc_start: 0.8979 (ttt) cc_final: 0.8468 (ptm) REVERT: H 434 LYS cc_start: 0.9094 (mtpt) cc_final: 0.8793 (mttt) REVERT: H 437 MET cc_start: 0.9395 (mtm) cc_final: 0.9094 (ttp) REVERT: H 440 ASN cc_start: 0.9143 (m-40) cc_final: 0.8816 (m110) REVERT: H 463 GLU cc_start: 0.9215 (pp20) cc_final: 0.8987 (pp20) REVERT: q 41 MET cc_start: 0.8439 (tmm) cc_final: 0.8017 (tmm) REVERT: q 49 CYS cc_start: 0.8289 (m) cc_final: 0.7507 (m) REVERT: q 87 MET cc_start: 0.9275 (mtm) cc_final: 0.8945 (mmt) REVERT: q 91 GLN cc_start: 0.9298 (tt0) cc_final: 0.8917 (tp40) REVERT: q 129 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8950 (tm-30) REVERT: q 144 GLU cc_start: 0.8765 (pp20) cc_final: 0.8497 (mp0) REVERT: q 226 MET cc_start: 0.5024 (mmp) cc_final: 0.4790 (mmp) REVERT: q 361 MET cc_start: 0.8067 (mtt) cc_final: 0.7720 (ttt) REVERT: q 429 GLU cc_start: 0.9666 (pt0) cc_final: 0.9412 (pp20) REVERT: q 430 LEU cc_start: 0.9604 (mt) cc_final: 0.9228 (mt) REVERT: q 451 GLN cc_start: 0.9424 (mt0) cc_final: 0.9047 (mt0) REVERT: q 456 PHE cc_start: 0.9335 (m-10) cc_final: 0.8703 (m-80) REVERT: q 473 GLU cc_start: 0.9331 (tt0) cc_final: 0.9018 (tt0) REVERT: q 518 TYR cc_start: 0.7792 (p90) cc_final: 0.6656 (p90) REVERT: q 519 ASP cc_start: 0.7805 (t70) cc_final: 0.6755 (t0) REVERT: q 533 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8908 (tm-30) REVERT: q 543 GLN cc_start: 0.9011 (pt0) cc_final: 0.8654 (pp30) REVERT: Q 38 LEU cc_start: 0.9562 (tp) cc_final: 0.9300 (tp) REVERT: Q 42 CYS cc_start: 0.9506 (m) cc_final: 0.8874 (p) REVERT: Q 49 CYS cc_start: 0.8714 (m) cc_final: 0.8220 (m) REVERT: Q 87 MET cc_start: 0.9552 (mpp) cc_final: 0.9120 (mpp) REVERT: Q 90 GLU cc_start: 0.9239 (mp0) cc_final: 0.8988 (mp0) REVERT: Q 92 GLN cc_start: 0.9365 (tp-100) cc_final: 0.9015 (tp40) REVERT: Q 103 VAL cc_start: 0.9567 (p) cc_final: 0.9152 (m) REVERT: Q 109 GLU cc_start: 0.9342 (tp30) cc_final: 0.9092 (tp30) REVERT: Q 113 VAL cc_start: 0.9564 (p) cc_final: 0.8804 (p) REVERT: Q 161 LYS cc_start: 0.9396 (mttt) cc_final: 0.8864 (mtmm) REVERT: Q 162 MET cc_start: 0.9153 (tmm) cc_final: 0.8605 (tmm) REVERT: Q 175 GLU cc_start: 0.8043 (mp0) cc_final: 0.7833 (mp0) REVERT: Q 213 MET cc_start: 0.3486 (mmp) cc_final: 0.2505 (mmp) REVERT: Q 230 ARG cc_start: 0.2036 (ttt180) cc_final: 0.0096 (mmp-170) REVERT: Q 374 GLU cc_start: 0.4991 (mt-10) cc_final: 0.4039 (pm20) REVERT: Q 465 GLU cc_start: 0.9544 (tt0) cc_final: 0.9323 (pp20) REVERT: Q 470 ASP cc_start: 0.9111 (t70) cc_final: 0.8534 (t70) REVERT: Q 472 ASN cc_start: 0.8878 (m-40) cc_final: 0.8451 (m-40) REVERT: Q 473 GLU cc_start: 0.9237 (pt0) cc_final: 0.8710 (pt0) REVERT: z 37 LEU cc_start: 0.9446 (tp) cc_final: 0.9084 (mt) REVERT: z 40 LYS cc_start: 0.9329 (mmpt) cc_final: 0.9064 (mmmt) REVERT: z 83 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8081 (tm-30) REVERT: z 215 LEU cc_start: 0.8183 (tp) cc_final: 0.7717 (tp) REVERT: z 246 GLU cc_start: 0.5461 (tt0) cc_final: 0.5202 (mp0) REVERT: z 364 PHE cc_start: 0.8401 (m-10) cc_final: 0.8121 (m-10) REVERT: z 372 ASP cc_start: 0.7635 (m-30) cc_final: 0.7347 (m-30) REVERT: z 392 LYS cc_start: 0.9572 (ptmm) cc_final: 0.9248 (ptmm) REVERT: z 419 TYR cc_start: 0.9234 (m-10) cc_final: 0.8862 (m-10) REVERT: z 452 LEU cc_start: 0.9566 (mp) cc_final: 0.9165 (mp) REVERT: z 456 LYS cc_start: 0.9691 (mtmm) cc_final: 0.9356 (mttp) REVERT: z 525 SER cc_start: 0.9478 (m) cc_final: 0.9010 (p) REVERT: z 526 ASN cc_start: 0.9574 (m110) cc_final: 0.9280 (m-40) REVERT: z 527 LEU cc_start: 0.9439 (mt) cc_final: 0.9085 (mt) REVERT: z 529 LEU cc_start: 0.9425 (mm) cc_final: 0.9081 (mm) REVERT: Z 22 ASN cc_start: 0.8881 (m110) cc_final: 0.8533 (m110) REVERT: Z 106 HIS cc_start: 0.8809 (t-90) cc_final: 0.8289 (t-90) REVERT: Z 165 ASP cc_start: 0.9354 (p0) cc_final: 0.8961 (t0) REVERT: Z 176 ASP cc_start: 0.8815 (m-30) cc_final: 0.8541 (m-30) REVERT: Z 366 TYR cc_start: 0.7531 (m-80) cc_final: 0.6923 (m-80) REVERT: Z 431 MET cc_start: 0.7384 (tpt) cc_final: 0.7134 (tpp) REVERT: Z 460 LYS cc_start: 0.9570 (mmmm) cc_final: 0.9296 (tppp) REVERT: Z 482 ASP cc_start: 0.8864 (m-30) cc_final: 0.8542 (m-30) REVERT: Z 504 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8700 (mm-30) outliers start: 1 outliers final: 0 residues processed: 1371 average time/residue: 0.5578 time to fit residues: 1332.9152 Evaluate side-chains 1107 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1107 time to evaluate : 5.481 ------------------------------------------------------------------------------- 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: 8.9990 chunk 742 optimal weight: 1.9990 chunk 677 optimal weight: 2.9990 chunk 722 optimal weight: 0.3980 chunk 434 optimal weight: 1.9990 chunk 314 optimal weight: 5.9990 chunk 567 optimal weight: 0.2980 chunk 221 optimal weight: 20.0000 chunk 652 optimal weight: 7.9990 chunk 682 optimal weight: 20.0000 chunk 719 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 172 HIS b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 HIS d 436 GLN ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 138 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 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 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 HIS ** G 568 GLN ** 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 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 ASN ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.8347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 62618 Z= 0.170 Angle : 0.585 10.208 84459 Z= 0.298 Chirality : 0.044 0.238 10166 Planarity : 0.003 0.070 10848 Dihedral : 3.941 24.069 8568 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 0.01 % Allowed : 0.38 % Favored : 99.61 % 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: 0.68 (0.08), residues: 3966 sheet: -0.46 (0.20), residues: 668 loop : -0.71 (0.10), residues: 3431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP d 440 HIS 0.011 0.001 HIS d 303 PHE 0.032 0.001 PHE Q 137 TYR 0.020 0.001 TYR Q 496 ARG 0.018 0.001 ARG D 380 *********************** 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 1360 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1359 time to evaluate : 5.647 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: a 34 MET cc_start: 0.9401 (tpp) cc_final: 0.8818 (tmm) REVERT: a 38 ASN cc_start: 0.9498 (t0) cc_final: 0.9259 (t0) REVERT: a 41 LYS cc_start: 0.9271 (ptpp) cc_final: 0.8856 (pttt) REVERT: a 44 LEU cc_start: 0.9353 (tp) cc_final: 0.9015 (tp) REVERT: a 49 LEU cc_start: 0.9329 (mm) cc_final: 0.9028 (mm) REVERT: a 51 LYS cc_start: 0.7972 (mmtp) cc_final: 0.7553 (mmtp) REVERT: a 69 ILE cc_start: 0.9729 (mt) cc_final: 0.9528 (mt) REVERT: a 73 LEU cc_start: 0.9121 (mt) cc_final: 0.8304 (mt) REVERT: a 109 LEU cc_start: 0.9216 (mm) cc_final: 0.8989 (mm) REVERT: a 117 LYS cc_start: 0.9059 (mppt) cc_final: 0.8854 (mptt) REVERT: a 135 GLU cc_start: 0.8855 (tm-30) cc_final: 0.6907 (tm-30) REVERT: a 175 PHE cc_start: 0.8068 (t80) cc_final: 0.7614 (t80) REVERT: a 179 MET cc_start: 0.7694 (mtp) cc_final: 0.7264 (mmm) REVERT: a 258 MET cc_start: 0.2123 (mmm) cc_final: 0.1382 (mpp) REVERT: a 398 MET cc_start: 0.5813 (ttt) cc_final: 0.5175 (ttp) REVERT: a 399 GLU cc_start: 0.6784 (tt0) cc_final: 0.6089 (pp20) REVERT: a 450 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8808 (mm-30) REVERT: a 451 PHE cc_start: 0.9325 (t80) cc_final: 0.8942 (t80) REVERT: a 460 LYS cc_start: 0.9039 (tptt) cc_final: 0.8815 (tptt) REVERT: a 469 ASP cc_start: 0.8861 (t0) cc_final: 0.7750 (t0) REVERT: a 472 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8507 (mm-30) REVERT: a 526 LYS cc_start: 0.9316 (mmtt) cc_final: 0.9099 (mmmt) REVERT: a 532 LEU cc_start: 0.9504 (mm) cc_final: 0.8998 (tt) REVERT: A 30 VAL cc_start: 0.9377 (p) cc_final: 0.9155 (m) REVERT: A 52 MET cc_start: 0.7553 (tpt) cc_final: 0.7113 (tpt) REVERT: A 108 LEU cc_start: 0.9414 (mt) cc_final: 0.9149 (mt) REVERT: A 181 VAL cc_start: 0.7207 (t) cc_final: 0.7006 (t) REVERT: A 320 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7139 (ptp90) REVERT: A 393 TYR cc_start: 0.7722 (m-80) cc_final: 0.7472 (m-80) REVERT: A 398 MET cc_start: 0.7032 (ttt) cc_final: 0.6349 (ptm) REVERT: A 444 GLU cc_start: 0.9463 (pm20) cc_final: 0.9192 (pm20) REVERT: A 533 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8732 (mm-30) REVERT: b 55 MET cc_start: 0.7296 (mtt) cc_final: 0.6949 (mtt) REVERT: b 59 ASP cc_start: 0.8977 (t0) cc_final: 0.8702 (t70) REVERT: b 62 THR cc_start: 0.9297 (t) cc_final: 0.9041 (t) REVERT: b 69 LEU cc_start: 0.8303 (mt) cc_final: 0.6969 (tp) REVERT: b 78 VAL cc_start: 0.9391 (t) cc_final: 0.9126 (t) REVERT: b 116 HIS cc_start: 0.6662 (t70) cc_final: 0.6292 (t-90) REVERT: b 148 MET cc_start: 0.8585 (ppp) cc_final: 0.8173 (ppp) REVERT: b 379 GLU cc_start: 0.8985 (pp20) cc_final: 0.8739 (pp20) REVERT: b 439 GLN cc_start: 0.9385 (mm110) cc_final: 0.9038 (mp10) REVERT: b 443 ILE cc_start: 0.9135 (mm) cc_final: 0.8718 (tp) REVERT: b 472 LEU cc_start: 0.9144 (mt) cc_final: 0.8869 (mt) REVERT: b 489 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9174 (mm-30) REVERT: B 155 HIS cc_start: 0.9258 (m90) cc_final: 0.8989 (m90) REVERT: B 175 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8173 (pm20) REVERT: B 269 MET cc_start: 0.0207 (mtm) cc_final: -0.0107 (mtm) REVERT: B 315 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 354 LEU cc_start: 0.5477 (mt) cc_final: 0.3988 (tp) REVERT: B 386 ASP cc_start: 0.8406 (m-30) cc_final: 0.7332 (t70) REVERT: B 409 MET cc_start: 0.9455 (tpp) cc_final: 0.9186 (ttm) REVERT: B 452 SER cc_start: 0.9047 (p) cc_final: 0.8741 (t) REVERT: B 472 LEU cc_start: 0.8564 (mt) cc_final: 0.8133 (mt) REVERT: d 19 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8591 (pm20) REVERT: d 91 ASP cc_start: 0.6590 (t0) cc_final: 0.6229 (m-30) REVERT: d 108 GLU cc_start: 0.9280 (tt0) cc_final: 0.9027 (tt0) REVERT: d 209 MET cc_start: 0.3862 (mtm) cc_final: 0.3534 (ttp) REVERT: d 311 MET cc_start: 0.3961 (mmm) cc_final: 0.3404 (mmm) REVERT: d 411 ILE cc_start: 0.8640 (mp) cc_final: 0.8269 (mm) REVERT: d 433 GLU cc_start: 0.8173 (pm20) cc_final: 0.7536 (tp30) REVERT: d 464 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9025 (ptmm) REVERT: d 502 LEU cc_start: 0.8963 (mt) cc_final: 0.8750 (mt) REVERT: D 29 ARG cc_start: 0.8848 (mtp85) cc_final: 0.8350 (mtp85) REVERT: D 33 ASP cc_start: 0.9197 (m-30) cc_final: 0.8933 (m-30) REVERT: D 44 MET cc_start: 0.8332 (mpp) cc_final: 0.8016 (mpp) REVERT: D 47 MET cc_start: 0.7137 (tpt) cc_final: 0.6753 (mmm) REVERT: D 103 LEU cc_start: 0.9474 (mm) cc_final: 0.9265 (mm) REVERT: D 104 LEU cc_start: 0.9268 (mt) cc_final: 0.9038 (mt) REVERT: D 108 GLU cc_start: 0.8017 (tt0) cc_final: 0.7690 (tt0) REVERT: D 133 ASP cc_start: 0.9478 (m-30) cc_final: 0.9205 (t0) REVERT: D 209 MET cc_start: 0.5310 (mmt) cc_final: 0.4900 (mmt) REVERT: D 379 ILE cc_start: 0.9005 (mp) cc_final: 0.8789 (mp) REVERT: D 509 THR cc_start: 0.9350 (t) cc_final: 0.9018 (t) REVERT: D 513 GLU cc_start: 0.9585 (mm-30) cc_final: 0.9102 (mp0) REVERT: e 50 HIS cc_start: 0.8564 (m-70) cc_final: 0.8351 (m-70) REVERT: e 107 LEU cc_start: 0.9455 (tp) cc_final: 0.9254 (tp) REVERT: e 113 ASP cc_start: 0.8415 (m-30) cc_final: 0.7690 (p0) REVERT: e 136 LEU cc_start: 0.8781 (mt) cc_final: 0.8493 (mt) REVERT: e 146 ILE cc_start: 0.9736 (mm) cc_final: 0.8768 (mm) REVERT: e 150 PHE cc_start: 0.9268 (m-10) cc_final: 0.8694 (m-80) REVERT: e 202 GLU cc_start: 0.8365 (pm20) cc_final: 0.7897 (tp30) REVERT: e 203 MET cc_start: 0.5028 (tmm) cc_final: 0.4093 (ptt) REVERT: e 210 ASN cc_start: 0.8804 (m-40) cc_final: 0.8444 (t0) REVERT: e 400 GLU cc_start: 0.5911 (tt0) cc_final: 0.5186 (mp0) REVERT: e 472 PHE cc_start: 0.9404 (t80) cc_final: 0.9115 (t80) REVERT: e 495 LEU cc_start: 0.9229 (tp) cc_final: 0.8555 (mt) REVERT: E 163 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9150 (mp0) REVERT: E 203 MET cc_start: 0.6490 (ptp) cc_final: 0.5807 (mpp) REVERT: E 226 MET cc_start: 0.6545 (pmm) cc_final: 0.6068 (pmm) REVERT: E 379 ARG cc_start: 0.7465 (mmt180) cc_final: 0.6434 (ptp-170) REVERT: E 392 MET cc_start: 0.7778 (mpp) cc_final: 0.7578 (mpp) REVERT: E 414 MET cc_start: 0.8704 (tpt) cc_final: 0.8394 (tmm) REVERT: E 481 MET cc_start: 0.9207 (mmm) cc_final: 0.8975 (tpt) REVERT: E 526 PHE cc_start: 0.6844 (m-10) cc_final: 0.6577 (m-10) REVERT: E 539 LEU cc_start: 0.9408 (tp) cc_final: 0.9140 (tp) REVERT: E 542 THR cc_start: 0.9302 (m) cc_final: 0.9089 (t) REVERT: E 553 ASN cc_start: 0.9359 (t0) cc_final: 0.8844 (p0) REVERT: g 24 ASN cc_start: 0.9520 (m-40) cc_final: 0.9195 (t0) REVERT: g 38 CYS cc_start: 0.9320 (m) cc_final: 0.8908 (m) REVERT: g 83 ARG cc_start: 0.8956 (ptm160) cc_final: 0.8744 (mtm-85) REVERT: g 102 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8574 (mm-30) REVERT: g 117 HIS cc_start: 0.8540 (t-90) cc_final: 0.8326 (t-90) REVERT: g 126 LYS cc_start: 0.9542 (mmpt) cc_final: 0.9338 (mmmt) REVERT: g 131 ASP cc_start: 0.9287 (p0) cc_final: 0.8824 (t0) REVERT: g 134 GLU cc_start: 0.9305 (pt0) cc_final: 0.8859 (pt0) REVERT: g 148 ASP cc_start: 0.8900 (m-30) cc_final: 0.8451 (m-30) REVERT: g 151 MET cc_start: 0.8190 (mpp) cc_final: 0.7320 (mpp) REVERT: g 163 TYR cc_start: 0.7044 (t80) cc_final: 0.6740 (t80) REVERT: g 467 MET cc_start: 0.9176 (mmp) cc_final: 0.8799 (tpt) REVERT: g 481 MET cc_start: 0.8716 (tpt) cc_final: 0.8248 (tpt) REVERT: g 505 VAL cc_start: 0.9657 (t) cc_final: 0.9443 (t) REVERT: g 509 MET cc_start: 0.9476 (mmm) cc_final: 0.8675 (tpp) REVERT: g 540 PHE cc_start: 0.7883 (p90) cc_final: 0.6859 (p90) REVERT: g 575 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8744 (pt0) REVERT: g 585 ASP cc_start: 0.8607 (m-30) cc_final: 0.7909 (m-30) REVERT: G 44 MET cc_start: 0.8406 (tpp) cc_final: 0.8057 (tpt) REVERT: G 45 LEU cc_start: 0.9217 (tp) cc_final: 0.8833 (tp) REVERT: G 49 LEU cc_start: 0.9139 (mt) cc_final: 0.8862 (tt) REVERT: G 52 MET cc_start: 0.8204 (tmm) cc_final: 0.7979 (tmm) REVERT: G 117 HIS cc_start: 0.9021 (t-90) cc_final: 0.8712 (t-90) REVERT: G 234 MET cc_start: 0.3738 (ttm) cc_final: 0.0257 (ptm) REVERT: G 507 ASP cc_start: 0.9217 (m-30) cc_final: 0.8852 (m-30) REVERT: G 574 ILE cc_start: 0.8470 (mp) cc_final: 0.8200 (mp) REVERT: G 578 CYS cc_start: 0.9522 (p) cc_final: 0.9170 (p) REVERT: G 584 ASP cc_start: 0.8797 (p0) cc_final: 0.8529 (p0) REVERT: G 585 ASP cc_start: 0.8329 (p0) cc_final: 0.8043 (p0) REVERT: h 166 MET cc_start: 0.8373 (mmp) cc_final: 0.6817 (mtp) REVERT: h 172 HIS cc_start: 0.5932 (t70) cc_final: 0.5578 (t70) REVERT: h 355 MET cc_start: 0.6222 (ptt) cc_final: 0.5744 (pmm) REVERT: h 362 TYR cc_start: 0.7513 (m-10) cc_final: 0.7300 (m-80) REVERT: h 418 MET cc_start: 0.8931 (ptp) cc_final: 0.8425 (ptp) REVERT: h 447 GLU cc_start: 0.9335 (pp20) cc_final: 0.8839 (tm-30) REVERT: h 451 ARG cc_start: 0.9375 (tpp80) cc_final: 0.8881 (tpp80) REVERT: h 465 LEU cc_start: 0.9535 (pp) cc_final: 0.9248 (pp) REVERT: H 44 LEU cc_start: 0.9475 (tp) cc_final: 0.9202 (tp) REVERT: H 85 ASP cc_start: 0.9529 (m-30) cc_final: 0.9145 (t70) REVERT: H 126 MET cc_start: 0.9203 (mmm) cc_final: 0.7739 (mmt) REVERT: H 402 ARG cc_start: 0.9507 (mpt180) cc_final: 0.9022 (mmt90) REVERT: H 418 MET cc_start: 0.8991 (ttt) cc_final: 0.8491 (ptm) REVERT: H 434 LYS cc_start: 0.9201 (mtpt) cc_final: 0.8885 (mttt) REVERT: H 437 MET cc_start: 0.9401 (mtm) cc_final: 0.9123 (ttp) REVERT: H 440 ASN cc_start: 0.9141 (m-40) cc_final: 0.8825 (m110) REVERT: H 449 ILE cc_start: 0.9488 (mp) cc_final: 0.9287 (mp) REVERT: H 494 LYS cc_start: 0.9253 (mmmt) cc_final: 0.8841 (mptt) REVERT: H 515 ASN cc_start: 0.9156 (t0) cc_final: 0.8881 (t0) REVERT: q 38 LEU cc_start: 0.9659 (tp) cc_final: 0.9375 (tp) REVERT: q 39 HIS cc_start: 0.9054 (t70) cc_final: 0.8581 (t70) REVERT: q 49 CYS cc_start: 0.8368 (m) cc_final: 0.7841 (m) REVERT: q 70 THR cc_start: 0.8717 (p) cc_final: 0.8413 (p) REVERT: q 73 ARG cc_start: 0.8852 (mtt180) cc_final: 0.8445 (ptp-170) REVERT: q 87 MET cc_start: 0.9309 (mtm) cc_final: 0.8992 (mmt) REVERT: q 89 THR cc_start: 0.9180 (m) cc_final: 0.8892 (m) REVERT: q 91 GLN cc_start: 0.9352 (tt0) cc_final: 0.8983 (tp40) REVERT: q 114 SER cc_start: 0.9273 (p) cc_final: 0.8947 (p) REVERT: q 115 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8526 (tm-30) REVERT: q 129 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8850 (pp30) REVERT: q 144 GLU cc_start: 0.8741 (pp20) cc_final: 0.8508 (mp0) REVERT: q 226 MET cc_start: 0.5150 (mmp) cc_final: 0.4914 (mmp) REVERT: q 361 MET cc_start: 0.8066 (mtt) cc_final: 0.7776 (ttt) REVERT: q 429 GLU cc_start: 0.9664 (pt0) cc_final: 0.9393 (pp20) REVERT: q 430 LEU cc_start: 0.9606 (mt) cc_final: 0.9218 (mt) REVERT: q 456 PHE cc_start: 0.9382 (m-10) cc_final: 0.8705 (m-80) REVERT: q 473 GLU cc_start: 0.9337 (tt0) cc_final: 0.9034 (tt0) REVERT: q 518 TYR cc_start: 0.7754 (p90) cc_final: 0.6880 (p90) REVERT: q 533 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8939 (tm-30) REVERT: q 543 GLN cc_start: 0.9029 (pt0) cc_final: 0.8693 (pp30) REVERT: Q 38 LEU cc_start: 0.9565 (tp) cc_final: 0.9330 (tp) REVERT: Q 42 CYS cc_start: 0.9518 (m) cc_final: 0.8977 (p) REVERT: Q 49 CYS cc_start: 0.8723 (m) cc_final: 0.8233 (m) REVERT: Q 92 GLN cc_start: 0.9287 (tp-100) cc_final: 0.9000 (tp40) REVERT: Q 103 VAL cc_start: 0.9532 (p) cc_final: 0.9122 (m) REVERT: Q 109 GLU cc_start: 0.9366 (tp30) cc_final: 0.9124 (tp30) REVERT: Q 161 LYS cc_start: 0.9379 (mttt) cc_final: 0.8825 (mtmm) REVERT: Q 162 MET cc_start: 0.9159 (tmm) cc_final: 0.8722 (tmm) REVERT: Q 175 GLU cc_start: 0.8221 (mp0) cc_final: 0.8020 (mp0) REVERT: Q 213 MET cc_start: 0.3845 (mmp) cc_final: 0.2595 (tpp) REVERT: Q 230 ARG cc_start: 0.2083 (ttt180) cc_final: 0.0130 (mmp-170) REVERT: Q 374 GLU cc_start: 0.5146 (mt-10) cc_final: 0.4159 (pm20) REVERT: Q 470 ASP cc_start: 0.9091 (t70) cc_final: 0.8499 (t70) REVERT: Q 472 ASN cc_start: 0.8772 (m-40) cc_final: 0.8359 (m-40) REVERT: Q 473 GLU cc_start: 0.9219 (pt0) cc_final: 0.8626 (pt0) REVERT: Q 545 ILE cc_start: 0.8759 (mm) cc_final: 0.8498 (mm) REVERT: z 37 LEU cc_start: 0.9484 (tp) cc_final: 0.9125 (mt) REVERT: z 40 LYS cc_start: 0.9345 (mmpt) cc_final: 0.9090 (mmmt) REVERT: z 66 MET cc_start: 0.5614 (tmm) cc_final: 0.4974 (tmm) REVERT: z 83 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8094 (tm-30) REVERT: z 100 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8662 (mm-30) REVERT: z 215 LEU cc_start: 0.8206 (tp) cc_final: 0.7811 (tp) REVERT: z 246 GLU cc_start: 0.5485 (tt0) cc_final: 0.5228 (mp0) REVERT: z 364 PHE cc_start: 0.8376 (m-10) cc_final: 0.8066 (m-10) REVERT: z 372 ASP cc_start: 0.7621 (m-30) cc_final: 0.7326 (m-30) REVERT: z 392 LYS cc_start: 0.9562 (ptmm) cc_final: 0.9299 (ptmm) REVERT: z 419 TYR cc_start: 0.9204 (m-10) cc_final: 0.8861 (m-10) REVERT: z 452 LEU cc_start: 0.9567 (mp) cc_final: 0.9148 (mp) REVERT: z 456 LYS cc_start: 0.9678 (mtmm) cc_final: 0.9347 (mttp) REVERT: z 525 SER cc_start: 0.9493 (m) cc_final: 0.8963 (p) REVERT: z 526 ASN cc_start: 0.9579 (m110) cc_final: 0.9282 (m-40) REVERT: z 527 LEU cc_start: 0.9419 (mt) cc_final: 0.9063 (mt) REVERT: z 529 LEU cc_start: 0.9399 (mm) cc_final: 0.9020 (mm) REVERT: Z 22 ASN cc_start: 0.8881 (m110) cc_final: 0.8470 (m110) REVERT: Z 114 HIS cc_start: 0.8665 (t-90) cc_final: 0.8458 (t-90) REVERT: Z 176 ASP cc_start: 0.8926 (m-30) cc_final: 0.8663 (m-30) REVERT: Z 366 TYR cc_start: 0.7585 (m-80) cc_final: 0.6953 (m-80) REVERT: Z 431 MET cc_start: 0.7404 (tpt) cc_final: 0.6876 (tmm) REVERT: Z 460 LYS cc_start: 0.9585 (mmmm) cc_final: 0.9305 (tppp) REVERT: Z 482 ASP cc_start: 0.8847 (m-30) cc_final: 0.8523 (m-30) REVERT: Z 504 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8701 (mm-30) outliers start: 1 outliers final: 0 residues processed: 1360 average time/residue: 0.5601 time to fit residues: 1327.4098 Evaluate side-chains 1097 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1097 time to evaluate : 5.625 ------------------------------------------------------------------------------- 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: 20.0000 chunk 763 optimal weight: 7.9990 chunk 466 optimal weight: 0.2980 chunk 362 optimal weight: 20.0000 chunk 530 optimal weight: 3.9990 chunk 800 optimal weight: 8.9990 chunk 737 optimal weight: 0.7980 chunk 637 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 492 optimal weight: 8.9990 chunk 391 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 375 GLN ** b 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 436 GLN ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 251 HIS ** e 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 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 188 GLN ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 HIS ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 491 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** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 543 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.8511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 62618 Z= 0.164 Angle : 0.590 10.368 84459 Z= 0.299 Chirality : 0.044 0.243 10166 Planarity : 0.003 0.061 10848 Dihedral : 3.909 22.120 8568 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 0.01 % Allowed : 0.19 % Favored : 99.80 % 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: -0.04 (0.09), residues: 8065 helix: 0.70 (0.08), residues: 3982 sheet: -0.43 (0.20), residues: 664 loop : -0.73 (0.10), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP d 440 HIS 0.011 0.001 HIS d 473 PHE 0.031 0.001 PHE Q 137 TYR 0.014 0.001 TYR z 355 ARG 0.015 0.000 ARG B 495 ********************** 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 1363 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1362 time to evaluate : 5.929 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: a 34 MET cc_start: 0.9438 (tpp) cc_final: 0.8814 (tmm) REVERT: a 38 ASN cc_start: 0.9525 (t0) cc_final: 0.9280 (t0) REVERT: a 41 LYS cc_start: 0.9306 (ptpp) cc_final: 0.8787 (pttt) REVERT: a 44 LEU cc_start: 0.9355 (tp) cc_final: 0.9015 (tp) REVERT: a 51 LYS cc_start: 0.7998 (mmtp) cc_final: 0.7622 (mmtp) REVERT: a 69 ILE cc_start: 0.9730 (mt) cc_final: 0.9526 (mt) REVERT: a 73 LEU cc_start: 0.9153 (mt) cc_final: 0.8338 (mt) REVERT: a 135 GLU cc_start: 0.8827 (tm-30) cc_final: 0.6746 (tm-30) REVERT: a 175 PHE cc_start: 0.8075 (t80) cc_final: 0.7616 (t80) REVERT: a 179 MET cc_start: 0.7741 (mtp) cc_final: 0.7351 (mmm) REVERT: a 258 MET cc_start: 0.1747 (mmm) cc_final: 0.1232 (mpp) REVERT: a 398 MET cc_start: 0.5874 (ttt) cc_final: 0.5212 (ttp) REVERT: a 399 GLU cc_start: 0.6776 (tt0) cc_final: 0.6074 (pp20) REVERT: a 444 GLU cc_start: 0.8642 (pm20) cc_final: 0.8363 (pm20) REVERT: a 450 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8797 (mm-30) REVERT: a 451 PHE cc_start: 0.9305 (t80) cc_final: 0.8994 (t80) REVERT: a 460 LYS cc_start: 0.9050 (tptt) cc_final: 0.8818 (tptt) REVERT: a 469 ASP cc_start: 0.8889 (t0) cc_final: 0.7777 (t0) REVERT: a 472 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8487 (mm-30) REVERT: a 526 LYS cc_start: 0.9333 (mmtt) cc_final: 0.9018 (mmmt) REVERT: a 538 ILE cc_start: 0.9029 (pt) cc_final: 0.8814 (mt) REVERT: A 30 VAL cc_start: 0.9412 (p) cc_final: 0.9175 (m) REVERT: A 52 MET cc_start: 0.7490 (tpt) cc_final: 0.7180 (tpt) REVERT: A 108 LEU cc_start: 0.9432 (mt) cc_final: 0.9162 (mt) REVERT: A 143 VAL cc_start: 0.8774 (p) cc_final: 0.8561 (m) REVERT: A 179 MET cc_start: 0.6140 (ptt) cc_final: 0.5411 (ptp) REVERT: A 320 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7122 (ptp90) REVERT: A 393 TYR cc_start: 0.7699 (m-80) cc_final: 0.7483 (m-80) REVERT: A 398 MET cc_start: 0.7030 (ttt) cc_final: 0.6290 (ptm) REVERT: A 444 GLU cc_start: 0.9417 (pm20) cc_final: 0.9176 (pm20) REVERT: A 533 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8631 (mm-30) REVERT: b 55 MET cc_start: 0.7310 (mtt) cc_final: 0.6935 (mtt) REVERT: b 59 ASP cc_start: 0.8975 (t0) cc_final: 0.8692 (t0) REVERT: b 62 THR cc_start: 0.9296 (t) cc_final: 0.9013 (t) REVERT: b 69 LEU cc_start: 0.8402 (mt) cc_final: 0.7095 (tp) REVERT: b 78 VAL cc_start: 0.9406 (t) cc_final: 0.9104 (t) REVERT: b 82 LYS cc_start: 0.9536 (mmtp) cc_final: 0.9328 (mmmm) REVERT: b 115 ILE cc_start: 0.8397 (mm) cc_final: 0.8073 (mm) REVERT: b 116 HIS cc_start: 0.6858 (t70) cc_final: 0.6335 (t-90) REVERT: b 148 MET cc_start: 0.8630 (ppp) cc_final: 0.8210 (ppp) REVERT: b 379 GLU cc_start: 0.8962 (pp20) cc_final: 0.8730 (pp20) REVERT: b 425 LYS cc_start: 0.8959 (tptm) cc_final: 0.8318 (tptm) REVERT: b 439 GLN cc_start: 0.9383 (mm110) cc_final: 0.9102 (mp10) REVERT: b 472 LEU cc_start: 0.9139 (mt) cc_final: 0.8900 (mt) REVERT: b 489 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9166 (mm-30) REVERT: B 107 GLU cc_start: 0.9042 (pp20) cc_final: 0.8836 (pp20) REVERT: B 155 HIS cc_start: 0.9258 (m90) cc_final: 0.8988 (m90) REVERT: B 269 MET cc_start: 0.0173 (mtm) cc_final: -0.0124 (mtm) REVERT: B 315 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7735 (mm-30) REVERT: B 354 LEU cc_start: 0.5498 (mt) cc_final: 0.4008 (tp) REVERT: B 386 ASP cc_start: 0.8400 (m-30) cc_final: 0.7345 (t70) REVERT: B 409 MET cc_start: 0.9487 (tpp) cc_final: 0.9183 (ttm) REVERT: B 452 SER cc_start: 0.9056 (p) cc_final: 0.8772 (t) REVERT: B 472 LEU cc_start: 0.8560 (mt) cc_final: 0.8153 (mt) REVERT: d 19 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8633 (pm20) REVERT: d 91 ASP cc_start: 0.6696 (t0) cc_final: 0.6327 (m-30) REVERT: d 108 GLU cc_start: 0.9302 (tt0) cc_final: 0.9038 (tt0) REVERT: d 116 HIS cc_start: 0.7952 (t-90) cc_final: 0.7671 (t-90) REVERT: d 209 MET cc_start: 0.3840 (mtm) cc_final: 0.3525 (ttp) REVERT: d 311 MET cc_start: 0.3926 (mmm) cc_final: 0.3392 (mmm) REVERT: d 411 ILE cc_start: 0.8625 (mp) cc_final: 0.8228 (mm) REVERT: d 433 GLU cc_start: 0.8276 (pm20) cc_final: 0.7590 (tp30) REVERT: d 464 LYS cc_start: 0.9627 (mmmt) cc_final: 0.8910 (ptmm) REVERT: d 502 LEU cc_start: 0.8969 (mt) cc_final: 0.8743 (mt) REVERT: D 29 ARG cc_start: 0.8855 (mtp85) cc_final: 0.8347 (mtp85) REVERT: D 33 ASP cc_start: 0.9186 (m-30) cc_final: 0.8905 (m-30) REVERT: D 44 MET cc_start: 0.8346 (mpp) cc_final: 0.8043 (mpp) REVERT: D 47 MET cc_start: 0.6822 (tpt) cc_final: 0.6526 (mmm) REVERT: D 104 LEU cc_start: 0.9264 (mt) cc_final: 0.9018 (mt) REVERT: D 108 GLU cc_start: 0.8032 (tt0) cc_final: 0.7716 (tt0) REVERT: D 133 ASP cc_start: 0.9483 (m-30) cc_final: 0.9212 (t0) REVERT: D 209 MET cc_start: 0.5383 (mmt) cc_final: 0.4974 (mmt) REVERT: D 379 ILE cc_start: 0.9057 (mp) cc_final: 0.8847 (mp) REVERT: D 509 THR cc_start: 0.9345 (t) cc_final: 0.8993 (t) REVERT: D 513 GLU cc_start: 0.9585 (mm-30) cc_final: 0.9111 (mp0) REVERT: e 50 HIS cc_start: 0.8529 (m-70) cc_final: 0.8279 (m-70) REVERT: e 113 ASP cc_start: 0.8431 (m-30) cc_final: 0.7747 (p0) REVERT: e 136 LEU cc_start: 0.8842 (mt) cc_final: 0.8498 (mt) REVERT: e 146 ILE cc_start: 0.9731 (mm) cc_final: 0.8761 (mm) REVERT: e 150 PHE cc_start: 0.9283 (m-10) cc_final: 0.8711 (m-80) REVERT: e 202 GLU cc_start: 0.8350 (pm20) cc_final: 0.7809 (tp30) REVERT: e 203 MET cc_start: 0.5040 (tmm) cc_final: 0.4041 (ptt) REVERT: e 210 ASN cc_start: 0.8788 (m-40) cc_final: 0.8444 (t0) REVERT: e 400 GLU cc_start: 0.5988 (tt0) cc_final: 0.5226 (mp0) REVERT: e 495 LEU cc_start: 0.9242 (tp) cc_final: 0.8638 (mt) REVERT: E 142 HIS cc_start: 0.9018 (t70) cc_final: 0.8753 (t-90) REVERT: E 163 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9096 (mp0) REVERT: E 203 MET cc_start: 0.6479 (ptp) cc_final: 0.5736 (mpp) REVERT: E 226 MET cc_start: 0.6549 (pmm) cc_final: 0.6087 (pmm) REVERT: E 379 ARG cc_start: 0.7529 (mmt180) cc_final: 0.6475 (ptp-170) REVERT: E 392 MET cc_start: 0.7706 (mpp) cc_final: 0.7474 (mpp) REVERT: E 414 MET cc_start: 0.8715 (tpt) cc_final: 0.8396 (tmm) REVERT: E 481 MET cc_start: 0.9202 (mmm) cc_final: 0.8914 (tpt) REVERT: E 526 PHE cc_start: 0.6871 (m-10) cc_final: 0.6617 (m-10) REVERT: E 539 LEU cc_start: 0.9403 (tp) cc_final: 0.9131 (tp) REVERT: E 542 THR cc_start: 0.9282 (m) cc_final: 0.9072 (t) REVERT: E 553 ASN cc_start: 0.9400 (t0) cc_final: 0.9118 (t0) REVERT: g 35 ILE cc_start: 0.9384 (pt) cc_final: 0.9115 (pt) REVERT: g 38 CYS cc_start: 0.9310 (m) cc_final: 0.8883 (m) REVERT: g 102 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8548 (mm-30) REVERT: g 110 TYR cc_start: 0.7721 (m-10) cc_final: 0.7441 (m-10) REVERT: g 131 ASP cc_start: 0.9266 (p0) cc_final: 0.8337 (t0) REVERT: g 134 GLU cc_start: 0.9286 (pt0) cc_final: 0.8873 (pp20) REVERT: g 148 ASP cc_start: 0.8878 (m-30) cc_final: 0.8407 (m-30) REVERT: g 151 MET cc_start: 0.8267 (mpp) cc_final: 0.7357 (mpp) REVERT: g 163 TYR cc_start: 0.7059 (t80) cc_final: 0.6760 (t80) REVERT: g 440 MET cc_start: 0.4955 (pmm) cc_final: 0.3886 (pmm) REVERT: g 467 MET cc_start: 0.9189 (mmp) cc_final: 0.8866 (mtt) REVERT: g 481 MET cc_start: 0.8704 (tpt) cc_final: 0.8256 (tpt) REVERT: g 500 TRP cc_start: 0.9086 (m100) cc_final: 0.8572 (m100) REVERT: g 509 MET cc_start: 0.9479 (mmm) cc_final: 0.8685 (tpp) REVERT: g 540 PHE cc_start: 0.7998 (p90) cc_final: 0.6970 (p90) REVERT: g 575 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8738 (pt0) REVERT: g 585 ASP cc_start: 0.8690 (m-30) cc_final: 0.7933 (m-30) REVERT: G 44 MET cc_start: 0.8354 (tpp) cc_final: 0.8021 (tpt) REVERT: G 45 LEU cc_start: 0.9187 (tp) cc_final: 0.8846 (tp) REVERT: G 49 LEU cc_start: 0.9181 (mt) cc_final: 0.8898 (tt) REVERT: G 52 MET cc_start: 0.8237 (tmm) cc_final: 0.8021 (tmm) REVERT: G 104 LEU cc_start: 0.9725 (mt) cc_final: 0.9523 (mt) REVERT: G 117 HIS cc_start: 0.9097 (t-90) cc_final: 0.8718 (t-90) REVERT: G 151 MET cc_start: 0.8950 (mpp) cc_final: 0.8639 (mpp) REVERT: G 234 MET cc_start: 0.3703 (ttm) cc_final: 0.0248 (ptm) REVERT: G 458 ASP cc_start: 0.9415 (m-30) cc_final: 0.9200 (t0) REVERT: G 512 ILE cc_start: 0.9198 (mm) cc_final: 0.8977 (mm) REVERT: G 574 ILE cc_start: 0.8512 (mp) cc_final: 0.8234 (mp) REVERT: G 578 CYS cc_start: 0.9528 (p) cc_final: 0.9235 (p) REVERT: G 584 ASP cc_start: 0.8758 (p0) cc_final: 0.8510 (p0) REVERT: G 585 ASP cc_start: 0.8331 (p0) cc_final: 0.8017 (p0) REVERT: h 166 MET cc_start: 0.8365 (mmp) cc_final: 0.8135 (mmm) REVERT: h 172 HIS cc_start: 0.5898 (t70) cc_final: 0.5631 (t70) REVERT: h 355 MET cc_start: 0.6164 (ptt) cc_final: 0.5692 (pmm) REVERT: h 362 TYR cc_start: 0.7539 (m-10) cc_final: 0.7305 (m-80) REVERT: h 418 MET cc_start: 0.8851 (ptp) cc_final: 0.8340 (ptp) REVERT: h 447 GLU cc_start: 0.9391 (pp20) cc_final: 0.8842 (tm-30) REVERT: h 451 ARG cc_start: 0.9406 (tpp80) cc_final: 0.8947 (tpp80) REVERT: h 465 LEU cc_start: 0.9544 (pp) cc_final: 0.9185 (pp) REVERT: H 44 LEU cc_start: 0.9478 (tp) cc_final: 0.9212 (tp) REVERT: H 103 ILE cc_start: 0.9468 (mm) cc_final: 0.9221 (mm) REVERT: H 110 LYS cc_start: 0.8488 (ptpp) cc_final: 0.8122 (ptpp) REVERT: H 166 MET cc_start: 0.4804 (mmp) cc_final: 0.4386 (mmp) REVERT: H 402 ARG cc_start: 0.9510 (mpt180) cc_final: 0.8994 (mmt-90) REVERT: H 418 MET cc_start: 0.8859 (ttt) cc_final: 0.8561 (ptm) REVERT: H 434 LYS cc_start: 0.9173 (mtpt) cc_final: 0.8871 (mttt) REVERT: H 437 MET cc_start: 0.9376 (mtm) cc_final: 0.9123 (ttp) REVERT: H 440 ASN cc_start: 0.9060 (m-40) cc_final: 0.8686 (m110) REVERT: H 492 PHE cc_start: 0.8049 (m-10) cc_final: 0.6959 (m-80) REVERT: H 494 LYS cc_start: 0.9245 (mmmt) cc_final: 0.8819 (mptt) REVERT: H 521 ASP cc_start: 0.8274 (t70) cc_final: 0.8043 (t0) REVERT: q 38 LEU cc_start: 0.9656 (tp) cc_final: 0.9400 (tp) REVERT: q 39 HIS cc_start: 0.9108 (t70) cc_final: 0.8838 (t70) REVERT: q 49 CYS cc_start: 0.8246 (m) cc_final: 0.7807 (m) REVERT: q 70 THR cc_start: 0.8694 (p) cc_final: 0.8444 (p) REVERT: q 73 ARG cc_start: 0.8876 (mtt180) cc_final: 0.8455 (ptp-170) REVERT: q 87 MET cc_start: 0.9306 (mtm) cc_final: 0.8803 (mmt) REVERT: q 89 THR cc_start: 0.9188 (m) cc_final: 0.8890 (m) REVERT: q 91 GLN cc_start: 0.9389 (tt0) cc_final: 0.8842 (tm-30) REVERT: q 96 MET cc_start: 0.8995 (ptp) cc_final: 0.8563 (ptm) REVERT: q 129 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8918 (tm-30) REVERT: q 145 MET cc_start: 0.7434 (ptp) cc_final: 0.6864 (ptp) REVERT: q 226 MET cc_start: 0.5224 (mmp) cc_final: 0.5001 (mmp) REVERT: q 361 MET cc_start: 0.8054 (mtt) cc_final: 0.7776 (ttt) REVERT: q 429 GLU cc_start: 0.9670 (pt0) cc_final: 0.9385 (pp20) REVERT: q 430 LEU cc_start: 0.9615 (mt) cc_final: 0.9204 (mt) REVERT: q 473 GLU cc_start: 0.9370 (tt0) cc_final: 0.9076 (tt0) REVERT: q 518 TYR cc_start: 0.7443 (p90) cc_final: 0.6922 (p90) REVERT: q 519 ASP cc_start: 0.8214 (t0) cc_final: 0.7978 (t0) REVERT: q 530 VAL cc_start: 0.9784 (m) cc_final: 0.9572 (m) REVERT: q 533 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8966 (tm-30) REVERT: q 543 GLN cc_start: 0.9046 (pt0) cc_final: 0.8708 (pp30) REVERT: Q 38 LEU cc_start: 0.9554 (tp) cc_final: 0.9328 (tp) REVERT: Q 42 CYS cc_start: 0.9475 (m) cc_final: 0.8902 (p) REVERT: Q 43 LEU cc_start: 0.9258 (mt) cc_final: 0.8990 (mt) REVERT: Q 49 CYS cc_start: 0.8672 (m) cc_final: 0.8229 (m) REVERT: Q 79 HIS cc_start: 0.7929 (t-90) cc_final: 0.7726 (t-90) REVERT: Q 87 MET cc_start: 0.9201 (mpp) cc_final: 0.8563 (mpp) REVERT: Q 109 GLU cc_start: 0.9362 (tp30) cc_final: 0.9141 (tp30) REVERT: Q 155 ASP cc_start: 0.8732 (t70) cc_final: 0.8481 (t70) REVERT: Q 161 LYS cc_start: 0.9446 (mttt) cc_final: 0.9101 (mtmm) REVERT: Q 162 MET cc_start: 0.8906 (tmm) cc_final: 0.8604 (tmm) REVERT: Q 213 MET cc_start: 0.2998 (mmp) cc_final: 0.2111 (tpp) REVERT: Q 230 ARG cc_start: 0.1896 (ttt180) cc_final: 0.0096 (mmp-170) REVERT: Q 374 GLU cc_start: 0.4964 (mt-10) cc_final: 0.3977 (pm20) REVERT: Q 472 ASN cc_start: 0.8775 (m-40) cc_final: 0.8364 (m-40) REVERT: Q 545 ILE cc_start: 0.8782 (mm) cc_final: 0.8533 (mm) REVERT: z 37 LEU cc_start: 0.9426 (tp) cc_final: 0.9078 (mt) REVERT: z 40 LYS cc_start: 0.9348 (mmpt) cc_final: 0.9049 (mmmt) REVERT: z 66 MET cc_start: 0.5862 (tmm) cc_final: 0.5335 (tmm) REVERT: z 83 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8083 (tm-30) REVERT: z 87 THR cc_start: 0.7483 (p) cc_final: 0.7108 (p) REVERT: z 100 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8624 (mm-30) REVERT: z 215 LEU cc_start: 0.8248 (tp) cc_final: 0.7786 (tp) REVERT: z 246 GLU cc_start: 0.5188 (tt0) cc_final: 0.4953 (mp0) REVERT: z 372 ASP cc_start: 0.7609 (m-30) cc_final: 0.7329 (m-30) REVERT: z 386 TYR cc_start: 0.8475 (p90) cc_final: 0.7950 (p90) REVERT: z 392 LYS cc_start: 0.9576 (ptmm) cc_final: 0.9267 (ptmm) REVERT: z 419 TYR cc_start: 0.9276 (m-10) cc_final: 0.8959 (m-10) REVERT: z 452 LEU cc_start: 0.9548 (mp) cc_final: 0.9118 (mp) REVERT: z 456 LYS cc_start: 0.9656 (mtmm) cc_final: 0.9403 (mttp) REVERT: z 525 SER cc_start: 0.9443 (m) cc_final: 0.8864 (p) REVERT: z 526 ASN cc_start: 0.9587 (m110) cc_final: 0.9294 (m-40) REVERT: z 527 LEU cc_start: 0.9503 (mt) cc_final: 0.9059 (mt) REVERT: z 529 LEU cc_start: 0.9404 (mm) cc_final: 0.8999 (mm) REVERT: Z 21 VAL cc_start: 0.9180 (t) cc_final: 0.8965 (p) REVERT: Z 22 ASN cc_start: 0.8920 (m110) cc_final: 0.8446 (m-40) REVERT: Z 168 GLU cc_start: 0.9588 (mp0) cc_final: 0.9376 (pm20) REVERT: Z 176 ASP cc_start: 0.8926 (m-30) cc_final: 0.8676 (m-30) REVERT: Z 366 TYR cc_start: 0.7579 (m-80) cc_final: 0.6957 (m-80) REVERT: Z 431 MET cc_start: 0.7382 (tpt) cc_final: 0.6882 (tmm) REVERT: Z 460 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9277 (tppp) REVERT: Z 482 ASP cc_start: 0.8881 (m-30) cc_final: 0.8595 (m-30) REVERT: Z 504 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8714 (mm-30) outliers start: 1 outliers final: 0 residues processed: 1363 average time/residue: 0.5613 time to fit residues: 1333.4059 Evaluate side-chains 1106 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1106 time to evaluate : 5.538 ------------------------------------------------------------------------------- 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: 3.9990 chunk 679 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 588 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 177 optimal weight: 0.8980 chunk 638 optimal weight: 0.9980 chunk 267 optimal weight: 20.0000 chunk 655 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 172 HIS b 375 GLN ** b 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 HIS d 436 GLN D 436 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 251 HIS ** e 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS E 397 GLN ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 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 ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 ASN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 HIS ** G 568 GLN ** 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** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 543 GLN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 543 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 = 0.4206 r_free = 0.4206 target = 0.132155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.107709 restraints weight = 290278.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.110274 restraints weight = 206201.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.111623 restraints weight = 147256.354| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.8768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 62618 Z= 0.176 Angle : 0.598 9.710 84459 Z= 0.304 Chirality : 0.044 0.338 10166 Planarity : 0.003 0.061 10848 Dihedral : 3.942 22.206 8568 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.31 % Rotamer: Outliers : 0.01 % Allowed : 0.28 % Favored : 99.71 % 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: -0.05 (0.09), residues: 8065 helix: 0.68 (0.08), residues: 3972 sheet: -0.38 (0.20), residues: 653 loop : -0.72 (0.10), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP d 440 HIS 0.011 0.001 HIS d 303 PHE 0.031 0.002 PHE Q 137 TYR 0.038 0.001 TYR e 467 ARG 0.012 0.001 ARG D 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19821.12 seconds wall clock time: 345 minutes 57.30 seconds (20757.30 seconds total)