Starting phenix.real_space_refine on Tue Mar 12 06:40:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/03_2024/6ks7_0759.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/03_2024/6ks7_0759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/03_2024/6ks7_0759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/03_2024/6ks7_0759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/03_2024/6ks7_0759.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/03_2024/6ks7_0759.pdb" } resolution = 4.62 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= 0.020 sd= 0.164 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 38930 2.51 5 N 10732 2.21 5 O 12044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 15": "NH1" <-> "NH2" Residue "z TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 62022 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 3878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3878 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 12, 'TRANS': 493} Chain: "a" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3879 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 10, 'TRANS': 503} Chain breaks: 1 Chain: "A" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3924 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 10, 'TRANS': 510} Chain breaks: 1 Chain: "b" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3833 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 10, 'TRANS': 494} Chain: "B" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3833 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 10, 'TRANS': 494} Chain: "d" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3687 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 470} Chain breaks: 2 Chain: "D" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3756 Classifications: {'peptide': 492} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 477} Chain breaks: 3 Chain: "e" Number of atoms: 3842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3842 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 1 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: "g" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3722 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 18, 'TRANS': 468} Chain breaks: 2 Chain: "G" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3905 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 18, 'TRANS': 489} Chain breaks: 1 Chain: "h" Number of atoms: 3658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3658 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 12, 'TRANS': 467} Chain breaks: 1 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: "Q" Number of atoms: 4005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4005 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 18, 'TRANS': 509} 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} 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: 24.18, per 1000 atoms: 0.39 Number of scatterers: 62022 At special positions: 0 Unit cell: (201.654, 204.29, 205.608, 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 12044 8.00 N 10732 7.00 C 38930 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: 17.52 Conformation dependent library (CDL) restraints added in 8.6 seconds 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15136 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 88 sheets defined 54.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'H' and resid 23 through 41 removed outlier: 3.683A pdb=" N ALA H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.534A pdb=" N LEU H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 94 Processing helix chain 'H' and resid 97 through 112 removed outlier: 3.944A pdb=" N THR H 102 " --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 removed outlier: 3.907A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 144 removed outlier: 3.692A pdb=" N ILE H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS H 131 " --> pdb=" O LYS H 127 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU H 142 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 167 removed outlier: 4.449A pdb=" N LEU H 158 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA H 162 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR H 164 " --> pdb=" O ARG H 160 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA H 165 " --> pdb=" O CYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 188 removed outlier: 4.194A pdb=" N LYS H 180 " --> pdb=" O ASP H 176 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET H 181 " --> pdb=" O PHE H 177 " (cutoff:3.500A) removed outlier: 3.648A 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: 3.596A pdb=" N GLU H 211 " --> pdb=" O ALA H 208 " (cutoff:3.500A) removed outlier: 3.606A 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 270 removed outlier: 4.417A pdb=" N ALA H 269 " --> pdb=" O GLU H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 272 No H-bonds generated for 'chain 'H' and resid 271 through 272' Processing helix chain 'H' and resid 273 through 277 Processing helix chain 'H' and resid 278 through 289 removed outlier: 4.066A pdb=" N GLN H 284 " --> pdb=" O GLU H 280 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 304 removed outlier: 3.857A pdb=" N ALA H 303 " --> pdb=" O GLY H 300 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR H 304 " --> pdb=" O ASP H 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 300 through 304' Processing helix chain 'H' and resid 305 through 310 removed outlier: 3.771A pdb=" N ASP H 309 " --> pdb=" O GLN H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 331 removed outlier: 3.566A pdb=" N MET H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN H 324 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG H 325 " --> pdb=" O ASP H 321 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL H 326 " --> pdb=" O ASP H 322 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE H 327 " --> pdb=" O MET H 323 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.597A pdb=" N GLU H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP H 395 " --> pdb=" O ARG H 391 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE H 399 " --> pdb=" O ASP H 395 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU H 404 " --> pdb=" O VAL H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 431 removed outlier: 3.568A pdb=" N GLU H 419 " --> pdb=" O ALA H 415 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER H 421 " --> pdb=" O GLU H 417 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H 424 " --> pdb=" O VAL H 420 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP H 426 " --> pdb=" O LYS H 422 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR H 430 " --> pdb=" O ASP H 426 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE H 431 " --> pdb=" O TYR H 427 " (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 472 removed outlier: 3.728A pdb=" N ARG H 469 " --> pdb=" O LEU H 465 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU H 470 " --> pdb=" O ASN H 466 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA H 471 " --> pdb=" O LYS H 467 " (cutoff:3.500A) Processing helix chain 'H' and resid 500 through 519 removed outlier: 3.723A pdb=" N LEU H 507 " --> pdb=" O LYS H 503 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN H 508 " --> pdb=" O ILE H 504 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE H 517 " --> pdb=" O ALA H 513 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 41 removed outlier: 3.781A pdb=" N ARG a 26 " --> pdb=" O GLY a 22 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL a 39 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL a 40 " --> pdb=" O VAL a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 44 No H-bonds generated for 'chain 'a' and resid 42 through 44' Processing helix chain 'a' and resid 66 through 73 removed outlier: 3.802A pdb=" N LEU a 70 " --> pdb=" O GLY a 66 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER a 71 " --> pdb=" O ALA a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 94 removed outlier: 3.571A pdb=" N ILE a 82 " --> pdb=" O PRO a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 111 removed outlier: 3.752A pdb=" N VAL a 102 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU a 109 " --> pdb=" O ALA a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 118 removed outlier: 3.920A pdb=" N LEU a 115 " --> pdb=" O ARG a 111 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS a 117 " --> pdb=" O ASN a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 144 removed outlier: 3.555A pdb=" N ILE a 137 " --> pdb=" O LEU a 133 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG a 138 " --> pdb=" O ARG a 134 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE a 139 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU a 142 " --> pdb=" O ARG a 138 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL a 143 " --> pdb=" O PHE a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 removed outlier: 4.309A pdb=" N ALA a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS a 161 " --> pdb=" O ILE a 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR a 162 " --> pdb=" O ASN a 158 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER a 163 " --> pdb=" O ILE a 159 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 171 Processing helix chain 'a' and resid 172 through 187 removed outlier: 4.446A pdb=" N ASN a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N MET a 179 " --> pdb=" O PHE a 175 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP a 182 " --> pdb=" O ASN a 178 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA a 186 " --> pdb=" O ASP a 182 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL a 187 " --> pdb=" O ALA a 183 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.582A pdb=" N SER a 216 " --> pdb=" O ALA a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 274 through 292 removed outlier: 4.124A pdb=" N ALA a 278 " --> pdb=" O ARG a 274 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL a 281 " --> pdb=" O GLU a 277 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU a 283 " --> pdb=" O GLY a 279 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG a 284 " --> pdb=" O ILE a 280 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE a 288 " --> pdb=" O ARG a 284 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE a 289 " --> pdb=" O VAL a 285 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 313 removed outlier: 3.836A pdb=" N GLU a 309 " --> pdb=" O LEU a 305 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE a 310 " --> pdb=" O CYS a 306 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU a 312 " --> pdb=" O LYS a 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 324 through 334 removed outlier: 4.261A pdb=" N ARG a 328 " --> pdb=" O GLU a 324 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG a 331 " --> pdb=" O ARG a 327 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 415 removed outlier: 3.520A pdb=" N GLU a 397 " --> pdb=" O TYR a 393 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG a 400 " --> pdb=" O ASP a 396 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS a 403 " --> pdb=" O GLU a 399 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP a 404 " --> pdb=" O ARG a 400 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL a 408 " --> pdb=" O ASP a 404 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL a 409 " --> pdb=" O SER a 405 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER a 415 " --> pdb=" O ARG a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 437 removed outlier: 3.802A pdb=" N ILE a 431 " --> pdb=" O ALA a 427 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR a 432 " --> pdb=" O ALA a 428 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP a 434 " --> pdb=" O ASN a 430 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN a 435 " --> pdb=" O ILE a 431 " (cutoff:3.500A) Processing helix chain 'a' and resid 443 through 454 removed outlier: 4.063A pdb=" N ALA a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) Processing helix chain 'a' and resid 456 through 466 removed outlier: 3.613A pdb=" N ASN a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) Processing helix chain 'a' and resid 469 through 485 removed outlier: 3.516A pdb=" N TYR a 480 " --> pdb=" O LYS a 476 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA a 483 " --> pdb=" O SER a 479 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN a 485 " --> pdb=" O HIS a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 511 through 516 Processing helix chain 'a' and resid 521 through 540 removed outlier: 3.695A pdb=" N ALA a 537 " --> pdb=" O GLU a 533 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE a 538 " --> pdb=" O ALA a 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 42 removed outlier: 4.008A pdb=" N ARG A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.777A pdb=" N ILE A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.764A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.567A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.714A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.964A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 4.243A pdb=" N ASP A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.848A pdb=" N SER A 216 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 290 removed outlier: 3.578A pdb=" N ILE A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.522A pdb=" N LYS A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.731A pdb=" N ARG A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 3.791A pdb=" N GLU A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.712A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.900A 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 444 through 454 Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.951A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.531A pdb=" N LEU A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 35 removed outlier: 3.511A pdb=" N GLY b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA b 26 " --> pdb=" O ALA b 22 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA b 28 " --> pdb=" O VAL b 24 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL b 29 " --> pdb=" O GLY b 25 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER b 35 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 67 removed outlier: 3.552A pdb=" N ILE b 63 " --> pdb=" O ASP b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 71 through 74 Processing helix chain 'b' and resid 75 through 88 removed outlier: 3.814A pdb=" N ASN b 79 " --> pdb=" O LYS b 75 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE b 80 " --> pdb=" O VAL b 76 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP b 86 " --> pdb=" O LYS b 82 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU b 87 " --> pdb=" O VAL b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 105 removed outlier: 3.862A pdb=" N THR b 96 " --> pdb=" O THR b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 138 removed outlier: 3.557A pdb=" N ALA b 130 " --> pdb=" O LEU b 126 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS b 137 " --> pdb=" O ASP b 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA b 138 " --> pdb=" O ALA b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 160 removed outlier: 3.580A pdb=" N GLU b 151 " --> pdb=" O THR b 147 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP b 152 " --> pdb=" O MET b 148 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU b 153 " --> pdb=" O PHE b 149 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE b 154 " --> pdb=" O ARG b 150 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS b 155 " --> pdb=" O GLU b 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR b 159 " --> pdb=" O HIS b 155 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR b 160 " --> pdb=" O ILE b 156 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 168 removed outlier: 3.564A pdb=" N GLN b 168 " --> pdb=" O ILE b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 183 removed outlier: 3.728A pdb=" N PHE b 173 " --> pdb=" O ASP b 169 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU b 176 " --> pdb=" O HIS b 172 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA b 177 " --> pdb=" O PHE b 173 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE b 181 " --> pdb=" O ALA b 177 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU b 182 " --> pdb=" O THR b 178 " (cutoff:3.500A) removed outlier: 3.738A 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 259 removed outlier: 3.834A pdb=" N ALA b 259 " --> pdb=" O THR b 255 " (cutoff:3.500A) Processing helix chain 'b' and resid 259 through 278 removed outlier: 4.161A pdb=" N LYS b 270 " --> pdb=" O ARG b 266 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN b 271 " --> pdb=" O GLU b 267 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS b 272 " --> pdb=" O LYS b 268 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS b 275 " --> pdb=" O ASN b 271 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE b 276 " --> pdb=" O LYS b 272 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 302 removed outlier: 3.529A pdb=" N PHE b 298 " --> pdb=" O PRO b 294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR b 299 " --> pdb=" O GLU b 295 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP b 300 " --> pdb=" O GLN b 296 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU b 301 " --> pdb=" O LEU b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 311 through 322 removed outlier: 3.647A pdb=" N ALA b 318 " --> pdb=" O VAL b 314 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 397 removed outlier: 3.725A pdb=" N LEU b 377 " --> pdb=" O THR b 373 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL b 390 " --> pdb=" O ASP b 386 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR b 395 " --> pdb=" O LEU b 391 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS b 396 " --> pdb=" O SER b 392 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 419 removed outlier: 3.734A pdb=" N SER b 412 " --> pdb=" O GLU b 408 " (cutoff:3.500A) Processing helix chain 'b' and resid 426 through 438 removed outlier: 3.619A pdb=" N ARG b 435 " --> pdb=" O GLU b 431 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA b 436 " --> pdb=" O ALA b 432 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG b 438 " --> pdb=" O ALA b 434 " (cutoff:3.500A) Processing helix chain 'b' and resid 438 through 447 removed outlier: 3.624A pdb=" N ASN b 447 " --> pdb=" O ILE b 443 " (cutoff:3.500A) Processing helix chain 'b' and resid 451 through 465 removed outlier: 3.564A pdb=" N LEU b 455 " --> pdb=" O ASP b 451 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER b 461 " --> pdb=" O SER b 457 " (cutoff:3.500A) removed outlier: 4.091A 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: 3.718A pdb=" N VAL b 507 " --> pdb=" O GLU b 503 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG b 510 " --> pdb=" O GLU b 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 35 removed outlier: 3.639A pdb=" N GLY B 25 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER B 35 " --> pdb=" O ASP B 31 " (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 LYS B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 removed outlier: 3.518A pdb=" N THR B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 138 removed outlier: 4.445A pdb=" N ILE B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.719A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B 152 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 159 " --> pdb=" O HIS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.664A pdb=" N GLN B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.880A pdb=" N PHE B 173 " --> pdb=" O ASP B 169 " (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 255 through 268 removed outlier: 4.315A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 4.424A pdb=" N LYS B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.539A pdb=" N PHE B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.533A pdb=" N VAL B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 394 removed outlier: 3.753A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.517A pdb=" N SER B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 removed outlier: 3.640A pdb=" N PHE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.808A pdb=" N THR B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 464 removed outlier: 3.504A pdb=" N SER B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 491 through 510 removed outlier: 3.713A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'd' and resid 18 through 37 removed outlier: 3.637A pdb=" N THR d 37 " --> pdb=" O ASP d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 68 Processing helix chain 'd' and resid 76 through 89 removed outlier: 3.998A pdb=" N GLU d 80 " --> pdb=" O ARG d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 107 removed outlier: 3.848A pdb=" N VAL d 97 " --> pdb=" O THR d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 113 removed outlier: 3.681A pdb=" N ASN d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 139 removed outlier: 3.546A pdb=" N ILE d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN d 125 " --> pdb=" O ALA d 121 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL d 132 " --> pdb=" O ALA d 128 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP d 133 " --> pdb=" O LYS d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 removed outlier: 3.556A pdb=" N ARG d 152 " --> pdb=" O GLU d 148 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 161 No H-bonds generated for 'chain 'd' and resid 159 through 161' Processing helix chain 'd' and resid 166 through 183 Proline residue: d 172 - end of helix removed outlier: 3.714A pdb=" N LYS d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE d 181 " --> pdb=" O SER d 177 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP d 183 " --> pdb=" O LEU d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 194 removed outlier: 3.824A pdb=" N ASP d 193 " --> pdb=" O ASP d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 281 removed outlier: 3.742A pdb=" N ASN d 273 " --> pdb=" O ALA d 269 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE d 274 " --> pdb=" O TYR d 270 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE d 278 " --> pdb=" O ILE d 274 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA d 281 " --> pdb=" O LYS d 277 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 309 removed outlier: 3.968A pdb=" N HIS d 303 " --> pdb=" O ASP d 299 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE d 304 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS d 307 " --> pdb=" O HIS d 303 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU d 308 " --> pdb=" O PHE d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 318 through 328 removed outlier: 4.396A pdb=" N GLU d 322 " --> pdb=" O ARG d 318 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE d 323 " --> pdb=" O GLU d 319 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS d 326 " --> pdb=" O GLU d 322 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY d 327 " --> pdb=" O PHE d 323 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU d 328 " --> pdb=" O LEU d 324 " (cutoff:3.500A) Processing helix chain 'd' and resid 383 through 407 removed outlier: 3.814A pdb=" N ILE d 387 " --> pdb=" O ASN d 383 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU d 389 " --> pdb=" O MET d 385 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP d 396 " --> pdb=" O ARG d 392 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU d 404 " --> pdb=" O VAL d 400 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL d 405 " --> pdb=" O ILE d 401 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS d 406 " --> pdb=" O ARG d 402 " (cutoff:3.500A) Processing helix chain 'd' and resid 415 through 429 removed outlier: 3.677A pdb=" N SER d 422 " --> pdb=" O GLU d 418 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG d 424 " --> pdb=" O GLU d 420 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER d 426 " --> pdb=" O SER d 422 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS d 427 " --> pdb=" O ARG d 423 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU d 428 " --> pdb=" O ARG d 424 " (cutoff:3.500A) Processing helix chain 'd' and resid 430 through 432 No H-bonds generated for 'chain 'd' and resid 430 through 432' Processing helix chain 'd' and resid 435 through 448 removed outlier: 3.769A pdb=" N ILE d 439 " --> pdb=" O VAL d 435 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN d 441 " --> pdb=" O ALA d 437 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER d 445 " --> pdb=" O GLN d 441 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU d 448 " --> pdb=" O ALA d 444 " (cutoff:3.500A) Processing helix chain 'd' and resid 448 through 458 removed outlier: 3.552A pdb=" N ALA d 458 " --> pdb=" O LEU d 454 " (cutoff:3.500A) Processing helix chain 'd' and resid 461 through 472 removed outlier: 3.554A pdb=" N LYS d 472 " --> pdb=" O GLU d 468 " (cutoff:3.500A) Processing helix chain 'd' and resid 473 through 475 No H-bonds generated for 'chain 'd' and resid 473 through 475' Processing helix chain 'd' and resid 500 through 519 removed outlier: 4.092A pdb=" N SER d 504 " --> pdb=" O PRO d 500 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE d 508 " --> pdb=" O SER d 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 37 removed outlier: 3.796A pdb=" N ARG D 21 " --> pdb=" O PRO D 17 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.602A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 113 removed outlier: 3.960A pdb=" N VAL D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 139 removed outlier: 3.541A pdb=" N PHE D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 4.211A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.805A pdb=" N SER D 168 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 183 removed outlier: 3.551A pdb=" N ALA D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 281 removed outlier: 3.872A pdb=" N ILE D 274 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 removed outlier: 3.518A pdb=" N HIS D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 4.504A pdb=" N GLU D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 327 " --> pdb=" O PHE D 323 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 383 through 407 removed outlier: 3.936A pdb=" N ILE D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.725A pdb=" N ILE D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 434 through 447 removed outlier: 4.145A pdb=" N PHE D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP D 440 " --> pdb=" O GLN D 436 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 447 " --> pdb=" O PHE D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.567A pdb=" N ALA D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 476 removed outlier: 3.510A pdb=" N VAL D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 474 " --> pdb=" O ARG D 470 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN D 475 " --> pdb=" O SER D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 520 removed outlier: 3.651A pdb=" N ILE D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 62 removed outlier: 3.544A pdb=" N LYS e 47 " --> pdb=" O GLY e 43 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS e 48 " --> pdb=" O LEU e 44 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU e 52 " --> pdb=" O LYS e 48 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE e 61 " --> pdb=" O VAL e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 93 Processing helix chain 'e' and resid 98 through 115 removed outlier: 3.532A pdb=" N LYS e 102 " --> pdb=" O ASN e 98 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU e 103 " --> pdb=" O GLU e 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU e 104 " --> pdb=" O ILE e 100 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL e 105 " --> pdb=" O ALA e 101 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER e 110 " --> pdb=" O GLN e 106 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU e 114 " --> pdb=" O SER e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 139 removed outlier: 3.547A pdb=" N VAL e 124 " --> pdb=" O THR e 120 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU e 136 " --> pdb=" O GLN e 132 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN e 138 " --> pdb=" O LEU e 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 164 removed outlier: 3.746A pdb=" N ILE e 146 " --> pdb=" O HIS e 142 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP e 151 " --> pdb=" O ALA e 147 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU e 152 " --> pdb=" O ASN e 148 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER e 159 " --> pdb=" O LYS e 155 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS e 160 " --> pdb=" O LEU e 156 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR e 164 " --> pdb=" O LYS e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 174 through 188 removed outlier: 4.465A pdb=" N ASP e 178 " --> pdb=" O GLU e 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU e 180 " --> pdb=" O PHE e 176 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA e 184 " --> pdb=" O LEU e 180 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS e 185 " --> pdb=" O LEU e 181 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR e 186 " --> pdb=" O ARG e 182 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 195 Processing helix chain 'e' and resid 196 through 211 removed outlier: 3.558A pdb=" N PHE e 200 " --> pdb=" O ASP e 196 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU e 202 " --> pdb=" O ASP e 198 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET e 203 " --> pdb=" O ARG e 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA e 204 " --> pdb=" O PHE e 200 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL e 205 " --> pdb=" O ALA e 201 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL e 208 " --> pdb=" O ALA e 204 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL e 211 " --> pdb=" O ALA e 207 " (cutoff:3.500A) Processing helix chain 'e' and resid 233 through 237 removed outlier: 3.799A pdb=" N ASP e 236 " --> pdb=" O SER e 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 302 through 317 removed outlier: 3.601A pdb=" N ASP e 311 " --> pdb=" O LYS e 307 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL e 313 " --> pdb=" O MET e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 328 through 338 removed outlier: 4.046A pdb=" N ASN e 332 " --> pdb=" O ASP e 328 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS e 333 " --> pdb=" O ASP e 329 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN e 337 " --> pdb=" O HIS e 333 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN e 338 " --> pdb=" O LEU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 349 through 358 removed outlier: 4.351A pdb=" N HIS e 353 " --> pdb=" O GLN e 349 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE e 354 " --> pdb=" O GLU e 350 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA e 355 " --> pdb=" O LEU e 351 " (cutoff:3.500A) Processing helix chain 'e' and resid 412 through 436 removed outlier: 3.616A pdb=" N ASP e 436 " --> pdb=" O ASN e 432 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 458 removed outlier: 3.551A pdb=" N VAL e 448 " --> pdb=" O GLY e 444 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL e 454 " --> pdb=" O MET e 450 " (cutoff:3.500A) Processing helix chain 'e' and resid 464 through 477 removed outlier: 3.949A pdb=" N ALA e 468 " --> pdb=" O ILE e 464 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG e 470 " --> pdb=" O GLN e 466 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP e 477 " --> pdb=" O ALA e 473 " (cutoff:3.500A) Processing helix chain 'e' and resid 477 through 487 Processing helix chain 'e' and resid 490 through 502 Processing helix chain 'e' and resid 521 through 526 removed outlier: 3.862A pdb=" N GLU e 524 " --> pdb=" O ASP e 521 " (cutoff:3.500A) Processing helix chain 'e' and resid 531 through 550 removed outlier: 3.545A pdb=" N ILE e 538 " --> pdb=" O LYS e 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 59 removed outlier: 3.753A pdb=" N ILE E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 4.209A pdb=" N THR E 63 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU E 65 " --> pdb=" O LYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.746A pdb=" N ILE E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 115 removed outlier: 3.978A pdb=" N VAL E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER E 110 " --> pdb=" O GLN E 106 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP E 112 " --> pdb=" O SER E 108 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 139 removed outlier: 3.795A pdb=" N VAL E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU E 135 " --> pdb=" O ASP E 131 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN E 138 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 165 removed outlier: 3.575A pdb=" N ASP E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 3.883A pdb=" N ARG E 177 " --> pdb=" O ASP E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.702A pdb=" N THR E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 196 through 202 removed outlier: 3.725A pdb=" N PHE E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 212 removed outlier: 4.166A pdb=" N GLU E 206 " --> pdb=" O GLU E 202 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE E 209 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN E 210 " --> pdb=" O GLU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 293 No H-bonds generated for 'chain 'E' and resid 291 through 293' Processing helix chain 'E' and resid 294 through 304 removed outlier: 3.583A pdb=" N GLN E 299 " --> pdb=" O TYR E 295 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR E 300 " --> pdb=" O GLN E 296 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN E 303 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP E 304 " --> pdb=" O THR E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 317 removed outlier: 4.117A pdb=" N MET E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP E 311 " --> pdb=" O LYS E 307 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL E 313 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 332 removed outlier: 4.130A pdb=" N ASN E 332 " --> pdb=" O ASP E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 332' Processing helix chain 'E' and resid 333 through 338 removed outlier: 3.907A pdb=" N GLN E 337 " --> pdb=" O HIS E 333 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 333 through 338' Processing helix chain 'E' and resid 349 through 358 removed outlier: 4.387A pdb=" N HIS E 353 " --> pdb=" O GLN E 349 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 436 removed outlier: 3.582A pdb=" N VAL E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 459 removed outlier: 3.662A pdb=" N VAL E 448 " --> pdb=" O GLY E 444 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 477 removed outlier: 3.542A pdb=" N ALA E 468 " --> pdb=" O ILE E 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP E 477 " --> pdb=" O ALA E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 487 Processing helix chain 'E' and resid 490 through 502 removed outlier: 3.592A pdb=" N THR E 497 " --> pdb=" O GLY E 493 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 502 " --> pdb=" O LEU E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 550 Processing helix chain 'g' and resid 18 through 33 removed outlier: 3.518A pdb=" N ILE g 25 " --> pdb=" O GLN g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 39 removed outlier: 3.980A pdb=" N LEU g 39 " --> pdb=" O ARG g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 66 removed outlier: 3.511A pdb=" N ILE g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG g 66 " --> pdb=" O HIS g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 89 removed outlier: 4.028A pdb=" N LYS g 76 " --> pdb=" O HIS g 72 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER g 77 " --> pdb=" O PRO g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 107 removed outlier: 3.556A pdb=" N VAL g 96 " --> pdb=" O GLY g 92 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE g 97 " --> pdb=" O THR g 93 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA g 105 " --> pdb=" O GLY g 101 " (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 156 removed outlier: 4.201A pdb=" N LYS g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) removed outlier: 3.811A 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: 4.136A pdb=" N HIS g 166 " --> pdb=" O TYR g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 183 removed outlier: 4.109A pdb=" N GLU g 173 " --> pdb=" O GLU g 169 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA g 178 " --> pdb=" O LEU g 174 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL g 182 " --> pdb=" O ALA g 178 " (cutoff:3.500A) Processing helix chain 'g' and resid 277 through 289 removed outlier: 3.559A pdb=" N GLN g 286 " --> pdb=" O LEU g 282 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE g 287 " --> pdb=" O MET g 283 " (cutoff:3.500A) Processing helix chain 'g' and resid 302 through 309 removed outlier: 3.597A pdb=" N GLN g 306 " --> pdb=" O SER g 302 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS g 307 " --> pdb=" O ASP g 303 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR g 308 " --> pdb=" O LEU g 304 " (cutoff:3.500A) Processing helix chain 'g' and resid 324 through 333 removed outlier: 3.631A pdb=" N ARG g 330 " --> pdb=" O ASN g 326 " (cutoff:3.500A) Processing helix chain 'g' and resid 339 through 343 Processing helix chain 'g' and resid 445 through 469 removed outlier: 3.839A pdb=" N ARG g 454 " --> pdb=" O ASN g 450 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER g 469 " --> pdb=" O ASN g 465 " (cutoff:3.500A) Processing helix chain 'g' and resid 477 through 491 removed outlier: 3.581A pdb=" N SER g 484 " --> pdb=" O GLU g 480 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS g 486 " --> pdb=" O ALA g 482 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA g 488 " --> pdb=" O SER g 484 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU g 489 " --> pdb=" O VAL g 485 " (cutoff:3.500A) Processing helix chain 'g' and resid 498 through 510 removed outlier: 3.706A pdb=" N VAL g 505 " --> pdb=" O PRO g 501 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA g 506 " --> pdb=" O TYR g 502 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP g 507 " --> pdb=" O GLN g 503 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA g 508 " --> pdb=" O ALA g 504 " (cutoff:3.500A) Processing helix chain 'g' and resid 510 through 521 Processing helix chain 'g' and resid 523 through 538 removed outlier: 3.512A pdb=" N GLN g 530 " --> pdb=" O ARG g 526 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA g 533 " --> pdb=" O SER g 529 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS g 535 " --> pdb=" O LEU g 531 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA g 536 " --> pdb=" O ARG g 532 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN g 537 " --> pdb=" O ALA g 533 " (cutoff:3.500A) Processing helix chain 'g' and resid 563 through 583 removed outlier: 3.827A pdb=" N VAL g 583 " --> pdb=" O LEU g 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 35 removed outlier: 3.757A pdb=" N ALA G 28 " --> pdb=" O ASN G 24 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 39 removed outlier: 3.856A pdb=" N LEU G 39 " --> pdb=" O ARG G 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 36 through 39' Processing helix chain 'G' and resid 60 through 68 removed outlier: 3.743A pdb=" N ARG G 66 " --> pdb=" O HIS G 62 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 89 removed outlier: 3.886A pdb=" N LYS G 76 " --> pdb=" O HIS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 3.620A pdb=" N VAL G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.938A 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: 3.736A pdb=" N THR G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 157 removed outlier: 3.670A pdb=" N LYS G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 166 removed outlier: 4.165A pdb=" N HIS G 166 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 removed outlier: 3.833A pdb=" N GLU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.590A pdb=" N GLU G 197 " --> pdb=" O PRO G 194 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 194 through 198' Processing helix chain 'G' and resid 265 through 267 No H-bonds generated for 'chain 'G' and resid 265 through 267' Processing helix chain 'G' and resid 268 through 288 removed outlier: 3.938A pdb=" N ILE G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL G 280 " --> pdb=" O GLU G 276 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN G 286 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE G 287 " --> pdb=" O MET G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 309 removed outlier: 4.191A pdb=" N HIS G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR G 308 " --> pdb=" O LEU G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 332 removed outlier: 3.529A pdb=" N ALA G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL G 331 " --> pdb=" O ARG G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 344 through 348 removed outlier: 3.669A pdb=" N ASP G 347 " --> pdb=" O LYS G 344 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL G 348 " --> pdb=" O GLU G 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 344 through 348' Processing helix chain 'G' and resid 445 through 468 removed outlier: 3.715A pdb=" N GLU G 451 " --> pdb=" O ASP G 447 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG G 454 " --> pdb=" O ASN G 450 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL G 462 " --> pdb=" O ASP G 458 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA G 463 " --> pdb=" O ALA G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 492 removed outlier: 3.575A pdb=" N VAL G 483 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER G 484 " --> pdb=" O GLU G 480 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 486 " --> pdb=" O ALA G 482 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU G 489 " --> pdb=" O VAL G 485 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS G 492 " --> pdb=" O ALA G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 510 removed outlier: 3.549A pdb=" N TYR G 502 " --> pdb=" O GLN G 498 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN G 503 " --> pdb=" O GLN G 499 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA G 504 " --> pdb=" O TRP G 500 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 520 removed outlier: 3.628A pdb=" N LEU G 516 " --> pdb=" O ILE G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 538 removed outlier: 3.574A pdb=" N LEU G 528 " --> pdb=" O PRO G 524 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 529 " --> pdb=" O ILE G 525 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS G 535 " --> pdb=" O LEU G 531 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA G 536 " --> pdb=" O ARG G 532 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN G 537 " --> pdb=" O ALA G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 563 through 582 removed outlier: 3.616A pdb=" N LEU G 581 " --> pdb=" O ALA G 577 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 41 removed outlier: 3.519A pdb=" N ILE h 27 " --> pdb=" O LYS h 23 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS h 33 " --> pdb=" O ASN h 29 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL h 36 " --> pdb=" O ALA h 32 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 72 Processing helix chain 'h' and resid 80 through 94 removed outlier: 3.962A pdb=" N VAL h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 112 removed outlier: 3.981A pdb=" N THR h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA h 112 " --> pdb=" O LEU h 108 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 118 removed outlier: 3.803A pdb=" N LEU h 116 " --> pdb=" O ALA h 112 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU h 118 " --> pdb=" O PRO h 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 112 through 118' Processing helix chain 'h' and resid 121 through 144 removed outlier: 3.749A pdb=" N ILE h 125 " --> pdb=" O SER h 121 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU h 138 " --> pdb=" O SER h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 155 through 162 removed outlier: 4.179A pdb=" N CYS h 161 " --> pdb=" O LEU h 157 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA h 162 " --> pdb=" O LEU h 158 " (cutoff:3.500A) Processing helix chain 'h' and resid 162 through 167 Processing helix chain 'h' and resid 174 through 188 removed outlier: 4.004A pdb=" N LYS h 180 " --> pdb=" O ASP h 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET h 181 " --> pdb=" O PHE h 177 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS h 182 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL h 183 " --> pdb=" O VAL h 179 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP h 184 " --> pdb=" O LYS h 180 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA h 185 " --> pdb=" O MET h 181 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL h 186 " --> pdb=" O CYS h 182 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER h 188 " --> pdb=" O ASP h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 208 through 212 removed outlier: 3.589A pdb=" N GLU h 211 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 3.784A 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 279 through 289 removed outlier: 3.502A pdb=" N VAL h 285 " --> pdb=" O LYS h 281 " (cutoff:3.500A) Processing helix chain 'h' and resid 300 through 310 removed outlier: 3.696A pdb=" N THR h 304 " --> pdb=" O GLY h 300 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE h 306 " --> pdb=" O LEU h 302 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP h 309 " --> pdb=" O GLN h 305 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG h 310 " --> pdb=" O PHE h 306 " (cutoff:3.500A) Processing helix chain 'h' and resid 319 through 331 removed outlier: 3.572A pdb=" N ASN h 324 " --> pdb=" O ALA h 320 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG h 325 " --> pdb=" O ASP h 321 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE h 327 " --> pdb=" O MET h 323 " (cutoff:3.500A) removed outlier: 3.822A 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: 3.505A pdb=" N ILE h 386 " --> pdb=" O ALA h 382 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP h 395 " --> pdb=" O ARG h 391 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA h 396 " --> pdb=" O SER h 392 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL h 400 " --> pdb=" O ALA h 396 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG h 402 " --> pdb=" O MET h 398 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA h 403 " --> pdb=" O ILE h 399 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN h 405 " --> pdb=" O LYS h 401 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN h 406 " --> pdb=" O ARG h 402 " (cutoff:3.500A) Processing helix chain 'h' and resid 414 through 429 removed outlier: 3.678A pdb=" N ARG h 425 " --> pdb=" O SER h 421 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP h 426 " --> pdb=" O LYS h 422 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 446 removed outlier: 3.541A pdb=" N ILE h 438 " --> pdb=" O LYS h 434 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 458 removed outlier: 3.511A pdb=" N LEU h 453 " --> pdb=" O ILE h 449 " (cutoff:3.500A) Processing helix chain 'h' and resid 460 through 473 removed outlier: 3.681A pdb=" N ASN h 466 " --> pdb=" O ILE h 462 " (cutoff:3.500A) removed outlier: 3.670A 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 removed outlier: 3.520A pdb=" N ILE h 517 " --> pdb=" O ALA h 513 " (cutoff:3.500A) Processing helix chain 'q' and resid 27 through 44 removed outlier: 3.724A pdb=" N ILE q 32 " --> pdb=" O ILE q 28 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU q 38 " --> pdb=" O ALA q 34 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS q 42 " --> pdb=" O LEU q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 75 removed outlier: 3.958A pdb=" N ARG q 73 " --> pdb=" O ALA q 69 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU q 74 " --> pdb=" O THR q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 95 removed outlier: 4.169A pdb=" N LEU q 85 " --> pdb=" O ALA q 81 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN q 92 " --> pdb=" O ALA q 88 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS q 93 " --> pdb=" O THR q 89 " (cutoff:3.500A) Processing helix chain 'q' and resid 99 through 121 removed outlier: 3.794A pdb=" N LEU q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN q 112 " --> pdb=" O GLY q 108 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS q 116 " --> pdb=" O ASN q 112 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU q 117 " --> pdb=" O VAL q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 123 through 142 removed outlier: 3.531A pdb=" N ILE q 127 " --> pdb=" O SER q 123 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) Processing helix chain 'q' and resid 159 through 168 Proline residue: q 165 - end of helix Processing helix chain 'q' and resid 176 through 190 removed outlier: 4.252A pdb=" N GLU q 180 " --> pdb=" O ASP q 176 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU q 181 " --> pdb=" O ILE q 177 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA q 185 " --> pdb=" O LEU q 181 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER q 187 " --> pdb=" O SER q 183 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS q 188 " --> pdb=" O GLU q 184 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL q 189 " --> pdb=" O ALA q 185 " (cutoff:3.500A) Processing helix chain 'q' and resid 270 through 294 removed outlier: 4.286A pdb=" N LEU q 274 " --> pdb=" O ALA q 270 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP q 275 " --> pdb=" O GLN q 271 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU q 290 " --> pdb=" O ALA q 286 " (cutoff:3.500A) Processing helix chain 'q' and resid 308 through 316 removed outlier: 3.970A pdb=" N TYR q 312 " --> pdb=" O LEU q 308 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU q 313 " --> pdb=" O ALA q 309 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN q 314 " --> pdb=" O LEU q 310 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG q 315 " --> pdb=" O HIS q 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR q 316 " --> pdb=" O TYR q 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 308 through 316' Processing helix chain 'q' and resid 325 through 334 removed outlier: 4.010A pdb=" N LEU q 329 " --> pdb=" O SER q 325 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG q 330 " --> pdb=" O LYS q 326 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG q 331 " --> pdb=" O PHE q 327 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG q 334 " --> pdb=" O ARG q 330 " (cutoff:3.500A) Processing helix chain 'q' and resid 390 through 410 removed outlier: 3.659A pdb=" N ASP q 395 " --> pdb=" O GLN q 391 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP q 402 " --> pdb=" O GLU q 398 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP q 403 " --> pdb=" O ARG q 399 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY q 404 " --> pdb=" O ALA q 400 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA q 406 " --> pdb=" O ASP q 402 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA q 407 " --> pdb=" O ASP q 403 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL q 408 " --> pdb=" O GLY q 404 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS q 409 " --> pdb=" O VAL q 405 " (cutoff:3.500A) Processing helix chain 'q' and resid 424 through 439 removed outlier: 3.518A pdb=" N ILE q 428 " --> pdb=" O GLY q 424 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE q 431 " --> pdb=" O GLU q 427 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER q 432 " --> pdb=" O ILE q 428 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG q 433 " --> pdb=" O GLU q 429 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR q 437 " --> pdb=" O ARG q 433 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU q 439 " --> pdb=" O THR q 435 " (cutoff:3.500A) Processing helix chain 'q' and resid 445 through 455 Processing helix chain 'q' and resid 457 through 467 Processing helix chain 'q' and resid 470 through 483 removed outlier: 3.551A pdb=" N LEU q 475 " --> pdb=" O VAL q 471 " (cutoff:3.500A) Proline residue: q 476 - end of helix removed outlier: 3.628A pdb=" N HIS q 482 " --> pdb=" O LEU q 478 " (cutoff:3.500A) Processing helix chain 'q' and resid 521 through 541 removed outlier: 3.690A pdb=" N ASN q 529 " --> pdb=" O LYS q 525 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL q 538 " --> pdb=" O ALA q 534 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 25 Processing helix chain 'Q' and resid 26 through 44 removed outlier: 3.681A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN Q 40 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS Q 42 " --> pdb=" O LEU Q 38 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 75 removed outlier: 3.728A pdb=" N MET Q 71 " --> pdb=" O ASP Q 67 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 95 removed outlier: 4.007A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN Q 91 " --> pdb=" O MET Q 87 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 114 removed outlier: 3.899A pdb=" N MET Q 104 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE Q 105 " --> pdb=" O ASN Q 101 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN Q 112 " --> pdb=" O GLY Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 120 Processing helix chain 'Q' and resid 123 through 142 removed outlier: 3.752A pdb=" N ILE Q 127 " --> pdb=" O SER Q 123 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS Q 136 " --> pdb=" O ASN Q 132 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 168 Proline residue: Q 165 - end of helix Processing helix chain 'Q' and resid 174 through 190 removed outlier: 4.265A pdb=" N GLU Q 180 " --> pdb=" O ASP Q 176 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU Q 181 " --> pdb=" O ILE Q 177 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER Q 187 " --> pdb=" O SER Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 294 removed outlier: 4.138A pdb=" N LEU Q 274 " --> pdb=" O ALA Q 270 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP Q 275 " --> pdb=" O GLN Q 271 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU Q 281 " --> pdb=" O SER Q 277 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS Q 282 " --> pdb=" O LYS Q 278 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET Q 294 " --> pdb=" O GLU Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 317 removed outlier: 3.829A pdb=" N LEU Q 310 " --> pdb=" O GLY Q 306 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS Q 311 " --> pdb=" O GLU Q 307 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR Q 312 " --> pdb=" O LEU Q 308 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN Q 314 " --> pdb=" O LEU Q 310 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG Q 315 " --> pdb=" O HIS Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 326 through 333 removed outlier: 4.147A pdb=" N ARG Q 330 " --> pdb=" O LYS Q 326 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG Q 331 " --> pdb=" O PHE Q 327 " (cutoff:3.500A) removed outlier: 3.573A 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 406 removed outlier: 3.597A pdb=" N LEU Q 394 " --> pdb=" O THR Q 390 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP Q 396 " --> pdb=" O ASN Q 392 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP Q 402 " --> pdb=" O GLU Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 407 through 412 removed outlier: 3.697A pdb=" N MET Q 412 " --> pdb=" O LYS Q 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 424 through 441 removed outlier: 3.737A pdb=" N ILE Q 428 " --> pdb=" O GLY Q 424 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE Q 431 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER Q 432 " --> pdb=" O ILE Q 428 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG Q 433 " --> pdb=" O GLU Q 429 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU Q 439 " --> pdb=" O THR Q 435 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG Q 440 " --> pdb=" O LYS Q 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 455 removed outlier: 4.387A 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 removed outlier: 3.629A pdb=" N VAL Q 474 " --> pdb=" O ASP Q 470 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU Q 475 " --> pdb=" O VAL Q 471 " (cutoff:3.500A) Proline residue: Q 476 - end of helix Processing helix chain 'Q' and resid 511 through 516 Processing helix chain 'Q' and resid 521 through 541 removed outlier: 3.548A pdb=" N PHE Q 526 " --> pdb=" O ALA Q 522 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN Q 529 " --> pdb=" O LYS Q 525 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL Q 530 " --> pdb=" O PHE Q 526 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL Q 538 " --> pdb=" O ALA Q 534 " (cutoff:3.500A) Processing helix chain 'z' and resid 20 through 35 removed outlier: 3.502A pdb=" N ALA z 26 " --> pdb=" O ASN z 22 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL z 32 " --> pdb=" O GLY z 28 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR z 35 " --> pdb=" O SER z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 65 removed outlier: 3.501A pdb=" N LEU z 63 " --> pdb=" O GLY z 59 " (cutoff:3.500A) Processing helix chain 'z' and resid 71 through 86 removed outlier: 4.044A pdb=" N LEU z 75 " --> pdb=" O PRO z 71 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE z 76 " --> pdb=" O THR z 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA z 81 " --> pdb=" O ALA z 77 " (cutoff:3.500A) Processing helix chain 'z' and resid 90 through 112 removed outlier: 3.708A pdb=" N VAL z 95 " --> pdb=" O THR z 91 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN z 104 " --> pdb=" O GLU z 100 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG z 107 " --> pdb=" O ARG z 103 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE z 108 " --> pdb=" O GLN z 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE z 109 " --> pdb=" O ALA z 105 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN z 110 " --> pdb=" O HIS z 106 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU z 111 " --> pdb=" O ARG z 107 " (cutoff:3.500A) Processing helix chain 'z' and resid 114 through 137 removed outlier: 3.860A pdb=" N LYS z 131 " --> pdb=" O LYS z 127 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE z 132 " --> pdb=" O GLU z 128 " (cutoff:3.500A) removed outlier: 3.593A 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: 4.199A pdb=" N GLN z 152 " --> pdb=" O GLU z 148 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER z 156 " --> pdb=" O GLN z 152 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER z 157 " --> pdb=" O VAL z 153 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU z 158 " --> pdb=" O ALA z 154 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR z 160 " --> pdb=" O SER z 156 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS z 161 " --> pdb=" O SER z 157 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL z 162 " --> pdb=" O LEU z 158 " (cutoff:3.500A) Processing helix chain 'z' and resid 166 through 182 Proline residue: z 172 - end of helix removed outlier: 3.920A pdb=" N VAL z 178 " --> pdb=" O VAL z 174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU z 179 " --> pdb=" O THR z 175 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL z 181 " --> pdb=" O ALA z 177 " (cutoff:3.500A) Processing helix chain 'z' and resid 203 through 207 removed outlier: 3.525A pdb=" N THR z 207 " --> pdb=" O PRO z 204 " (cutoff:3.500A) Processing helix chain 'z' and resid 255 through 263 removed outlier: 4.281A pdb=" N ASP z 260 " --> pdb=" O ALA z 256 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS z 261 " --> pdb=" O ASP z 257 " (cutoff:3.500A) Processing helix chain 'z' and resid 263 through 284 removed outlier: 4.743A pdb=" N PHE z 269 " --> pdb=" O SER z 265 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL z 270 " --> pdb=" O GLU z 266 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS z 273 " --> pdb=" O PHE z 269 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS z 276 " --> pdb=" O ALA z 272 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP z 279 " --> pdb=" O LYS z 275 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU z 280 " --> pdb=" O LYS z 276 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS z 281 " --> pdb=" O ILE z 277 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN z 282 " --> pdb=" O ILE z 278 " (cutoff:3.500A) Processing helix chain 'z' and resid 303 through 312 removed outlier: 4.427A pdb=" N ASP z 307 " --> pdb=" O PRO z 303 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL z 308 " --> pdb=" O MET z 304 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS z 311 " --> pdb=" O ASP z 307 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS z 312 " --> pdb=" O VAL z 308 " (cutoff:3.500A) Processing helix chain 'z' and resid 321 through 332 removed outlier: 3.535A pdb=" N GLU z 326 " --> pdb=" O ARG z 322 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG z 327 " --> pdb=" O ARG z 323 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN z 329 " --> pdb=" O MET z 325 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU z 330 " --> pdb=" O GLU z 326 " (cutoff:3.500A) Processing helix chain 'z' and resid 344 through 348 removed outlier: 3.734A pdb=" N LEU z 348 " --> pdb=" O PRO z 345 " (cutoff:3.500A) Processing helix chain 'z' and resid 384 through 408 removed outlier: 3.734A pdb=" N LEU z 388 " --> pdb=" O THR z 384 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN z 404 " --> pdb=" O ARG z 400 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL z 405 " --> pdb=" O ALA z 401 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU z 406 " --> pdb=" O VAL z 402 " (cutoff:3.500A) Processing helix chain 'z' and resid 416 through 434 removed outlier: 3.516A pdb=" N ARG z 427 " --> pdb=" O SER z 423 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER z 428 " --> pdb=" O ARG z 424 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN z 430 " --> pdb=" O LEU z 426 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET z 431 " --> pdb=" O ARG z 427 " (cutoff:3.500A) Processing helix chain 'z' and resid 439 through 451 removed outlier: 4.238A pdb=" N GLY z 443 " --> pdb=" O LYS z 439 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA z 446 " --> pdb=" O THR z 442 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE z 447 " --> pdb=" O GLY z 443 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU z 451 " --> pdb=" O PHE z 447 " (cutoff:3.500A) Processing helix chain 'z' and resid 452 through 462 removed outlier: 3.525A pdb=" N LYS z 456 " --> pdb=" O LEU z 452 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL z 459 " --> pdb=" O PRO z 455 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER z 462 " --> pdb=" O LEU z 458 " (cutoff:3.500A) Processing helix chain 'z' and resid 465 through 483 removed outlier: 3.895A pdb=" N ASP z 479 " --> pdb=" O ASP z 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA z 480 " --> pdb=" O GLU z 476 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP z 482 " --> pdb=" O ASP z 478 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER z 483 " --> pdb=" O ASP z 479 " (cutoff:3.500A) Processing helix chain 'z' and resid 500 through 505 Processing helix chain 'z' and resid 510 through 529 removed outlier: 3.544A pdb=" N ILE z 517 " --> pdb=" O LEU z 513 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR z 518 " --> pdb=" O ARG z 514 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY z 522 " --> pdb=" O THR z 518 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU z 527 " --> pdb=" O ILE z 523 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU z 528 " --> pdb=" O ALA z 524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 18 No H-bonds generated for 'chain 'Z' and resid 16 through 18' Processing helix chain 'Z' and resid 19 through 35 removed outlier: 3.521A pdb=" N VAL Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU Z 29 " --> pdb=" O SER Z 25 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR Z 35 " --> pdb=" O SER Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 65 removed outlier: 3.577A pdb=" N LEU Z 62 " --> pdb=" O ASP Z 58 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU Z 65 " --> pdb=" O VAL Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 80 removed outlier: 3.668A pdb=" N VAL Z 74 " --> pdb=" O SER Z 70 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU Z 75 " --> pdb=" O PRO Z 71 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE Z 76 " --> pdb=" O THR Z 72 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA Z 80 " --> pdb=" O ILE Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 85 removed outlier: 3.555A pdb=" N GLU Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.509A pdb=" N LEU Z 102 " --> pdb=" O VAL Z 98 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG Z 107 " --> pdb=" O ARG Z 103 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE Z 108 " --> pdb=" O GLN Z 104 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU Z 111 " --> pdb=" O ARG Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 137 removed outlier: 3.508A pdb=" N GLU Z 123 " --> pdb=" O THR Z 119 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS Z 131 " --> pdb=" O LYS Z 127 " (cutoff:3.500A) removed outlier: 3.849A 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: 4.388A pdb=" N GLN Z 152 " --> pdb=" O GLU Z 148 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL Z 153 " --> pdb=" O PHE Z 149 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER Z 156 " --> pdb=" O GLN Z 152 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER Z 157 " --> pdb=" O VAL Z 153 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS Z 161 " --> pdb=" O SER Z 157 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL Z 162 " --> pdb=" O LEU Z 158 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 182 Proline residue: Z 172 - end of helix removed outlier: 3.890A pdb=" N VAL Z 178 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU Z 179 " --> pdb=" O THR Z 175 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER Z 180 " --> pdb=" O ASP Z 176 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL Z 181 " --> pdb=" O ALA Z 177 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 192 No H-bonds generated for 'chain 'Z' and resid 190 through 192' Processing helix chain 'Z' and resid 203 through 207 Processing helix chain 'Z' and resid 255 through 284 removed outlier: 3.593A pdb=" N ARG Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP Z 260 " --> pdb=" O ALA Z 256 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS Z 261 " --> pdb=" O ASP Z 257 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU Z 266 " --> pdb=" O LEU Z 262 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE Z 269 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL Z 270 " --> pdb=" O GLU Z 266 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS Z 273 " --> pdb=" O PHE Z 269 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS Z 276 " --> pdb=" O ALA Z 272 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP Z 279 " --> pdb=" O LYS Z 275 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU Z 280 " --> pdb=" O LYS Z 276 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS Z 281 " --> pdb=" O ILE Z 277 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN Z 282 " --> pdb=" O ILE Z 278 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL Z 284 " --> pdb=" O LEU Z 280 " (cutoff:3.500A) Processing helix chain 'Z' and resid 304 through 312 removed outlier: 3.925A pdb=" N VAL Z 308 " --> pdb=" O MET Z 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS Z 311 " --> pdb=" O ASP Z 307 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS Z 312 " --> pdb=" O VAL Z 308 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 333 removed outlier: 3.841A pdb=" N GLU Z 326 " --> pdb=" O ARG Z 322 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG Z 327 " --> pdb=" O ARG Z 323 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU Z 330 " --> pdb=" O GLU Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 344 through 348 removed outlier: 3.625A pdb=" N LEU Z 348 " --> pdb=" O PRO Z 345 " (cutoff:3.500A) Processing helix chain 'Z' and resid 385 through 408 removed outlier: 3.531A pdb=" N ALA Z 389 " --> pdb=" O HIS Z 385 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR Z 391 " --> pdb=" O ALA Z 387 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN Z 404 " --> pdb=" O ARG Z 400 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL Z 405 " --> pdb=" O ALA Z 401 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 434 removed outlier: 3.574A pdb=" N SER Z 428 " --> pdb=" O ARG Z 424 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN Z 430 " --> pdb=" O LEU Z 426 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N MET Z 431 " --> pdb=" O ARG Z 427 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN Z 432 " --> pdb=" O SER Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 440 through 451 removed outlier: 3.515A pdb=" N LEU Z 451 " --> pdb=" O PHE Z 447 " (cutoff:3.500A) Processing helix chain 'Z' and resid 452 through 463 removed outlier: 3.570A pdb=" N LYS Z 456 " --> pdb=" O LEU Z 452 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL Z 459 " --> pdb=" O PRO Z 455 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER Z 462 " --> pdb=" O LEU Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 465 through 483 removed outlier: 3.520A pdb=" N VAL Z 469 " --> pdb=" O ASP Z 465 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP Z 478 " --> pdb=" O GLU Z 474 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP Z 479 " --> pdb=" O ASP Z 475 " (cutoff:3.500A) removed outlier: 3.716A 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: 3.815A pdb=" N LEU Z 528 " --> pdb=" O ALA Z 524 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Z 529 " --> pdb=" O SER Z 525 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.854A pdb=" N THR H 61 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 53 " --> pdb=" O THR H 61 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER H 63 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE H 51 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 555 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 199 through 205 removed outlier: 6.550A pdb=" N GLY H 200 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU H 378 " --> pdb=" O GLY H 200 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS H 202 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY H 380 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE H 204 " --> pdb=" O GLY H 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 241 through 244 removed outlier: 3.996A pdb=" N LEU H 294 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 351 through 355 removed outlier: 3.711A pdb=" N GLU H 353 " --> pdb=" O LEU H 364 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU H 364 " --> pdb=" O GLU H 353 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 409 through 411 Processing sheet with id=AA6, first strand: chain 'H' and resid 479 through 481 removed outlier: 3.810A pdb=" N GLY H 489 " --> pdb=" O GLY H 480 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 523 through 525 Processing sheet with id=AA8, first strand: chain 'a' and resid 19 through 20 removed outlier: 4.002A pdb=" N ILE a 541 " --> pdb=" O ASP d 45 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET d 47 " --> pdb=" O ILE a 541 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR a 543 " --> pdb=" O MET d 47 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LYS d 49 " --> pdb=" O THR a 543 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE a 545 " --> pdb=" O LYS d 49 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS d 46 " --> pdb=" O SER d 58 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER d 58 " --> pdb=" O LYS d 46 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE d 48 " --> pdb=" O ILE d 56 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE d 56 " --> pdb=" O ILE d 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 62 through 63 removed outlier: 4.358A pdb=" N THR a 63 " --> pdb=" O LYS a 51 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS a 51 " --> pdb=" O THR a 63 " (cutoff:3.500A) removed outlier: 3.635A 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: 5.998A pdb=" N ASN a 204 " --> pdb=" O ILE a 385 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU a 387 " --> pdb=" O ASN a 204 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU a 206 " --> pdb=" O LEU a 387 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER a 384 " --> pdb=" O VAL a 219 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL a 219 " --> pdb=" O SER a 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'a' and resid 222 through 225 removed outlier: 7.819A pdb=" N GLY a 376 " --> pdb=" O ASP a 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 244 through 246 removed outlier: 3.735A pdb=" N LEU a 297 " --> pdb=" O ALA a 245 " (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 'A' and resid 18 through 21 removed outlier: 6.140A pdb=" N THR A 543 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LYS D 49 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A 545 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS D 46 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER D 58 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D 48 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'A' and resid 206 through 208 removed outlier: 6.095A pdb=" N LEU A 206 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 384 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 219 " --> pdb=" O SER A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 222 through 225 removed outlier: 3.667A pdb=" N LYS A 375 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 360 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR A 377 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N CYS A 358 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.612A pdb=" N LEU A 247 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 298 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AC2, first strand: chain 'b' and resid 55 through 57 removed outlier: 3.832A pdb=" N MET b 55 " --> pdb=" O LEU b 46 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU b 46 " --> pdb=" O MET b 55 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR b 57 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS b 44 " --> pdb=" O THR b 57 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP b 43 " --> pdb=" O ILE d 521 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASP d 523 " --> pdb=" O ASP b 43 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU b 45 " --> pdb=" O ASP d 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA d 525 " --> pdb=" O LEU b 45 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'b' and resid 193 through 198 removed outlier: 6.210A pdb=" N GLN b 194 " --> pdb=" O ILE b 367 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU b 369 " --> pdb=" O GLN b 194 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE b 196 " --> pdb=" O LEU b 369 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 225 through 229 removed outlier: 7.125A pdb=" N ASP b 341 " --> pdb=" O ASN b 228 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N CYS b 340 " --> pdb=" O CYS b 359 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS b 359 " --> pdb=" O CYS b 340 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b' and resid 231 through 233 removed outlier: 7.320A pdb=" N LEU b 232 " --> pdb=" O ILE b 285 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 400 through 402 Processing sheet with id=AC7, first strand: chain 'b' and resid 470 through 473 removed outlier: 3.568A pdb=" N THR b 478 " --> pdb=" O ASP b 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 55 through 57 removed outlier: 3.687A pdb=" N MET B 55 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR B 57 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS B 44 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP B 43 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP D 523 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 45 " --> pdb=" O ASP D 523 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA D 525 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 193 through 199 removed outlier: 3.631A pdb=" N VAL B 368 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE B 207 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 212 through 215 removed outlier: 6.032A pdb=" N CYS B 359 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS B 340 " --> pdb=" O CYS B 359 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 338 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 342 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU B 227 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLU B 344 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ARG B 225 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 212 through 215 Processing sheet with id=AD3, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AD4, first strand: chain 'B' and resid 400 through 402 Processing sheet with id=AD5, first strand: chain 'B' and resid 470 through 473 Processing sheet with id=AD6, first strand: chain 'B' and resid 511 through 514 removed outlier: 7.951A pdb=" N ILE E 73 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE B 514 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ILE E 75 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS E 72 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR E 84 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 197 through 200 removed outlier: 6.291A pdb=" N VAL d 197 " --> pdb=" O ILE d 379 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLY d 381 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS d 199 " --> pdb=" O GLY d 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'd' and resid 213 through 214 removed outlier: 3.690A pdb=" N VAL d 213 " --> pdb=" O VAL d 363 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL d 363 " --> pdb=" O VAL d 213 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE d 360 " --> pdb=" O ILE d 353 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU d 351 " --> pdb=" O ARG d 362 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR d 364 " --> pdb=" O LEU d 349 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU d 349 " --> pdb=" O THR d 364 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP d 348 " --> pdb=" O LYS d 231 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 234 through 237 removed outlier: 4.301A pdb=" N GLY d 235 " --> pdb=" O VAL d 285 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU d 287 " --> pdb=" O GLY d 235 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN d 289 " --> pdb=" O ILE d 237 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU d 286 " --> pdb=" O VAL d 313 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASP d 315 " --> pdb=" O LEU d 286 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE d 288 " --> pdb=" O ASP d 315 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 196 through 200 removed outlier: 3.738A pdb=" N GLY D 381 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 213 through 214 removed outlier: 3.849A pdb=" N VAL D 363 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 360 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU D 351 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR D 364 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 4.311A 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=AE3, first strand: chain 'D' and resid 285 through 289 removed outlier: 10.011A pdb=" N LEU D 286 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ILE D 316 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE D 288 " --> pdb=" O ILE D 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 410 through 411 Processing sheet with id=AE5, first strand: chain 'e' and resid 72 through 75 removed outlier: 3.625A pdb=" N LYS e 72 " --> pdb=" O THR e 84 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR e 84 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR e 82 " --> pdb=" O LEU e 74 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'e' and resid 166 through 167 removed outlier: 3.705A pdb=" N ASP e 166 " --> pdb=" O VAL e 439 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'e' and resid 224 through 230 removed outlier: 6.417A pdb=" N LYS e 225 " --> pdb=" O CYS e 406 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL e 408 " --> pdb=" O LYS e 225 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLN e 227 " --> pdb=" O VAL e 408 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N GLY e 410 " --> pdb=" O GLN e 227 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG e 229 " --> pdb=" O GLY e 410 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 342 through 343 removed outlier: 6.511A pdb=" N VAL e 321 " --> pdb=" O VAL e 343 " (cutoff:3.500A) removed outlier: 3.659A 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: 4.378A pdb=" N ARG e 379 " --> pdb=" O GLU e 396 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU e 396 " --> pdb=" O ARG e 379 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR e 381 " --> pdb=" O ILE e 394 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'e' and resid 554 through 556 removed outlier: 7.199A pdb=" N ILE e 555 " --> pdb=" O VAL h 54 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE h 51 " --> pdb=" O SER h 63 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER h 63 " --> pdb=" O ILE h 51 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE h 53 " --> pdb=" O THR h 61 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR h 61 " --> pdb=" O ILE h 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 224 through 230 removed outlier: 6.322A pdb=" N LYS E 225 " --> pdb=" O CYS E 406 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL E 408 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN E 227 " --> pdb=" O VAL E 408 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N GLY E 410 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG E 229 " --> pdb=" O GLY E 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 269 through 272 removed outlier: 6.307A pdb=" N VAL E 321 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 380 through 382 Processing sheet with id=AF5, first strand: chain 'g' and resid 55 through 56 Processing sheet with id=AF6, first strand: chain 'g' and resid 141 through 142 Processing sheet with id=AF7, first strand: chain 'g' and resid 206 through 208 removed outlier: 3.800A pdb=" N GLU g 207 " --> pdb=" O ILE g 439 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU g 441 " --> pdb=" O GLU g 207 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 224 through 225 removed outlier: 3.789A pdb=" N LEU g 225 " --> pdb=" O SER g 366 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 294 through 296 Processing sheet with id=AG1, first strand: chain 'g' and resid 542 through 544 removed outlier: 3.722A pdb=" N VAL g 552 " --> pdb=" O GLY g 543 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 55 through 56 removed outlier: 4.259A pdb=" N VAL G 56 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU G 48 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AG4, first strand: chain 'G' and resid 206 through 208 Processing sheet with id=AG5, first strand: chain 'G' and resid 294 through 296 Processing sheet with id=AG6, first strand: chain 'G' and resid 542 through 544 removed outlier: 3.502A pdb=" N VAL G 552 " --> pdb=" O GLY G 543 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 201 through 205 removed outlier: 3.691A pdb=" N LEU h 378 " --> pdb=" O LYS h 202 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY h 380 " --> pdb=" O ILE h 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR h 375 " --> pdb=" O ILE h 215 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE h 215 " --> pdb=" O THR h 375 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU h 377 " --> pdb=" O LEU h 213 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU h 213 " --> pdb=" O LEU h 377 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'h' and resid 241 through 243 removed outlier: 6.211A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'h' and resid 351 through 355 removed outlier: 3.696A pdb=" N LEU h 351 " --> pdb=" O GLN h 366 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN h 366 " --> pdb=" O LEU h 351 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU h 353 " --> pdb=" O LEU h 364 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU h 364 " --> pdb=" O GLU h 353 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 409 through 411 Processing sheet with id=AH2, first strand: chain 'h' and resid 479 through 481 removed outlier: 3.887A pdb=" N GLY h 489 " --> pdb=" O GLY h 480 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'q' and resid 53 through 56 removed outlier: 3.682A pdb=" N LYS q 53 " --> pdb=" O THR q 65 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR q 65 " --> pdb=" O LYS q 53 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE q 55 " --> pdb=" O ILE q 63 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'q' and resid 207 through 213 removed outlier: 3.508A pdb=" N VAL q 210 " --> pdb=" O ILE q 384 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE q 212 " --> pdb=" O LEU q 386 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY q 388 " --> pdb=" O ILE q 212 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR q 383 " --> pdb=" O ILE q 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE q 223 " --> pdb=" O THR q 383 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'q' and resid 319 through 322 removed outlier: 7.427A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N LEU q 341 " --> pdb=" O VAL q 247 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL q 249 " --> pdb=" O LEU q 341 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'q' and resid 319 through 322 removed outlier: 7.427A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'q' and resid 360 through 363 removed outlier: 4.006A pdb=" N ASP q 366 " --> pdb=" O ILE q 363 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'q' and resid 419 through 421 Processing sheet with id=AH9, first strand: chain 'q' and resid 544 through 545 removed outlier: 4.028A pdb=" N ILE q 545 " --> pdb=" O MET z 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'Q' and resid 207 through 213 removed outlier: 3.911A pdb=" N ILE Q 384 " --> pdb=" O ARG Q 208 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL Q 210 " --> pdb=" O ILE Q 384 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU Q 386 " --> pdb=" O VAL Q 210 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE Q 212 " --> pdb=" O LEU Q 386 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY Q 388 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE Q 385 " --> pdb=" O THR Q 221 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR Q 221 " --> pdb=" O ILE Q 385 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 319 through 322 removed outlier: 3.551A pdb=" N LEU Q 321 " --> pdb=" O ILE Q 299 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N LEU Q 341 " --> pdb=" O VAL Q 247 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL Q 249 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 319 through 322 removed outlier: 3.551A pdb=" N LEU Q 321 " --> pdb=" O ILE Q 299 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 357 through 363 removed outlier: 3.962A pdb=" N THR Q 357 " --> pdb=" O LYS Q 372 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS Q 372 " --> pdb=" O THR Q 357 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS Q 359 " --> pdb=" O VAL Q 370 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP Q 366 " --> pdb=" O ILE Q 363 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 419 through 421 Processing sheet with id=AI6, first strand: chain 'Q' and resid 544 through 545 removed outlier: 6.196A pdb=" N ILE Q 545 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS Z 54 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'z' and resid 138 through 139 Processing sheet with id=AI8, first strand: chain 'z' and resid 194 through 199 removed outlier: 6.452A pdb=" N GLU z 195 " --> pdb=" O ILE z 378 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE z 380 " --> pdb=" O GLU z 195 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N MET z 197 " --> pdb=" O ILE z 380 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'z' and resid 227 through 228 Processing sheet with id=AJ1, first strand: chain 'z' and resid 231 through 234 removed outlier: 5.963A pdb=" N TYR z 232 " --> pdb=" O VAL z 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'z' and resid 490 through 491 Processing sheet with id=AJ3, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AJ4, first strand: chain 'Z' and resid 194 through 197 removed outlier: 6.235A pdb=" N GLU Z 195 " --> pdb=" O ILE Z 378 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Z' and resid 227 through 228 Processing sheet with id=AJ6, first strand: chain 'Z' and resid 292 through 295 removed outlier: 6.032A pdb=" N TYR Z 232 " --> pdb=" O VAL Z 294 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N GLN Z 337 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE Z 235 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'Z' and resid 490 through 491 2511 hydrogen bonds defined for protein. 7281 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: 19.95 Time building geometry restraints manager: 19.46 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: 20992 1.34 - 1.46: 11340 1.46 - 1.58: 29853 1.58 - 1.69: 0 1.69 - 1.81: 512 Bond restraints: 62697 Sorted by residual: bond pdb=" C ALA q 346 " pdb=" N PRO q 347 " ideal model delta sigma weight residual 1.334 1.433 -0.100 2.34e-02 1.83e+03 1.81e+01 bond pdb=" C VAL a 219 " pdb=" N PRO a 220 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.16e+00 bond pdb=" C SER G 469 " pdb=" N PRO G 470 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.80e+00 bond pdb=" CA ARG Z 15 " pdb=" C ARG Z 15 " ideal model delta sigma weight residual 1.520 1.532 -0.012 1.16e-02 7.43e+03 1.02e+00 bond pdb=" CA ARG Z 14 " pdb=" CB ARG Z 14 " ideal model delta sigma weight residual 1.530 1.545 -0.014 1.54e-02 4.22e+03 8.85e-01 ... (remaining 62692 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.23: 1380 107.23 - 113.91: 37313 113.91 - 120.60: 25118 120.60 - 127.28: 20361 127.28 - 133.96: 388 Bond angle restraints: 84560 Sorted by residual: angle pdb=" C SER Z 12 " pdb=" CA SER Z 12 " pdb=" CB SER Z 12 " ideal model delta sigma weight residual 115.79 109.77 6.02 1.19e+00 7.06e-01 2.56e+01 angle pdb=" C ASP Z 187 " pdb=" CA ASP Z 187 " pdb=" CB ASP Z 187 " ideal model delta sigma weight residual 116.54 110.98 5.56 1.15e+00 7.56e-01 2.33e+01 angle pdb=" CA ASP Z 187 " pdb=" C ASP Z 187 " pdb=" N ASN Z 188 " ideal model delta sigma weight residual 119.52 116.67 2.85 7.90e-01 1.60e+00 1.30e+01 angle pdb=" C LEU Z 13 " pdb=" N ARG Z 14 " pdb=" CA ARG Z 14 " ideal model delta sigma weight residual 122.08 127.36 -5.28 1.47e+00 4.63e-01 1.29e+01 angle pdb=" N GLU Z 11 " pdb=" CA GLU Z 11 " pdb=" C GLU Z 11 " ideal model delta sigma weight residual 108.38 112.73 -4.35 1.35e+00 5.49e-01 1.04e+01 ... (remaining 84555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 38344 16.18 - 32.36: 334 32.36 - 48.54: 199 48.54 - 64.72: 59 64.72 - 80.90: 3 Dihedral angle restraints: 38939 sinusoidal: 15590 harmonic: 23349 Sorted by residual: dihedral pdb=" CA PHE E 276 " pdb=" C PHE E 276 " pdb=" N GLU E 277 " pdb=" CA GLU E 277 " ideal model delta harmonic sigma weight residual -180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ALA H 273 " pdb=" C ALA H 273 " pdb=" N GLU H 274 " pdb=" CA GLU H 274 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ASP H 272 " pdb=" C ASP H 272 " pdb=" N ALA H 273 " pdb=" CA ALA H 273 " ideal model delta harmonic sigma weight residual 180.00 -158.29 -21.71 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 38936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 7152 0.034 - 0.069: 2193 0.069 - 0.103: 490 0.103 - 0.138: 335 0.138 - 0.172: 5 Chirality restraints: 10175 Sorted by residual: chirality pdb=" CB ILE e 244 " pdb=" CA ILE e 244 " pdb=" CG1 ILE e 244 " pdb=" CG2 ILE e 244 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CB ILE A 196 " pdb=" CA ILE A 196 " pdb=" CG1 ILE A 196 " pdb=" CG2 ILE A 196 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.38e-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 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 10172 not shown) Planarity restraints: 10863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 276 " 0.016 2.00e-02 2.50e+03 1.46e-02 3.72e+00 pdb=" CG PHE E 276 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE E 276 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE E 276 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 276 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 276 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 372 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO D 373 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 373 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 373 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 270 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" C ILE H 270 " 0.018 2.00e-02 2.50e+03 pdb=" O ILE H 270 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL H 271 " -0.006 2.00e-02 2.50e+03 ... (remaining 10860 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 11351 2.77 - 3.30: 57385 3.30 - 3.84: 91825 3.84 - 4.37: 108870 4.37 - 4.90: 187043 Nonbonded interactions: 456474 Sorted by model distance: nonbonded pdb=" O LEU H 198 " pdb=" OG1 THR H 373 " model vdw 2.241 2.440 nonbonded pdb=" O ILE H 62 " pdb=" NH1 ARG H 391 " model vdw 2.267 2.520 nonbonded pdb=" O VAL Z 367 " pdb=" ND2 ASN Z 370 " model vdw 2.274 2.520 nonbonded pdb=" O ILE E 354 " pdb=" OG1 THR E 358 " model vdw 2.279 2.440 nonbonded pdb=" O PRO q 421 " pdb=" OG1 THR q 426 " model vdw 2.280 2.440 ... (remaining 456469 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' and (resid 18 through 256 or resid 273 through 547)) selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'D' and (resid 17 through 246 or resid 263 through 479 or resid 492 throu \ gh 528)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 43 through 281 or resid 301 through 560)) selection = (chain 'e' and resid 43 through 560) } ncs_group { reference = (chain 'G' and (resid 18 through 253 or resid 276 through 590)) selection = (chain 'g' and resid 18 through 590) } ncs_group { reference = (chain 'H' and (resid 23 through 250 or resid 278 through 528)) selection = (chain 'h' and resid 23 through 528) } ncs_group { reference = (chain 'Q' and resid 26 through 549) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } 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: 0.750 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: 5.980 Check model and map are aligned: 0.690 Set scattering table: 0.420 Process input model: 121.010 Find NCS groups from input model: 5.600 Set up NCS constraints: 0.370 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 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 0.100 62697 Z= 0.082 Angle : 0.391 9.163 84560 Z= 0.222 Chirality : 0.039 0.172 10175 Planarity : 0.001 0.036 10863 Dihedral : 7.113 80.896 23803 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -3.50 (0.07), residues: 8076 helix: -3.60 (0.04), residues: 3560 sheet: -0.82 (0.20), residues: 528 loop : -1.11 (0.08), residues: 3988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP E 325 HIS 0.003 0.000 HIS Q 39 PHE 0.034 0.001 PHE E 276 TYR 0.008 0.001 TYR G 502 ARG 0.002 0.000 ARG a 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2816 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2816 time to evaluate : 5.315 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: H 30 ILE cc_start: 0.9250 (mt) cc_final: 0.9014 (mt) REVERT: H 33 CYS cc_start: 0.8995 (m) cc_final: 0.8594 (m) REVERT: H 37 GLN cc_start: 0.8919 (tt0) cc_final: 0.8309 (tt0) REVERT: H 49 SER cc_start: 0.9064 (m) cc_final: 0.8734 (m) REVERT: H 163 ARG cc_start: 0.7414 (mtt-85) cc_final: 0.5979 (ptp90) REVERT: H 195 ASP cc_start: 0.7195 (t0) cc_final: 0.6940 (t0) REVERT: H 226 TYR cc_start: 0.5866 (m-80) cc_final: 0.5620 (m-80) REVERT: H 281 LYS cc_start: 0.7175 (mttt) cc_final: 0.6715 (ptpt) REVERT: H 452 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8204 (mm-40) REVERT: H 462 ILE cc_start: 0.8556 (mt) cc_final: 0.8292 (mp) REVERT: H 479 TYR cc_start: 0.6118 (m-10) cc_final: 0.5566 (m-80) REVERT: H 481 VAL cc_start: 0.7094 (t) cc_final: 0.6578 (t) REVERT: H 509 SER cc_start: 0.8882 (m) cc_final: 0.8309 (p) REVERT: a 81 LYS cc_start: 0.8468 (mttt) cc_final: 0.8241 (mtmt) REVERT: a 98 THR cc_start: 0.8647 (m) cc_final: 0.8071 (t) REVERT: a 121 HIS cc_start: 0.7689 (t-90) cc_final: 0.7238 (t-90) REVERT: a 201 LYS cc_start: 0.6128 (pttt) cc_final: 0.5728 (tptt) REVERT: a 280 ILE cc_start: 0.3890 (mt) cc_final: 0.3500 (tp) REVERT: a 315 ILE cc_start: 0.3859 (mt) cc_final: 0.3620 (mt) REVERT: a 341 MET cc_start: -0.1619 (mtp) cc_final: -0.2488 (ptt) REVERT: a 486 MET cc_start: 0.8398 (mtt) cc_final: 0.8046 (ppp) REVERT: a 497 TYR cc_start: 0.7102 (m-80) cc_final: 0.6806 (m-10) REVERT: a 526 LYS cc_start: 0.9306 (mttt) cc_final: 0.9011 (mmmt) REVERT: a 540 ARG cc_start: 0.7374 (mtp85) cc_final: 0.7152 (mmm160) REVERT: A 27 ASN cc_start: 0.8469 (m-40) cc_final: 0.8028 (p0) REVERT: A 125 ILE cc_start: 0.9374 (mt) cc_final: 0.9168 (mt) REVERT: A 129 PHE cc_start: 0.9090 (m-10) cc_final: 0.8710 (m-80) REVERT: A 243 LYS cc_start: 0.7338 (mttt) cc_final: 0.6672 (mmtt) REVERT: A 360 GLU cc_start: 0.2629 (tt0) cc_final: 0.1902 (pt0) REVERT: A 406 LEU cc_start: 0.8052 (tp) cc_final: 0.7743 (mm) REVERT: A 411 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7577 (mmm-85) REVERT: A 526 LYS cc_start: 0.8868 (mttt) cc_final: 0.8419 (tttt) REVERT: A 532 LEU cc_start: 0.9489 (mp) cc_final: 0.8681 (tp) REVERT: b 97 VAL cc_start: 0.9461 (t) cc_final: 0.9149 (p) REVERT: b 107 GLU cc_start: 0.8672 (tt0) cc_final: 0.8409 (pt0) REVERT: b 120 ILE cc_start: 0.8092 (mt) cc_final: 0.7113 (mt) REVERT: b 121 ILE cc_start: 0.9160 (mt) cc_final: 0.8178 (mt) REVERT: b 124 TYR cc_start: 0.8720 (m-10) cc_final: 0.8486 (m-80) REVERT: b 212 PHE cc_start: 0.6913 (t80) cc_final: 0.6668 (m-80) REVERT: b 402 LEU cc_start: 0.9326 (mt) cc_final: 0.9106 (mt) REVERT: b 409 MET cc_start: 0.8466 (tpp) cc_final: 0.6700 (tpp) REVERT: b 431 GLU cc_start: 0.8955 (tt0) cc_final: 0.8721 (tt0) REVERT: B 45 LEU cc_start: 0.7897 (mt) cc_final: 0.6938 (mt) REVERT: B 154 ILE cc_start: 0.3626 (tt) cc_final: 0.3242 (mt) REVERT: B 156 ILE cc_start: 0.5717 (mt) cc_final: 0.5361 (tp) REVERT: B 268 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8501 (tmtt) REVERT: B 328 THR cc_start: 0.5431 (p) cc_final: 0.4586 (t) REVERT: B 457 SER cc_start: 0.8841 (m) cc_final: 0.8598 (p) REVERT: B 472 LEU cc_start: 0.6409 (mt) cc_final: 0.5517 (mt) REVERT: d 116 HIS cc_start: 0.6565 (t-90) cc_final: 0.6358 (t-90) REVERT: d 166 TYR cc_start: 0.8385 (m-80) cc_final: 0.8127 (m-80) REVERT: d 305 LEU cc_start: 0.5318 (mt) cc_final: 0.5113 (pp) REVERT: d 385 MET cc_start: 0.5586 (mmm) cc_final: 0.5375 (mmm) REVERT: d 439 ILE cc_start: 0.9119 (mt) cc_final: 0.8469 (mt) REVERT: d 448 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8587 (mt-10) REVERT: d 513 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8338 (mp0) REVERT: d 522 ASP cc_start: 0.7522 (p0) cc_final: 0.7269 (p0) REVERT: D 38 SER cc_start: 0.9293 (m) cc_final: 0.8985 (t) REVERT: D 72 HIS cc_start: 0.7860 (t-90) cc_final: 0.6430 (m90) REVERT: D 74 VAL cc_start: 0.9372 (t) cc_final: 0.8868 (t) REVERT: D 85 GLN cc_start: 0.8979 (tp40) cc_final: 0.8390 (tm-30) REVERT: D 111 LEU cc_start: 0.9195 (mt) cc_final: 0.8836 (mt) REVERT: D 112 ASN cc_start: 0.8727 (m-40) cc_final: 0.8440 (p0) REVERT: D 148 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7948 (tt0) REVERT: D 198 LYS cc_start: 0.7122 (mtmt) cc_final: 0.6824 (mtpt) REVERT: D 260 MET cc_start: 0.5972 (ttp) cc_final: 0.5675 (tpt) REVERT: D 315 ASP cc_start: 0.4607 (m-30) cc_final: 0.3923 (m-30) REVERT: D 388 ASP cc_start: 0.6235 (m-30) cc_final: 0.5863 (m-30) REVERT: D 399 CYS cc_start: 0.8010 (m) cc_final: 0.7501 (p) REVERT: D 447 LEU cc_start: 0.9322 (mt) cc_final: 0.8941 (tp) REVERT: D 465 VAL cc_start: 0.9023 (t) cc_final: 0.8688 (p) REVERT: e 94 MET cc_start: 0.6994 (mtp) cc_final: 0.6655 (tpt) REVERT: e 103 LEU cc_start: 0.8884 (mt) cc_final: 0.8604 (mm) REVERT: e 115 ILE cc_start: 0.8594 (mt) cc_final: 0.7296 (mt) REVERT: e 122 VAL cc_start: 0.9060 (t) cc_final: 0.8733 (p) REVERT: e 127 SER cc_start: 0.9676 (m) cc_final: 0.9256 (p) REVERT: e 130 LEU cc_start: 0.9020 (mt) cc_final: 0.8444 (tt) REVERT: e 132 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7925 (mm-40) REVERT: e 229 ARG cc_start: 0.7370 (mmt-90) cc_final: 0.7007 (mtp180) REVERT: e 353 HIS cc_start: 0.7349 (m-70) cc_final: 0.7093 (m-70) REVERT: e 405 THR cc_start: 0.7786 (m) cc_final: 0.7234 (p) REVERT: e 464 ILE cc_start: 0.8434 (mt) cc_final: 0.8197 (mt) REVERT: e 467 TYR cc_start: 0.8047 (m-10) cc_final: 0.7844 (m-10) REVERT: e 477 ASP cc_start: 0.8682 (m-30) cc_final: 0.8435 (t70) REVERT: e 478 THR cc_start: 0.9284 (m) cc_final: 0.8745 (t) REVERT: e 479 ILE cc_start: 0.9077 (mm) cc_final: 0.8804 (mm) REVERT: e 486 ASN cc_start: 0.8934 (m-40) cc_final: 0.8051 (t0) REVERT: e 495 LEU cc_start: 0.8483 (tp) cc_final: 0.8061 (tp) REVERT: e 544 LEU cc_start: 0.8875 (tp) cc_final: 0.8517 (tp) REVERT: e 552 ASP cc_start: 0.7882 (p0) cc_final: 0.7587 (p0) REVERT: E 51 ILE cc_start: 0.8636 (mm) cc_final: 0.8420 (mm) REVERT: E 120 THR cc_start: 0.8541 (m) cc_final: 0.8320 (m) REVERT: E 130 LEU cc_start: 0.9038 (mt) cc_final: 0.8563 (tt) REVERT: E 144 ILE cc_start: 0.8432 (mm) cc_final: 0.7983 (mm) REVERT: E 160 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7397 (tptt) REVERT: E 185 LYS cc_start: 0.8341 (tttt) cc_final: 0.8116 (mttm) REVERT: E 406 CYS cc_start: 0.6781 (m) cc_final: 0.6455 (m) REVERT: E 454 VAL cc_start: 0.9466 (t) cc_final: 0.9248 (p) REVERT: E 477 ASP cc_start: 0.8507 (m-30) cc_final: 0.8130 (t0) REVERT: E 481 MET cc_start: 0.8261 (mtp) cc_final: 0.6702 (mtp) REVERT: E 544 LEU cc_start: 0.9167 (tp) cc_final: 0.8927 (tp) REVERT: E 547 MET cc_start: 0.8718 (mtp) cc_final: 0.8248 (mtp) REVERT: g 115 ASN cc_start: 0.8331 (t0) cc_final: 0.7952 (p0) REVERT: g 153 LYS cc_start: 0.8981 (mttt) cc_final: 0.8392 (pttm) REVERT: g 171 MET cc_start: 0.0691 (mmm) cc_final: 0.0019 (tpt) REVERT: g 242 ARG cc_start: 0.5987 (mtm-85) cc_final: 0.5413 (ttp-170) REVERT: g 295 VAL cc_start: 0.1470 (t) cc_final: 0.1169 (t) REVERT: g 364 TYR cc_start: 0.6943 (m-80) cc_final: 0.6706 (m-10) REVERT: g 445 SER cc_start: 0.6039 (p) cc_final: 0.5736 (t) REVERT: g 531 LEU cc_start: 0.9574 (tp) cc_final: 0.8806 (tp) REVERT: g 555 VAL cc_start: 0.8657 (t) cc_final: 0.8238 (t) REVERT: g 584 ASP cc_start: 0.6671 (p0) cc_final: 0.5899 (p0) REVERT: G 45 LEU cc_start: 0.9096 (mt) cc_final: 0.8753 (mt) REVERT: G 48 LEU cc_start: 0.8413 (mp) cc_final: 0.7799 (mp) REVERT: G 79 LEU cc_start: 0.9326 (mt) cc_final: 0.9109 (mt) REVERT: G 85 GLN cc_start: 0.8424 (tp40) cc_final: 0.7382 (tm-30) REVERT: G 152 LYS cc_start: 0.8505 (mttt) cc_final: 0.8087 (pptt) REVERT: G 166 HIS cc_start: 0.6944 (m-70) cc_final: 0.6629 (t70) REVERT: G 202 ARG cc_start: 0.8186 (mtm180) cc_final: 0.7690 (mtm110) REVERT: G 359 MET cc_start: -0.0207 (ttp) cc_final: -0.0879 (ttp) REVERT: G 515 THR cc_start: 0.9008 (m) cc_final: 0.8749 (m) REVERT: G 531 LEU cc_start: 0.9326 (tp) cc_final: 0.8223 (tp) REVERT: G 554 MET cc_start: 0.8688 (mmp) cc_final: 0.8198 (mmt) REVERT: h 28 SER cc_start: 0.9240 (t) cc_final: 0.8822 (p) REVERT: h 41 LYS cc_start: 0.9012 (mttt) cc_final: 0.8770 (mtpt) REVERT: h 44 LEU cc_start: 0.8901 (tp) cc_final: 0.8407 (tp) REVERT: h 108 LEU cc_start: 0.9257 (tp) cc_final: 0.8891 (tt) REVERT: h 139 LYS cc_start: 0.8681 (tptt) cc_final: 0.8349 (tptm) REVERT: h 143 LEU cc_start: 0.9101 (mt) cc_final: 0.8739 (mt) REVERT: h 159 GLU cc_start: 0.4989 (mt-10) cc_final: 0.3430 (tt0) REVERT: h 190 ASP cc_start: 0.3112 (t0) cc_final: 0.2824 (t70) REVERT: h 215 ILE cc_start: 0.7594 (mm) cc_final: 0.7321 (mp) REVERT: h 216 ASN cc_start: 0.4524 (m-40) cc_final: 0.3668 (t0) REVERT: h 322 ASP cc_start: 0.6489 (m-30) cc_final: 0.5518 (t0) REVERT: h 362 TYR cc_start: 0.2460 (m-80) cc_final: 0.1962 (m-10) REVERT: h 438 ILE cc_start: 0.9386 (mt) cc_final: 0.8499 (mt) REVERT: h 439 ILE cc_start: 0.9546 (mt) cc_final: 0.9231 (mm) REVERT: h 449 ILE cc_start: 0.9037 (mt) cc_final: 0.8824 (mp) REVERT: h 452 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8076 (mm-40) REVERT: h 460 ASP cc_start: 0.8120 (t0) cc_final: 0.7723 (t0) REVERT: h 476 GLU cc_start: 0.8177 (tp30) cc_final: 0.7899 (tt0) REVERT: h 512 GLU cc_start: 0.8637 (tt0) cc_final: 0.7965 (tp30) REVERT: q 76 ASP cc_start: 0.8078 (t0) cc_final: 0.7649 (p0) REVERT: q 83 LYS cc_start: 0.9234 (mttt) cc_final: 0.8861 (mptt) REVERT: q 87 MET cc_start: 0.8322 (mtp) cc_final: 0.7471 (tpt) REVERT: q 92 GLN cc_start: 0.7619 (tp40) cc_final: 0.6875 (tp40) REVERT: q 136 LYS cc_start: 0.8572 (mttt) cc_final: 0.8211 (ttmt) REVERT: q 170 LYS cc_start: 0.8245 (mttm) cc_final: 0.8030 (mptt) REVERT: q 240 SER cc_start: 0.7773 (p) cc_final: 0.6650 (t) REVERT: q 241 GLU cc_start: 0.4195 (mt-10) cc_final: 0.3810 (pm20) REVERT: q 431 ILE cc_start: 0.9733 (mt) cc_final: 0.9409 (tp) REVERT: q 432 SER cc_start: 0.9303 (m) cc_final: 0.8907 (p) REVERT: q 436 LYS cc_start: 0.9081 (tttt) cc_final: 0.8831 (mmtm) REVERT: q 451 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8162 (mm110) REVERT: q 454 VAL cc_start: 0.9374 (t) cc_final: 0.8720 (p) REVERT: q 461 ARG cc_start: 0.8322 (ttm110) cc_final: 0.8024 (mtm110) REVERT: q 470 ASP cc_start: 0.7646 (t0) cc_final: 0.7311 (t0) REVERT: q 523 THR cc_start: 0.8471 (m) cc_final: 0.8033 (p) REVERT: Q 86 VAL cc_start: 0.9701 (t) cc_final: 0.9478 (p) REVERT: Q 104 MET cc_start: 0.7647 (mmm) cc_final: 0.7242 (mmm) REVERT: Q 109 GLU cc_start: 0.8625 (tp30) cc_final: 0.8407 (tp30) REVERT: Q 128 ILE cc_start: 0.9366 (mt) cc_final: 0.8887 (tp) REVERT: Q 135 ARG cc_start: 0.7803 (ttp-170) cc_final: 0.7405 (ttm110) REVERT: Q 152 ASP cc_start: 0.7203 (m-30) cc_final: 0.6695 (m-30) REVERT: Q 153 LYS cc_start: 0.7928 (tttt) cc_final: 0.7387 (mmtt) REVERT: Q 161 LYS cc_start: 0.9024 (mttt) cc_final: 0.8635 (ttpt) REVERT: Q 162 MET cc_start: 0.7749 (tpp) cc_final: 0.6714 (tpp) REVERT: Q 202 PHE cc_start: 0.7226 (t80) cc_final: 0.6983 (t80) REVERT: Q 204 VAL cc_start: 0.7813 (t) cc_final: 0.7592 (m) REVERT: Q 227 VAL cc_start: 0.7805 (t) cc_final: 0.7571 (t) REVERT: Q 230 ARG cc_start: 0.5651 (mtp85) cc_final: 0.5347 (ptm160) REVERT: Q 235 HIS cc_start: 0.7265 (m170) cc_final: 0.6898 (t70) REVERT: Q 287 MET cc_start: 0.5854 (mmp) cc_final: 0.5496 (tmm) REVERT: Q 313 LEU cc_start: 0.8314 (mt) cc_final: 0.7913 (mt) REVERT: Q 331 ARG cc_start: 0.5951 (mtm180) cc_final: 0.5076 (ptp-110) REVERT: Q 429 GLU cc_start: 0.8392 (tt0) cc_final: 0.7932 (tm-30) REVERT: Q 447 LEU cc_start: 0.9190 (mt) cc_final: 0.8926 (mt) REVERT: Q 451 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8330 (tp40) REVERT: Q 454 VAL cc_start: 0.9503 (t) cc_final: 0.8408 (p) REVERT: Q 458 VAL cc_start: 0.9321 (p) cc_final: 0.8710 (p) REVERT: Q 525 LYS cc_start: 0.8819 (tttt) cc_final: 0.8613 (ptmt) REVERT: z 30 GLN cc_start: 0.8598 (tt0) cc_final: 0.7744 (tp40) REVERT: z 36 ASN cc_start: 0.8430 (m-40) cc_final: 0.7907 (m-40) REVERT: z 37 LEU cc_start: 0.8438 (tp) cc_final: 0.8141 (tt) REVERT: z 42 THR cc_start: 0.8987 (p) cc_final: 0.8625 (p) REVERT: z 122 PHE cc_start: 0.8952 (m-10) cc_final: 0.8659 (m-10) REVERT: z 174 VAL cc_start: 0.9620 (t) cc_final: 0.9291 (p) REVERT: z 242 TYR cc_start: 0.5193 (m-10) cc_final: 0.3877 (p90) REVERT: z 412 ILE cc_start: 0.9450 (mt) cc_final: 0.9200 (tp) REVERT: z 431 MET cc_start: 0.7344 (mtt) cc_final: 0.7135 (ptp) REVERT: z 469 VAL cc_start: 0.9603 (m) cc_final: 0.9346 (p) REVERT: z 478 ASP cc_start: 0.8751 (m-30) cc_final: 0.8354 (p0) REVERT: z 500 ASP cc_start: 0.7931 (t0) cc_final: 0.7523 (t0) REVERT: z 533 LEU cc_start: 0.8186 (tp) cc_final: 0.7684 (tp) REVERT: Z 40 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8294 (mttm) REVERT: Z 43 LEU cc_start: 0.7433 (tp) cc_final: 0.7133 (tp) REVERT: Z 62 LEU cc_start: 0.7116 (mt) cc_final: 0.6896 (mt) REVERT: Z 119 THR cc_start: 0.9459 (m) cc_final: 0.9232 (m) REVERT: Z 132 PHE cc_start: 0.6515 (m-10) cc_final: 0.6097 (m-80) REVERT: Z 134 ASP cc_start: 0.9419 (m-30) cc_final: 0.9087 (m-30) REVERT: Z 151 LEU cc_start: 0.9028 (mt) cc_final: 0.8734 (tt) REVERT: Z 176 ASP cc_start: 0.8425 (m-30) cc_final: 0.7183 (p0) REVERT: Z 223 ASP cc_start: 0.7212 (m-30) cc_final: 0.6998 (t0) REVERT: Z 224 MET cc_start: 0.1152 (mtt) cc_final: 0.0839 (tmm) REVERT: Z 374 LYS cc_start: 0.6913 (mttt) cc_final: 0.6592 (mmmt) REVERT: Z 412 ILE cc_start: 0.9473 (mt) cc_final: 0.9074 (tp) REVERT: Z 477 LEU cc_start: 0.8319 (mt) cc_final: 0.8000 (mt) REVERT: Z 482 ASP cc_start: 0.8455 (m-30) cc_final: 0.7595 (p0) REVERT: Z 500 ASP cc_start: 0.8595 (t0) cc_final: 0.7938 (t70) REVERT: Z 523 ILE cc_start: 0.8958 (mm) cc_final: 0.8710 (mm) outliers start: 0 outliers final: 0 residues processed: 2816 average time/residue: 0.6193 time to fit residues: 2819.9369 Evaluate side-chains 1463 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1463 time to evaluate : 5.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 5.9990 chunk 610 optimal weight: 3.9990 chunk 338 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 411 optimal weight: 9.9990 chunk 325 optimal weight: 2.9990 chunk 630 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 383 optimal weight: 9.9990 chunk 469 optimal weight: 9.9990 chunk 731 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 ASN H 356 GLN ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 64 ASN a 88 GLN a 191 ASN ** a 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 252 GLN A 261 GLN A 403 HIS b 118 GLN b 222 GLN b 260 GLN b 286 ASN b 385 HIS b 393 GLN B 304 ASN d 112 ASN ** d 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 499 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 238 GLN D 284 ASN ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 HIS ** e 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 383 GLN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 502 GLN ** E 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN g 21 GLN ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 279 GLN g 503 GLN g 535 HIS G 85 GLN G 156 GLN G 188 GLN G 530 GLN ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 GLN h 58 GLN h 90 GLN h 216 ASN h 345 HIS h 394 HIS ** h 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 27 GLN q 91 GLN q 311 HIS Q 58 HIS Q 66 ASN Q 92 GLN Q 258 ASN ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 142 ASN Z 145 ASN Z 185 GLN Z 297 ASN ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 430 ASN Z 515 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 62697 Z= 0.259 Angle : 0.679 11.370 84560 Z= 0.358 Chirality : 0.045 0.214 10175 Planarity : 0.005 0.075 10863 Dihedral : 3.742 21.144 8578 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.60 % Favored : 97.35 % Rotamer: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % 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: -1.34 (0.08), residues: 8076 helix: -0.85 (0.07), residues: 3716 sheet: -0.58 (0.18), residues: 690 loop : -0.82 (0.09), residues: 3670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 478 HIS 0.011 0.001 HIS G 535 PHE 0.029 0.002 PHE e 179 TYR 0.027 0.002 TYR Z 425 ARG 0.016 0.001 ARG Z 323 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1813 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1806 time to evaluate : 5.325 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: H 33 CYS cc_start: 0.8773 (m) cc_final: 0.8437 (m) REVERT: H 37 GLN cc_start: 0.8577 (tt0) cc_final: 0.8350 (tt0) REVERT: H 103 ILE cc_start: 0.9252 (mt) cc_final: 0.9002 (mt) REVERT: H 163 ARG cc_start: 0.6960 (mtt-85) cc_final: 0.5598 (ptp90) REVERT: H 195 ASP cc_start: 0.7438 (t0) cc_final: 0.7029 (t0) REVERT: H 447 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7423 (tm-30) REVERT: H 452 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8312 (mm-40) REVERT: H 459 PHE cc_start: 0.8075 (m-10) cc_final: 0.7637 (m-10) REVERT: H 460 ASP cc_start: 0.8587 (p0) cc_final: 0.8377 (p0) REVERT: H 462 ILE cc_start: 0.8894 (mt) cc_final: 0.7420 (tp) REVERT: a 34 MET cc_start: 0.8684 (mmp) cc_final: 0.8268 (mmm) REVERT: a 159 ILE cc_start: 0.8657 (tp) cc_final: 0.8378 (mp) REVERT: a 341 MET cc_start: -0.0633 (mtp) cc_final: -0.2186 (ptp) REVERT: a 398 MET cc_start: 0.2856 (mmp) cc_final: 0.2618 (mmm) REVERT: a 403 HIS cc_start: 0.8091 (m-70) cc_final: 0.7581 (m-70) REVERT: a 497 TYR cc_start: 0.7282 (m-80) cc_final: 0.6708 (m-10) REVERT: A 27 ASN cc_start: 0.8727 (m-40) cc_final: 0.8407 (p0) REVERT: A 108 LEU cc_start: 0.8924 (mt) cc_final: 0.8704 (mt) REVERT: A 124 THR cc_start: 0.9368 (m) cc_final: 0.8984 (p) REVERT: A 125 ILE cc_start: 0.9609 (mt) cc_final: 0.9350 (mt) REVERT: A 129 PHE cc_start: 0.9357 (m-10) cc_final: 0.9072 (m-80) REVERT: A 175 PHE cc_start: 0.8224 (m-80) cc_final: 0.7059 (t80) REVERT: A 176 PHE cc_start: 0.7556 (m-10) cc_final: 0.7184 (m-10) REVERT: A 233 MET cc_start: 0.3202 (ptp) cc_final: 0.2655 (ptp) REVERT: A 243 LYS cc_start: 0.6989 (mttt) cc_final: 0.6758 (mmtt) REVERT: A 411 ARG cc_start: 0.8388 (mtt180) cc_final: 0.7488 (mmm160) REVERT: A 526 LYS cc_start: 0.9027 (mttt) cc_final: 0.8778 (tttt) REVERT: A 529 LYS cc_start: 0.9481 (tttt) cc_final: 0.9255 (ttpt) REVERT: A 532 LEU cc_start: 0.9395 (mp) cc_final: 0.8881 (tp) REVERT: A 544 MET cc_start: 0.7503 (ttp) cc_final: 0.7064 (ttt) REVERT: b 65 LYS cc_start: 0.8685 (pttm) cc_final: 0.8457 (pttt) REVERT: b 107 GLU cc_start: 0.8724 (tt0) cc_final: 0.8481 (pt0) REVERT: b 120 ILE cc_start: 0.8214 (mt) cc_final: 0.6810 (mt) REVERT: b 121 ILE cc_start: 0.9125 (mt) cc_final: 0.8518 (mt) REVERT: b 124 TYR cc_start: 0.9282 (m-10) cc_final: 0.8172 (m-80) REVERT: b 148 MET cc_start: -0.0980 (ppp) cc_final: -0.1284 (ppp) REVERT: b 347 MET cc_start: 0.7330 (mmm) cc_final: 0.6182 (ptt) REVERT: b 409 MET cc_start: 0.8989 (tpp) cc_final: 0.8375 (tpp) REVERT: b 413 LYS cc_start: 0.9476 (tttt) cc_final: 0.9058 (ttmm) REVERT: b 425 LYS cc_start: 0.8777 (mttt) cc_final: 0.8550 (mmtt) REVERT: b 433 PHE cc_start: 0.9012 (t80) cc_final: 0.8792 (t80) REVERT: b 503 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8629 (mt-10) REVERT: b 506 GLU cc_start: 0.7853 (tt0) cc_final: 0.7558 (mt-10) REVERT: b 508 LEU cc_start: 0.9355 (mm) cc_final: 0.8856 (tt) REVERT: B 116 HIS cc_start: 0.7789 (m-70) cc_final: 0.7401 (m-70) REVERT: B 173 PHE cc_start: 0.4883 (t80) cc_final: 0.4679 (t80) REVERT: B 509 LEU cc_start: 0.9142 (mm) cc_final: 0.8798 (mm) REVERT: d 29 ARG cc_start: 0.9069 (mtp85) cc_final: 0.8815 (mtp-110) REVERT: d 33 ASP cc_start: 0.8428 (t0) cc_final: 0.7268 (t0) REVERT: d 36 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8193 (ptp-170) REVERT: d 39 LEU cc_start: 0.8879 (tp) cc_final: 0.8679 (tp) REVERT: d 48 ILE cc_start: 0.8538 (mt) cc_final: 0.8333 (mt) REVERT: d 62 HIS cc_start: 0.8081 (t-170) cc_final: 0.7774 (t-170) REVERT: d 91 ASP cc_start: 0.6690 (t0) cc_final: 0.6250 (t70) REVERT: d 108 GLU cc_start: 0.7952 (pm20) cc_final: 0.7735 (mt-10) REVERT: d 109 ARG cc_start: 0.8469 (tpp80) cc_final: 0.7938 (tpp80) REVERT: d 116 HIS cc_start: 0.7451 (t-90) cc_final: 0.7157 (t-90) REVERT: d 166 TYR cc_start: 0.7939 (m-80) cc_final: 0.7609 (m-80) REVERT: d 209 MET cc_start: 0.0539 (tpt) cc_final: -0.0133 (tpt) REVERT: d 305 LEU cc_start: 0.5785 (mt) cc_final: 0.5513 (pp) REVERT: d 311 MET cc_start: 0.2674 (ppp) cc_final: 0.2310 (ppp) REVERT: d 394 LEU cc_start: 0.7800 (mm) cc_final: 0.7563 (mm) REVERT: d 461 ASN cc_start: 0.9489 (t0) cc_final: 0.9147 (t0) REVERT: d 466 VAL cc_start: 0.9471 (t) cc_final: 0.9253 (p) REVERT: d 496 HIS cc_start: 0.6570 (p-80) cc_final: 0.6226 (p-80) REVERT: d 513 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8639 (mp0) REVERT: D 33 ASP cc_start: 0.9044 (p0) cc_final: 0.8631 (p0) REVERT: D 38 SER cc_start: 0.9538 (m) cc_final: 0.9064 (t) REVERT: D 66 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8525 (mtmm) REVERT: D 103 LEU cc_start: 0.9151 (mt) cc_final: 0.8635 (mt) REVERT: D 108 GLU cc_start: 0.8571 (tp30) cc_final: 0.8341 (tp30) REVERT: D 133 ASP cc_start: 0.8130 (m-30) cc_final: 0.7854 (t0) REVERT: D 209 MET cc_start: 0.5034 (tmm) cc_final: 0.4676 (tmm) REVERT: D 311 MET cc_start: -0.0696 (mtm) cc_final: -0.1030 (mpp) REVERT: e 94 MET cc_start: 0.7949 (mtp) cc_final: 0.7686 (tpt) REVERT: e 127 SER cc_start: 0.9386 (m) cc_final: 0.8973 (p) REVERT: e 159 SER cc_start: 0.9339 (m) cc_final: 0.8860 (t) REVERT: e 229 ARG cc_start: 0.7766 (mmt-90) cc_final: 0.7041 (mtm110) REVERT: e 405 THR cc_start: 0.7783 (m) cc_final: 0.7493 (p) REVERT: e 425 ASP cc_start: 0.8586 (m-30) cc_final: 0.8288 (m-30) REVERT: e 441 TYR cc_start: 0.7233 (m-80) cc_final: 0.6849 (m-80) REVERT: e 478 THR cc_start: 0.9356 (m) cc_final: 0.8982 (p) REVERT: e 486 ASN cc_start: 0.9002 (m-40) cc_final: 0.8100 (t0) REVERT: e 549 LEU cc_start: 0.9434 (mm) cc_final: 0.9217 (mm) REVERT: e 554 VAL cc_start: 0.8340 (t) cc_final: 0.8072 (t) REVERT: E 130 LEU cc_start: 0.8998 (mt) cc_final: 0.8696 (tt) REVERT: E 144 ILE cc_start: 0.8396 (mm) cc_final: 0.7966 (mm) REVERT: E 428 CYS cc_start: 0.9042 (t) cc_final: 0.8609 (t) REVERT: E 432 ASN cc_start: 0.8267 (m110) cc_final: 0.7794 (t0) REVERT: E 454 VAL cc_start: 0.9598 (t) cc_final: 0.9333 (p) REVERT: E 481 MET cc_start: 0.8488 (mtp) cc_final: 0.7083 (mtp) REVERT: E 521 ASP cc_start: 0.7726 (t0) cc_final: 0.7412 (t0) REVERT: g 25 ILE cc_start: 0.9481 (mt) cc_final: 0.9216 (mm) REVERT: g 106 GLN cc_start: 0.7389 (mp-120) cc_final: 0.6956 (mm110) REVERT: g 110 TYR cc_start: 0.8095 (m-80) cc_final: 0.7874 (m-10) REVERT: g 112 ILE cc_start: 0.9258 (mt) cc_final: 0.8904 (mt) REVERT: g 115 ASN cc_start: 0.8484 (t0) cc_final: 0.7843 (p0) REVERT: g 117 HIS cc_start: 0.8418 (t-90) cc_final: 0.8182 (t-90) REVERT: g 133 LEU cc_start: 0.9486 (mt) cc_final: 0.9166 (mt) REVERT: g 153 LYS cc_start: 0.8959 (mttt) cc_final: 0.8537 (pttm) REVERT: g 170 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7763 (mppt) REVERT: g 242 ARG cc_start: 0.5991 (mtm-85) cc_final: 0.5712 (tmm-80) REVERT: g 364 TYR cc_start: 0.6695 (m-10) cc_final: 0.6255 (m-80) REVERT: g 481 MET cc_start: 0.8844 (ttt) cc_final: 0.7184 (ttt) REVERT: g 507 ASP cc_start: 0.8128 (m-30) cc_final: 0.7916 (t0) REVERT: g 512 ILE cc_start: 0.9645 (mp) cc_final: 0.9407 (mp) REVERT: g 553 ASP cc_start: 0.8724 (p0) cc_final: 0.8495 (p0) REVERT: g 555 VAL cc_start: 0.8916 (t) cc_final: 0.8486 (m) REVERT: g 585 ASP cc_start: 0.6934 (m-30) cc_final: 0.6655 (m-30) REVERT: G 48 LEU cc_start: 0.8999 (mp) cc_final: 0.8785 (mp) REVERT: G 87 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8560 (tm-30) REVERT: G 99 LEU cc_start: 0.8709 (mp) cc_final: 0.8477 (mm) REVERT: G 106 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8195 (tp40) REVERT: G 111 LEU cc_start: 0.8787 (tp) cc_final: 0.8569 (tp) REVERT: G 116 ILE cc_start: 0.9383 (mm) cc_final: 0.8949 (tp) REVERT: G 120 ILE cc_start: 0.9168 (mm) cc_final: 0.8884 (mm) REVERT: G 202 ARG cc_start: 0.8378 (mtm180) cc_final: 0.7840 (mtm110) REVERT: G 359 MET cc_start: -0.0233 (ttp) cc_final: -0.0785 (ttm) REVERT: G 481 MET cc_start: 0.8253 (ttt) cc_final: 0.7910 (ttt) REVERT: G 517 ILE cc_start: 0.9082 (mm) cc_final: 0.8815 (mm) REVERT: G 531 LEU cc_start: 0.9067 (tp) cc_final: 0.8866 (tp) REVERT: G 572 THR cc_start: 0.9560 (p) cc_final: 0.9131 (p) REVERT: G 583 VAL cc_start: 0.9274 (t) cc_final: 0.9055 (p) REVERT: h 44 LEU cc_start: 0.9058 (tp) cc_final: 0.8465 (tp) REVERT: h 84 VAL cc_start: 0.8169 (t) cc_final: 0.7902 (t) REVERT: h 99 THR cc_start: 0.9527 (p) cc_final: 0.9316 (p) REVERT: h 216 ASN cc_start: 0.3798 (m110) cc_final: 0.3463 (t0) REVERT: h 322 ASP cc_start: 0.6012 (m-30) cc_final: 0.5784 (t0) REVERT: h 418 MET cc_start: 0.6359 (ttt) cc_final: 0.6137 (ttt) REVERT: h 434 LYS cc_start: 0.9346 (mtpt) cc_final: 0.8977 (mtpt) REVERT: h 449 ILE cc_start: 0.9039 (mt) cc_final: 0.8747 (mt) REVERT: h 453 LEU cc_start: 0.9311 (mt) cc_final: 0.9090 (mt) REVERT: h 460 ASP cc_start: 0.8596 (t0) cc_final: 0.6814 (t0) REVERT: h 463 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7360 (mt-10) REVERT: q 76 ASP cc_start: 0.8303 (t0) cc_final: 0.8044 (p0) REVERT: q 87 MET cc_start: 0.8982 (mtp) cc_final: 0.8583 (tpt) REVERT: q 106 LEU cc_start: 0.8967 (tp) cc_final: 0.8752 (tp) REVERT: q 139 LEU cc_start: 0.9005 (mt) cc_final: 0.8071 (tt) REVERT: q 153 LYS cc_start: 0.8997 (tttm) cc_final: 0.8757 (ptpt) REVERT: q 176 ASP cc_start: 0.8863 (p0) cc_final: 0.8601 (p0) REVERT: q 431 ILE cc_start: 0.9564 (mt) cc_final: 0.9115 (tp) REVERT: q 451 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8706 (mm-40) REVERT: q 454 VAL cc_start: 0.9559 (t) cc_final: 0.9302 (p) REVERT: q 458 VAL cc_start: 0.9417 (p) cc_final: 0.9195 (p) REVERT: q 461 ARG cc_start: 0.8338 (ttm110) cc_final: 0.7728 (ttp-110) REVERT: Q 72 LEU cc_start: 0.8976 (mt) cc_final: 0.8722 (mt) REVERT: Q 104 MET cc_start: 0.7991 (mmm) cc_final: 0.7763 (mmm) REVERT: Q 128 ILE cc_start: 0.9263 (mt) cc_final: 0.8936 (tp) REVERT: Q 140 LYS cc_start: 0.8766 (tppt) cc_final: 0.8485 (tppt) REVERT: Q 161 LYS cc_start: 0.9177 (mttt) cc_final: 0.8726 (ttmt) REVERT: Q 227 VAL cc_start: 0.7807 (t) cc_final: 0.7520 (t) REVERT: Q 235 HIS cc_start: 0.7376 (m170) cc_final: 0.6894 (t70) REVERT: Q 237 LYS cc_start: 0.8318 (mptt) cc_final: 0.7669 (mmtt) REVERT: Q 282 LYS cc_start: 0.4592 (mttt) cc_final: 0.4153 (tptp) REVERT: Q 287 MET cc_start: 0.6356 (mmp) cc_final: 0.5645 (tmm) REVERT: Q 288 MET cc_start: 0.3469 (ttp) cc_final: 0.2843 (ttt) REVERT: Q 311 HIS cc_start: 0.9061 (m-70) cc_final: 0.8638 (m-70) REVERT: Q 367 ARG cc_start: 0.7644 (mpp80) cc_final: 0.7056 (ttt90) REVERT: Q 409 LYS cc_start: 0.6096 (tptt) cc_final: 0.5674 (tppt) REVERT: Q 451 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8337 (mm110) REVERT: Q 458 VAL cc_start: 0.9337 (p) cc_final: 0.8702 (p) REVERT: Q 463 LEU cc_start: 0.9629 (mt) cc_final: 0.9365 (tp) REVERT: Q 540 SER cc_start: 0.9359 (m) cc_final: 0.8923 (p) REVERT: z 34 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8082 (mt-10) REVERT: z 36 ASN cc_start: 0.8695 (m-40) cc_final: 0.8425 (m-40) REVERT: z 37 LEU cc_start: 0.7797 (tp) cc_final: 0.7390 (tt) REVERT: z 91 THR cc_start: 0.8550 (p) cc_final: 0.8287 (t) REVERT: z 127 LYS cc_start: 0.9245 (mttt) cc_final: 0.8590 (tptt) REVERT: z 199 MET cc_start: 0.7770 (ppp) cc_final: 0.7111 (ppp) REVERT: z 283 GLU cc_start: 0.8429 (pt0) cc_final: 0.8058 (pt0) REVERT: z 369 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8007 (tm-30) REVERT: z 376 CYS cc_start: 0.6612 (m) cc_final: 0.6366 (m) REVERT: z 431 MET cc_start: 0.7913 (mtt) cc_final: 0.7571 (ptm) REVERT: z 441 LYS cc_start: 0.8225 (ptpp) cc_final: 0.7790 (mttm) REVERT: z 468 ASP cc_start: 0.9007 (t0) cc_final: 0.8702 (t70) REVERT: z 500 ASP cc_start: 0.8493 (t0) cc_final: 0.7526 (t70) REVERT: z 503 ILE cc_start: 0.9438 (mt) cc_final: 0.9201 (mt) REVERT: Z 24 THR cc_start: 0.9090 (m) cc_final: 0.8774 (m) REVERT: Z 40 LYS cc_start: 0.9205 (mmtt) cc_final: 0.8551 (mttp) REVERT: Z 102 LEU cc_start: 0.8868 (mt) cc_final: 0.8632 (mt) REVERT: Z 118 ILE cc_start: 0.9369 (mm) cc_final: 0.8531 (mm) REVERT: Z 122 PHE cc_start: 0.9021 (m-10) cc_final: 0.8534 (m-10) REVERT: Z 131 LYS cc_start: 0.8802 (mttt) cc_final: 0.8520 (ttpt) REVERT: Z 192 HIS cc_start: 0.8486 (m90) cc_final: 0.8224 (m90) REVERT: Z 193 MET cc_start: 0.7883 (ppp) cc_final: 0.7470 (ppp) REVERT: Z 223 ASP cc_start: 0.7363 (m-30) cc_final: 0.7089 (t0) REVERT: Z 412 ILE cc_start: 0.9500 (mt) cc_final: 0.9258 (tp) REVERT: Z 431 MET cc_start: 0.6986 (mpp) cc_final: 0.6667 (mpp) REVERT: Z 442 THR cc_start: 0.8806 (p) cc_final: 0.8392 (t) REVERT: Z 465 ASP cc_start: 0.8693 (t0) cc_final: 0.8475 (t0) REVERT: Z 475 ASP cc_start: 0.8534 (m-30) cc_final: 0.8319 (t70) REVERT: Z 482 ASP cc_start: 0.8998 (m-30) cc_final: 0.8207 (p0) outliers start: 7 outliers final: 1 residues processed: 1810 average time/residue: 0.5699 time to fit residues: 1729.7970 Evaluate side-chains 1339 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1338 time to evaluate : 5.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 608 optimal weight: 6.9990 chunk 497 optimal weight: 0.7980 chunk 201 optimal weight: 4.9990 chunk 732 optimal weight: 0.9990 chunk 791 optimal weight: 5.9990 chunk 652 optimal weight: 2.9990 chunk 726 optimal weight: 8.9990 chunk 249 optimal weight: 0.4980 chunk 587 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 466 ASN b 228 ASN b 286 ASN B 168 GLN B 172 HIS d 112 ASN d 289 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN e 138 GLN e 537 GLN ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 503 GLN G 166 HIS ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 568 GLN h 90 GLN h 345 HIS ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 66 ASN q 91 GLN ** q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 145 ASN ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 356 GLN Z 430 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 62697 Z= 0.178 Angle : 0.566 9.367 84560 Z= 0.291 Chirality : 0.043 0.189 10175 Planarity : 0.004 0.075 10863 Dihedral : 3.648 20.700 8578 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.27 % 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: -0.50 (0.09), residues: 8076 helix: 0.11 (0.08), residues: 3749 sheet: -0.41 (0.19), residues: 651 loop : -0.67 (0.10), residues: 3676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 560 HIS 0.006 0.001 HIS E 50 PHE 0.027 0.002 PHE z 122 TYR 0.035 0.002 TYR Q 131 ARG 0.015 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1701 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1696 time to evaluate : 6.431 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: H 33 CYS cc_start: 0.8890 (m) cc_final: 0.8422 (m) REVERT: H 37 GLN cc_start: 0.8525 (tt0) cc_final: 0.8206 (tt0) REVERT: H 113 LYS cc_start: 0.9497 (mtpt) cc_final: 0.9031 (mtpt) REVERT: H 150 GLU cc_start: 0.7592 (tm-30) cc_final: 0.6220 (mp0) REVERT: H 163 ARG cc_start: 0.6971 (mtt-85) cc_final: 0.5639 (ttp-110) REVERT: H 195 ASP cc_start: 0.7557 (t0) cc_final: 0.7148 (t0) REVERT: H 355 MET cc_start: 0.5383 (pmm) cc_final: 0.4389 (ppp) REVERT: H 364 LEU cc_start: 0.7901 (pp) cc_final: 0.7635 (pp) REVERT: H 388 GLU cc_start: 0.6825 (pp20) cc_final: 0.5930 (mp0) REVERT: H 452 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8605 (mm-40) REVERT: H 467 LYS cc_start: 0.8701 (ptpp) cc_final: 0.8363 (ptpp) REVERT: a 34 MET cc_start: 0.8627 (mmp) cc_final: 0.8034 (mmm) REVERT: a 121 HIS cc_start: 0.8090 (t-90) cc_final: 0.7831 (t-90) REVERT: a 123 THR cc_start: 0.8877 (m) cc_final: 0.8610 (m) REVERT: a 159 ILE cc_start: 0.8502 (tp) cc_final: 0.8195 (mp) REVERT: a 176 PHE cc_start: 0.8694 (t80) cc_final: 0.8031 (m-10) REVERT: a 341 MET cc_start: -0.1289 (mtp) cc_final: -0.2720 (ptp) REVERT: a 497 TYR cc_start: 0.7333 (m-80) cc_final: 0.6763 (m-10) REVERT: a 529 LYS cc_start: 0.9015 (tptp) cc_final: 0.8708 (tptp) REVERT: a 544 MET cc_start: 0.8420 (tpp) cc_final: 0.7983 (tpp) REVERT: A 27 ASN cc_start: 0.8696 (m-40) cc_final: 0.8431 (p0) REVERT: A 108 LEU cc_start: 0.8975 (mt) cc_final: 0.8474 (mt) REVERT: A 125 ILE cc_start: 0.9571 (mt) cc_final: 0.9301 (mt) REVERT: A 129 PHE cc_start: 0.9384 (m-10) cc_final: 0.9174 (m-80) REVERT: A 175 PHE cc_start: 0.8272 (m-80) cc_final: 0.7180 (t80) REVERT: A 176 PHE cc_start: 0.7756 (m-10) cc_final: 0.7136 (m-10) REVERT: A 233 MET cc_start: 0.3257 (ptp) cc_final: 0.2599 (ptm) REVERT: A 236 ARG cc_start: 0.6928 (ttp-110) cc_final: 0.6421 (tmt-80) REVERT: A 387 LEU cc_start: 0.7673 (tt) cc_final: 0.7408 (tt) REVERT: A 410 LYS cc_start: 0.8686 (tptt) cc_final: 0.8467 (tptp) REVERT: A 411 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7349 (mmm160) REVERT: A 526 LYS cc_start: 0.9119 (mttt) cc_final: 0.8553 (mmtm) REVERT: b 79 ASN cc_start: 0.7689 (p0) cc_final: 0.7454 (p0) REVERT: b 107 GLU cc_start: 0.8846 (tt0) cc_final: 0.8448 (pt0) REVERT: b 120 ILE cc_start: 0.8212 (mt) cc_final: 0.6522 (mt) REVERT: b 121 ILE cc_start: 0.9156 (mt) cc_final: 0.8514 (mt) REVERT: b 124 TYR cc_start: 0.9160 (m-10) cc_final: 0.8394 (m-80) REVERT: b 402 LEU cc_start: 0.9497 (mt) cc_final: 0.9263 (tp) REVERT: b 409 MET cc_start: 0.9165 (tpp) cc_final: 0.8564 (tpp) REVERT: b 413 LYS cc_start: 0.9518 (tttt) cc_final: 0.8983 (ttmm) REVERT: b 503 GLU cc_start: 0.9367 (mt-10) cc_final: 0.8789 (mt-10) REVERT: b 506 GLU cc_start: 0.7803 (tt0) cc_final: 0.7585 (mt-10) REVERT: b 508 LEU cc_start: 0.9333 (mm) cc_final: 0.8824 (tt) REVERT: B 81 SER cc_start: 0.9071 (m) cc_final: 0.8751 (p) REVERT: B 121 ILE cc_start: 0.8843 (mm) cc_final: 0.8630 (mm) REVERT: B 269 MET cc_start: 0.3809 (ptm) cc_final: 0.3460 (ttp) REVERT: B 426 LYS cc_start: 0.8967 (mttt) cc_final: 0.8719 (mtpp) REVERT: B 451 ASP cc_start: 0.8217 (t0) cc_final: 0.7994 (t0) REVERT: d 39 LEU cc_start: 0.8838 (tp) cc_final: 0.8637 (tp) REVERT: d 48 ILE cc_start: 0.8376 (mt) cc_final: 0.7958 (mt) REVERT: d 66 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8690 (mmmt) REVERT: d 67 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7753 (tp-100) REVERT: d 77 MET cc_start: 0.7760 (ppp) cc_final: 0.7319 (ppp) REVERT: d 91 ASP cc_start: 0.6916 (t0) cc_final: 0.6482 (t70) REVERT: d 116 HIS cc_start: 0.7501 (t-90) cc_final: 0.7150 (t-90) REVERT: d 120 ILE cc_start: 0.9137 (mp) cc_final: 0.8565 (mp) REVERT: d 124 PHE cc_start: 0.9276 (m-10) cc_final: 0.8957 (m-80) REVERT: d 130 ARG cc_start: 0.8515 (mtp-110) cc_final: 0.8286 (mtp-110) REVERT: d 165 GLN cc_start: 0.6930 (mt0) cc_final: 0.6507 (mm-40) REVERT: d 166 TYR cc_start: 0.7720 (m-80) cc_final: 0.7467 (m-80) REVERT: d 209 MET cc_start: 0.0435 (tpt) cc_final: -0.0099 (tpt) REVERT: d 305 LEU cc_start: 0.5990 (mt) cc_final: 0.5689 (pp) REVERT: d 389 GLU cc_start: 0.8188 (pp20) cc_final: 0.7239 (pm20) REVERT: d 394 LEU cc_start: 0.7762 (mm) cc_final: 0.7395 (mt) REVERT: d 510 LEU cc_start: 0.8966 (mt) cc_final: 0.7907 (mt) REVERT: d 513 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8875 (pp20) REVERT: D 33 ASP cc_start: 0.8823 (p0) cc_final: 0.8458 (p0) REVERT: D 38 SER cc_start: 0.9568 (m) cc_final: 0.9136 (t) REVERT: D 86 ASP cc_start: 0.8624 (m-30) cc_final: 0.8312 (p0) REVERT: D 91 ASP cc_start: 0.7646 (t0) cc_final: 0.6795 (t70) REVERT: D 133 ASP cc_start: 0.8239 (m-30) cc_final: 0.7937 (t0) REVERT: D 183 ASP cc_start: 0.8082 (t0) cc_final: 0.7860 (t70) REVERT: e 127 SER cc_start: 0.9423 (m) cc_final: 0.8995 (p) REVERT: e 132 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8085 (tp40) REVERT: e 159 SER cc_start: 0.9440 (m) cc_final: 0.9071 (t) REVERT: e 229 ARG cc_start: 0.7774 (mmt-90) cc_final: 0.7060 (mtm110) REVERT: e 392 MET cc_start: 0.2874 (mtm) cc_final: 0.1930 (ptm) REVERT: e 394 ILE cc_start: 0.7363 (mt) cc_final: 0.7001 (mt) REVERT: e 405 THR cc_start: 0.7888 (m) cc_final: 0.7535 (p) REVERT: e 441 TYR cc_start: 0.7270 (m-80) cc_final: 0.7016 (m-80) REVERT: e 465 ASP cc_start: 0.8654 (m-30) cc_final: 0.8445 (m-30) REVERT: e 477 ASP cc_start: 0.8245 (p0) cc_final: 0.8039 (p0) REVERT: e 481 MET cc_start: 0.8304 (mmp) cc_final: 0.7845 (mmp) REVERT: e 486 ASN cc_start: 0.8952 (m-40) cc_final: 0.8204 (t0) REVERT: e 550 LYS cc_start: 0.9314 (mmpt) cc_final: 0.9110 (mmmt) REVERT: e 552 ASP cc_start: 0.8826 (p0) cc_final: 0.8455 (p0) REVERT: E 71 ASP cc_start: 0.7810 (m-30) cc_final: 0.7573 (m-30) REVERT: E 146 ILE cc_start: 0.8803 (mt) cc_final: 0.8358 (mt) REVERT: E 200 PHE cc_start: 0.7884 (m-10) cc_final: 0.7674 (m-80) REVERT: E 225 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7965 (mmtt) REVERT: E 412 ASN cc_start: 0.7347 (t0) cc_final: 0.7139 (t0) REVERT: E 428 CYS cc_start: 0.8923 (t) cc_final: 0.8530 (t) REVERT: E 432 ASN cc_start: 0.8067 (m110) cc_final: 0.7771 (t0) REVERT: E 454 VAL cc_start: 0.9470 (t) cc_final: 0.9237 (p) REVERT: E 477 ASP cc_start: 0.8923 (t0) cc_final: 0.7896 (t0) REVERT: E 481 MET cc_start: 0.7984 (mtp) cc_final: 0.6992 (mtp) REVERT: E 485 GLU cc_start: 0.8591 (tp30) cc_final: 0.7999 (tm-30) REVERT: E 521 ASP cc_start: 0.7838 (t0) cc_final: 0.7492 (t0) REVERT: g 111 LEU cc_start: 0.9244 (tp) cc_final: 0.8960 (tp) REVERT: g 117 HIS cc_start: 0.8415 (t-90) cc_final: 0.8169 (t-90) REVERT: g 242 ARG cc_start: 0.6000 (mtm-85) cc_final: 0.5690 (tmm-80) REVERT: g 364 TYR cc_start: 0.6919 (m-10) cc_final: 0.6480 (m-80) REVERT: g 509 MET cc_start: 0.9452 (mmp) cc_final: 0.9074 (mmt) REVERT: g 510 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8515 (mm-30) REVERT: g 511 CYS cc_start: 0.9347 (t) cc_final: 0.9128 (p) REVERT: g 555 VAL cc_start: 0.8980 (t) cc_final: 0.8540 (m) REVERT: g 585 ASP cc_start: 0.6825 (m-30) cc_final: 0.6430 (m-30) REVERT: G 25 ILE cc_start: 0.9316 (mm) cc_final: 0.9049 (mm) REVERT: G 87 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8598 (tm-30) REVERT: G 120 ILE cc_start: 0.8866 (mm) cc_final: 0.7539 (mm) REVERT: G 122 ILE cc_start: 0.9298 (mt) cc_final: 0.9057 (mt) REVERT: G 202 ARG cc_start: 0.8451 (mtm180) cc_final: 0.7851 (mtm110) REVERT: G 481 MET cc_start: 0.8735 (ttt) cc_final: 0.8494 (ttm) REVERT: G 517 ILE cc_start: 0.9173 (mm) cc_final: 0.8918 (mm) REVERT: G 531 LEU cc_start: 0.9279 (tp) cc_final: 0.8925 (tp) REVERT: G 554 MET cc_start: 0.8535 (mmt) cc_final: 0.8304 (mmp) REVERT: G 572 THR cc_start: 0.9511 (p) cc_final: 0.9007 (p) REVERT: h 44 LEU cc_start: 0.9119 (tp) cc_final: 0.8775 (tp) REVERT: h 110 LYS cc_start: 0.9335 (ttpt) cc_final: 0.9097 (ttpp) REVERT: h 143 LEU cc_start: 0.8546 (mt) cc_final: 0.8319 (mt) REVERT: h 209 MET cc_start: -0.2390 (ttp) cc_final: -0.3670 (ptp) REVERT: h 216 ASN cc_start: 0.3774 (m110) cc_final: 0.3485 (t0) REVERT: h 322 ASP cc_start: 0.6011 (m-30) cc_final: 0.5598 (t0) REVERT: h 323 MET cc_start: -0.0700 (tmm) cc_final: -0.0923 (tmm) REVERT: h 362 TYR cc_start: 0.1948 (m-80) cc_final: 0.1434 (m-80) REVERT: h 437 MET cc_start: 0.8807 (ppp) cc_final: 0.8081 (ppp) REVERT: h 438 ILE cc_start: 0.9217 (mt) cc_final: 0.8849 (mm) REVERT: h 460 ASP cc_start: 0.8621 (t0) cc_final: 0.8380 (t0) REVERT: h 490 ASP cc_start: 0.7522 (p0) cc_final: 0.6674 (p0) REVERT: q 39 HIS cc_start: 0.7634 (t70) cc_final: 0.6703 (t-90) REVERT: q 86 VAL cc_start: 0.9547 (m) cc_final: 0.9327 (p) REVERT: q 87 MET cc_start: 0.9125 (mtp) cc_final: 0.8511 (tpt) REVERT: q 105 ILE cc_start: 0.8873 (mt) cc_final: 0.8461 (mt) REVERT: q 106 LEU cc_start: 0.9125 (tp) cc_final: 0.8774 (tp) REVERT: q 109 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8206 (mm-30) REVERT: q 113 VAL cc_start: 0.9257 (m) cc_final: 0.9005 (m) REVERT: q 133 MET cc_start: 0.9455 (ttp) cc_final: 0.8675 (tmm) REVERT: q 139 LEU cc_start: 0.8901 (mt) cc_final: 0.8144 (tt) REVERT: q 176 ASP cc_start: 0.8857 (p0) cc_final: 0.8536 (p0) REVERT: q 451 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8406 (tp40) REVERT: q 454 VAL cc_start: 0.9620 (t) cc_final: 0.9115 (p) REVERT: Q 109 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8228 (mm-30) REVERT: Q 112 ASN cc_start: 0.8178 (t0) cc_final: 0.7739 (t0) REVERT: Q 128 ILE cc_start: 0.9259 (mt) cc_final: 0.8876 (tp) REVERT: Q 140 LYS cc_start: 0.8839 (tppt) cc_final: 0.8425 (tppt) REVERT: Q 167 ILE cc_start: 0.8907 (pt) cc_final: 0.8283 (tp) REVERT: Q 237 LYS cc_start: 0.8388 (mptt) cc_final: 0.8086 (mmtt) REVERT: Q 282 LYS cc_start: 0.4735 (mttt) cc_final: 0.4230 (tptp) REVERT: Q 311 HIS cc_start: 0.9082 (m-70) cc_final: 0.8696 (m-70) REVERT: Q 361 MET cc_start: 0.7971 (tpp) cc_final: 0.7748 (tpp) REVERT: Q 458 VAL cc_start: 0.9367 (p) cc_final: 0.8970 (p) REVERT: Q 473 GLU cc_start: 0.9037 (pt0) cc_final: 0.8804 (pp20) REVERT: Q 530 VAL cc_start: 0.9482 (m) cc_final: 0.9133 (p) REVERT: Q 540 SER cc_start: 0.9377 (m) cc_final: 0.8693 (p) REVERT: z 34 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8219 (mt-10) REVERT: z 37 LEU cc_start: 0.7484 (tp) cc_final: 0.7033 (tt) REVERT: z 127 LYS cc_start: 0.9224 (mtpp) cc_final: 0.8761 (tptt) REVERT: z 199 MET cc_start: 0.7908 (ppp) cc_final: 0.7078 (ppp) REVERT: z 283 GLU cc_start: 0.8372 (pt0) cc_final: 0.8024 (pt0) REVERT: z 369 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7716 (tt0) REVERT: z 376 CYS cc_start: 0.6541 (m) cc_final: 0.6336 (m) REVERT: z 431 MET cc_start: 0.7826 (mtt) cc_final: 0.7462 (ptp) REVERT: z 441 LYS cc_start: 0.8232 (ptpp) cc_final: 0.7597 (mmtm) REVERT: z 468 ASP cc_start: 0.9084 (t0) cc_final: 0.8785 (t70) REVERT: z 477 LEU cc_start: 0.8881 (mt) cc_final: 0.8228 (pp) REVERT: z 500 ASP cc_start: 0.8441 (t0) cc_final: 0.7958 (t0) REVERT: Z 24 THR cc_start: 0.8852 (m) cc_final: 0.8501 (p) REVERT: Z 40 LYS cc_start: 0.9199 (mmtt) cc_final: 0.8685 (mmmt) REVERT: Z 113 VAL cc_start: 0.9165 (t) cc_final: 0.8953 (p) REVERT: Z 122 PHE cc_start: 0.8980 (m-10) cc_final: 0.8422 (m-10) REVERT: Z 130 MET cc_start: 0.8898 (tpp) cc_final: 0.8489 (tpp) REVERT: Z 131 LYS cc_start: 0.8997 (mttt) cc_final: 0.8492 (ttpt) REVERT: Z 151 LEU cc_start: 0.9450 (mt) cc_final: 0.9074 (tt) REVERT: Z 192 HIS cc_start: 0.8522 (m90) cc_final: 0.8268 (m90) REVERT: Z 193 MET cc_start: 0.7887 (ppp) cc_final: 0.7177 (ppp) REVERT: Z 223 ASP cc_start: 0.7329 (m-30) cc_final: 0.6991 (t0) REVERT: Z 224 MET cc_start: 0.3187 (mmt) cc_final: 0.2759 (mmm) REVERT: Z 384 THR cc_start: 0.8301 (p) cc_final: 0.7910 (p) REVERT: Z 412 ILE cc_start: 0.9531 (mt) cc_final: 0.9319 (tp) REVERT: Z 431 MET cc_start: 0.7092 (mpp) cc_final: 0.6726 (mpp) REVERT: Z 442 THR cc_start: 0.9014 (p) cc_final: 0.8635 (t) REVERT: Z 465 ASP cc_start: 0.8893 (t0) cc_final: 0.8651 (t0) REVERT: Z 478 ASP cc_start: 0.8584 (m-30) cc_final: 0.8254 (m-30) REVERT: Z 482 ASP cc_start: 0.8954 (m-30) cc_final: 0.8194 (p0) outliers start: 5 outliers final: 1 residues processed: 1699 average time/residue: 0.6224 time to fit residues: 1811.0855 Evaluate side-chains 1329 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1328 time to evaluate : 5.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 0.8980 chunk 550 optimal weight: 1.9990 chunk 380 optimal weight: 0.0470 chunk 81 optimal weight: 0.9980 chunk 349 optimal weight: 5.9990 chunk 491 optimal weight: 0.4980 chunk 734 optimal weight: 0.0070 chunk 778 optimal weight: 0.7980 chunk 383 optimal weight: 6.9990 chunk 696 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 209 HIS ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN b 286 ASN B 118 GLN B 192 HIS d 62 HIS D 59 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 238 GLN D 284 ASN ** e 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN E 536 GLN ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 503 GLN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 568 GLN h 90 GLN h 345 HIS ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 91 GLN ** q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 ASN q 392 ASN q 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 62697 Z= 0.150 Angle : 0.539 8.349 84560 Z= 0.273 Chirality : 0.042 0.169 10175 Planarity : 0.003 0.065 10863 Dihedral : 3.583 19.848 8578 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Rotamer: Outliers : 0.04 % Allowed : 1.77 % Favored : 98.19 % 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: 8076 helix: 0.44 (0.08), residues: 3748 sheet: -0.24 (0.19), residues: 676 loop : -0.59 (0.10), residues: 3652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 560 HIS 0.009 0.001 HIS A 121 PHE 0.019 0.001 PHE z 418 TYR 0.024 0.001 TYR b 491 ARG 0.008 0.000 ARG Q 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1632 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1629 time to evaluate : 5.306 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: H 33 CYS cc_start: 0.9011 (m) cc_final: 0.8720 (m) REVERT: H 37 GLN cc_start: 0.8471 (tt0) cc_final: 0.8075 (tt0) REVERT: H 113 LYS cc_start: 0.9537 (mtpt) cc_final: 0.8962 (mtpt) REVERT: H 163 ARG cc_start: 0.6456 (mtt-85) cc_final: 0.5625 (ttp-110) REVERT: H 317 ARG cc_start: 0.6008 (ptm160) cc_final: 0.5727 (ptt180) REVERT: H 434 LYS cc_start: 0.9254 (mmtm) cc_final: 0.8850 (mmtm) REVERT: H 452 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8161 (mm-40) REVERT: H 467 LYS cc_start: 0.8718 (ptpp) cc_final: 0.8375 (ptpp) REVERT: H 485 THR cc_start: 0.7965 (p) cc_final: 0.7749 (p) REVERT: a 34 MET cc_start: 0.8551 (mmp) cc_final: 0.7960 (mmm) REVERT: a 130 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8204 (mmt180) REVERT: a 159 ILE cc_start: 0.8495 (tp) cc_final: 0.8200 (mp) REVERT: a 164 MET cc_start: 0.6060 (ttt) cc_final: 0.5184 (tpp) REVERT: a 176 PHE cc_start: 0.8738 (t80) cc_final: 0.8165 (m-10) REVERT: a 341 MET cc_start: -0.1414 (mtp) cc_final: -0.3049 (ptt) REVERT: a 398 MET cc_start: 0.2899 (mmp) cc_final: 0.2505 (mmp) REVERT: a 403 HIS cc_start: 0.8071 (m-70) cc_final: 0.7531 (m-70) REVERT: a 446 LEU cc_start: 0.8853 (mt) cc_final: 0.8581 (mt) REVERT: a 450 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7462 (mm-30) REVERT: a 497 TYR cc_start: 0.7350 (m-80) cc_final: 0.6850 (m-10) REVERT: a 526 LYS cc_start: 0.9011 (mmpt) cc_final: 0.8706 (mmmt) REVERT: a 529 LYS cc_start: 0.9050 (tptp) cc_final: 0.8674 (tptp) REVERT: A 27 ASN cc_start: 0.8759 (m-40) cc_final: 0.8399 (p0) REVERT: A 108 LEU cc_start: 0.8752 (mt) cc_final: 0.8263 (mt) REVERT: A 113 ASN cc_start: 0.7963 (t0) cc_final: 0.7557 (t0) REVERT: A 125 ILE cc_start: 0.9594 (mt) cc_final: 0.9290 (mt) REVERT: A 129 PHE cc_start: 0.9420 (m-10) cc_final: 0.9179 (m-80) REVERT: A 175 PHE cc_start: 0.8245 (m-80) cc_final: 0.7184 (t80) REVERT: A 176 PHE cc_start: 0.7693 (m-10) cc_final: 0.7342 (m-10) REVERT: A 179 MET cc_start: 0.6672 (ptt) cc_final: 0.6371 (ptt) REVERT: A 233 MET cc_start: 0.3219 (ptp) cc_final: 0.2545 (ptm) REVERT: A 236 ARG cc_start: 0.6896 (ttp-110) cc_final: 0.6418 (tmt-80) REVERT: A 387 LEU cc_start: 0.7578 (tt) cc_final: 0.7251 (tt) REVERT: A 398 MET cc_start: 0.6884 (mmp) cc_final: 0.6644 (mmp) REVERT: A 410 LYS cc_start: 0.8653 (tptt) cc_final: 0.8369 (tptp) REVERT: A 411 ARG cc_start: 0.8288 (mtt180) cc_final: 0.7211 (mmm160) REVERT: A 518 LEU cc_start: 0.9161 (tp) cc_final: 0.8943 (tp) REVERT: A 526 LYS cc_start: 0.9130 (mttt) cc_final: 0.8574 (mmtm) REVERT: b 79 ASN cc_start: 0.7827 (p0) cc_final: 0.7547 (p0) REVERT: b 107 GLU cc_start: 0.8797 (tt0) cc_final: 0.8521 (pt0) REVERT: b 120 ILE cc_start: 0.8250 (mt) cc_final: 0.6485 (mt) REVERT: b 121 ILE cc_start: 0.9144 (mt) cc_final: 0.8506 (mt) REVERT: b 124 TYR cc_start: 0.9126 (m-10) cc_final: 0.8498 (m-80) REVERT: b 347 MET cc_start: 0.6707 (tpp) cc_final: 0.6118 (ptp) REVERT: b 402 LEU cc_start: 0.9465 (mt) cc_final: 0.9256 (tp) REVERT: b 409 MET cc_start: 0.9260 (tpp) cc_final: 0.8678 (tpp) REVERT: b 413 LYS cc_start: 0.9439 (tttt) cc_final: 0.9011 (ttmm) REVERT: b 433 PHE cc_start: 0.8864 (t80) cc_final: 0.8640 (t80) REVERT: b 482 MET cc_start: 0.7640 (mmp) cc_final: 0.7395 (mmm) REVERT: b 494 LYS cc_start: 0.8552 (tmmt) cc_final: 0.8318 (tmmt) REVERT: b 503 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8793 (mt-10) REVERT: b 506 GLU cc_start: 0.7792 (tt0) cc_final: 0.7506 (mt-10) REVERT: b 508 LEU cc_start: 0.9294 (mm) cc_final: 0.8808 (tt) REVERT: B 45 LEU cc_start: 0.8261 (mt) cc_final: 0.7971 (mt) REVERT: B 81 SER cc_start: 0.9098 (m) cc_final: 0.8793 (p) REVERT: B 269 MET cc_start: 0.3689 (ptm) cc_final: 0.3279 (ttp) REVERT: B 443 ILE cc_start: 0.9087 (pt) cc_final: 0.8858 (pt) REVERT: B 447 ASN cc_start: 0.9099 (m-40) cc_final: 0.8576 (p0) REVERT: B 451 ASP cc_start: 0.8193 (t0) cc_final: 0.7920 (t0) REVERT: d 47 MET cc_start: 0.6786 (ppp) cc_final: 0.6020 (ppp) REVERT: d 77 MET cc_start: 0.7838 (ppp) cc_final: 0.7285 (ppp) REVERT: d 91 ASP cc_start: 0.6881 (t0) cc_final: 0.6449 (t70) REVERT: d 116 HIS cc_start: 0.7344 (t-90) cc_final: 0.6961 (t-90) REVERT: d 120 ILE cc_start: 0.9110 (mp) cc_final: 0.8565 (mp) REVERT: d 124 PHE cc_start: 0.9300 (m-10) cc_final: 0.8986 (m-80) REVERT: d 125 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7897 (mm-40) REVERT: d 165 GLN cc_start: 0.6842 (mt0) cc_final: 0.6370 (mm-40) REVERT: d 166 TYR cc_start: 0.7746 (m-80) cc_final: 0.7442 (m-80) REVERT: d 305 LEU cc_start: 0.5954 (mt) cc_final: 0.5655 (pp) REVERT: d 394 LEU cc_start: 0.7768 (mm) cc_final: 0.7441 (mt) REVERT: d 513 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8916 (mm-30) REVERT: D 33 ASP cc_start: 0.8687 (p0) cc_final: 0.8434 (p0) REVERT: D 38 SER cc_start: 0.9589 (m) cc_final: 0.9103 (t) REVERT: D 44 MET cc_start: 0.7176 (tpt) cc_final: 0.6823 (tpt) REVERT: D 91 ASP cc_start: 0.7764 (t0) cc_final: 0.6871 (t70) REVERT: D 209 MET cc_start: 0.4374 (tmm) cc_final: 0.4092 (tmm) REVERT: e 127 SER cc_start: 0.9495 (m) cc_final: 0.9011 (p) REVERT: e 132 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8522 (tp40) REVERT: e 135 GLU cc_start: 0.8831 (pm20) cc_final: 0.8577 (pm20) REVERT: e 137 ILE cc_start: 0.9557 (mm) cc_final: 0.9350 (mt) REVERT: e 159 SER cc_start: 0.9411 (m) cc_final: 0.9140 (p) REVERT: e 203 MET cc_start: 0.6354 (ptp) cc_final: 0.5665 (ptp) REVERT: e 229 ARG cc_start: 0.7665 (mmt-90) cc_final: 0.7055 (mtm110) REVERT: e 392 MET cc_start: 0.2970 (mtm) cc_final: 0.2106 (ptm) REVERT: e 394 ILE cc_start: 0.7321 (mt) cc_final: 0.7050 (mt) REVERT: e 405 THR cc_start: 0.7890 (m) cc_final: 0.7553 (p) REVERT: e 481 MET cc_start: 0.7989 (mmp) cc_final: 0.7759 (mmp) REVERT: e 486 ASN cc_start: 0.8339 (m-40) cc_final: 0.8024 (t0) REVERT: e 524 GLU cc_start: 0.8637 (pm20) cc_final: 0.8427 (pm20) REVERT: e 537 GLN cc_start: 0.8808 (tt0) cc_final: 0.8597 (tt0) REVERT: e 548 ILE cc_start: 0.9402 (mm) cc_final: 0.8793 (mm) REVERT: e 550 LYS cc_start: 0.9281 (mmpt) cc_final: 0.9044 (mmmt) REVERT: e 552 ASP cc_start: 0.8773 (p0) cc_final: 0.8432 (p0) REVERT: E 61 ILE cc_start: 0.9548 (pt) cc_final: 0.9332 (pt) REVERT: E 94 MET cc_start: 0.5919 (tpt) cc_final: 0.5526 (tpp) REVERT: E 150 PHE cc_start: 0.7923 (m-80) cc_final: 0.7134 (m-80) REVERT: E 225 LYS cc_start: 0.8318 (mtmt) cc_final: 0.7878 (mmtt) REVERT: E 428 CYS cc_start: 0.8872 (t) cc_final: 0.8455 (t) REVERT: E 432 ASN cc_start: 0.8147 (m-40) cc_final: 0.7673 (t0) REVERT: E 454 VAL cc_start: 0.9468 (t) cc_final: 0.9199 (p) REVERT: E 477 ASP cc_start: 0.8790 (t0) cc_final: 0.7478 (t0) REVERT: E 481 MET cc_start: 0.8049 (mtp) cc_final: 0.7104 (mtp) REVERT: E 485 GLU cc_start: 0.8599 (tp30) cc_final: 0.8038 (tm-30) REVERT: E 521 ASP cc_start: 0.7708 (t0) cc_final: 0.7398 (t0) REVERT: g 35 ILE cc_start: 0.9755 (pt) cc_final: 0.9431 (mp) REVERT: g 107 CYS cc_start: 0.7868 (p) cc_final: 0.7152 (p) REVERT: g 112 ILE cc_start: 0.9128 (mt) cc_final: 0.8767 (mt) REVERT: g 117 HIS cc_start: 0.8383 (t-90) cc_final: 0.8167 (t-90) REVERT: g 133 LEU cc_start: 0.9472 (mt) cc_final: 0.9107 (mt) REVERT: g 137 LYS cc_start: 0.9400 (mmtm) cc_final: 0.9183 (mmtm) REVERT: g 242 ARG cc_start: 0.5971 (mtm-85) cc_final: 0.5687 (tmm-80) REVERT: g 364 TYR cc_start: 0.6918 (m-10) cc_final: 0.6457 (m-80) REVERT: g 507 ASP cc_start: 0.8471 (m-30) cc_final: 0.8168 (t0) REVERT: g 510 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8591 (mm-30) REVERT: g 525 ILE cc_start: 0.9236 (mt) cc_final: 0.9026 (pt) REVERT: g 545 ASP cc_start: 0.7500 (p0) cc_final: 0.7262 (p0) REVERT: g 555 VAL cc_start: 0.8992 (t) cc_final: 0.8551 (m) REVERT: g 585 ASP cc_start: 0.6848 (m-30) cc_final: 0.6464 (m-30) REVERT: G 52 MET cc_start: 0.7034 (mmm) cc_final: 0.6652 (mmm) REVERT: G 87 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8629 (tm-30) REVERT: G 120 ILE cc_start: 0.8841 (mm) cc_final: 0.7580 (mm) REVERT: G 166 HIS cc_start: 0.8148 (t-90) cc_final: 0.7938 (t70) REVERT: G 202 ARG cc_start: 0.8417 (mtm180) cc_final: 0.7797 (mtm110) REVERT: G 481 MET cc_start: 0.8864 (ttt) cc_final: 0.8656 (ttm) REVERT: G 509 MET cc_start: 0.9036 (mmp) cc_final: 0.8674 (mmm) REVERT: G 511 CYS cc_start: 0.9139 (p) cc_final: 0.8642 (p) REVERT: G 531 LEU cc_start: 0.9279 (tp) cc_final: 0.8802 (tp) REVERT: G 554 MET cc_start: 0.8444 (mmt) cc_final: 0.8215 (mmp) REVERT: G 572 THR cc_start: 0.9521 (p) cc_final: 0.9091 (p) REVERT: h 28 SER cc_start: 0.9472 (t) cc_final: 0.9101 (p) REVERT: h 216 ASN cc_start: 0.3757 (m110) cc_final: 0.3471 (t0) REVERT: h 322 ASP cc_start: 0.6123 (m-30) cc_final: 0.5738 (t0) REVERT: h 323 MET cc_start: -0.0715 (tmm) cc_final: -0.0941 (tmm) REVERT: h 362 TYR cc_start: 0.1780 (m-80) cc_final: 0.1126 (m-80) REVERT: h 401 LYS cc_start: 0.6898 (mttt) cc_final: 0.6601 (mttt) REVERT: h 434 LYS cc_start: 0.9221 (mtpt) cc_final: 0.8538 (ttpt) REVERT: h 437 MET cc_start: 0.8745 (ppp) cc_final: 0.8046 (ppp) REVERT: h 438 ILE cc_start: 0.9148 (mt) cc_final: 0.8818 (mm) REVERT: h 440 ASN cc_start: 0.8961 (t0) cc_final: 0.8746 (t0) REVERT: h 449 ILE cc_start: 0.9393 (mt) cc_final: 0.9188 (mt) REVERT: h 464 ILE cc_start: 0.8720 (pt) cc_final: 0.8384 (pt) REVERT: h 504 ILE cc_start: 0.9245 (mt) cc_final: 0.8994 (tp) REVERT: q 39 HIS cc_start: 0.7710 (t70) cc_final: 0.6741 (t-90) REVERT: q 71 MET cc_start: 0.8872 (ppp) cc_final: 0.8448 (ppp) REVERT: q 87 MET cc_start: 0.9127 (mtp) cc_final: 0.8553 (tpt) REVERT: q 91 GLN cc_start: 0.8310 (tt0) cc_final: 0.7978 (tt0) REVERT: q 105 ILE cc_start: 0.8883 (mt) cc_final: 0.8492 (mt) REVERT: q 106 LEU cc_start: 0.9071 (tp) cc_final: 0.8772 (tp) REVERT: q 109 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8339 (mm-30) REVERT: q 133 MET cc_start: 0.9381 (ttp) cc_final: 0.8818 (tmm) REVERT: q 139 LEU cc_start: 0.8831 (mt) cc_final: 0.8032 (tt) REVERT: q 176 ASP cc_start: 0.8871 (p0) cc_final: 0.8583 (p0) REVERT: q 393 ASN cc_start: 0.8226 (m-40) cc_final: 0.7557 (m-40) REVERT: q 451 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8599 (tp40) REVERT: Q 112 ASN cc_start: 0.8238 (t0) cc_final: 0.7982 (t0) REVERT: Q 128 ILE cc_start: 0.9146 (mt) cc_final: 0.8935 (mm) REVERT: Q 140 LYS cc_start: 0.8847 (tppt) cc_final: 0.8376 (tppt) REVERT: Q 167 ILE cc_start: 0.8963 (pt) cc_final: 0.8333 (tp) REVERT: Q 282 LYS cc_start: 0.4734 (mttt) cc_final: 0.4277 (tptp) REVERT: Q 287 MET cc_start: 0.6775 (mmp) cc_final: 0.5640 (tmm) REVERT: Q 288 MET cc_start: 0.4228 (ttt) cc_final: 0.3509 (ttm) REVERT: Q 311 HIS cc_start: 0.9074 (m-70) cc_final: 0.8638 (m-70) REVERT: Q 437 TYR cc_start: 0.7254 (m-10) cc_final: 0.7036 (m-10) REVERT: Q 451 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8271 (mm110) REVERT: Q 473 GLU cc_start: 0.9022 (pt0) cc_final: 0.8705 (pp20) REVERT: Q 521 LEU cc_start: 0.9197 (tp) cc_final: 0.8899 (mt) REVERT: Q 540 SER cc_start: 0.9309 (m) cc_final: 0.8813 (p) REVERT: z 34 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8053 (mt-10) REVERT: z 66 MET cc_start: 0.8087 (ppp) cc_final: 0.7829 (ppp) REVERT: z 122 PHE cc_start: 0.9443 (m-80) cc_final: 0.9241 (m-80) REVERT: z 127 LYS cc_start: 0.9084 (mtpp) cc_final: 0.8688 (tptt) REVERT: z 155 ARG cc_start: 0.8842 (mtm-85) cc_final: 0.8458 (ttm110) REVERT: z 193 MET cc_start: 0.6963 (ptp) cc_final: 0.6392 (ttm) REVERT: z 199 MET cc_start: 0.8074 (ppp) cc_final: 0.7428 (ppp) REVERT: z 283 GLU cc_start: 0.8238 (pt0) cc_final: 0.7902 (pt0) REVERT: z 369 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7739 (tt0) REVERT: z 399 LEU cc_start: 0.9722 (mt) cc_final: 0.9413 (pp) REVERT: z 431 MET cc_start: 0.7796 (mtt) cc_final: 0.7452 (ptp) REVERT: z 441 LYS cc_start: 0.8189 (ptpp) cc_final: 0.7537 (mmtm) REVERT: z 474 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8929 (mm-30) REVERT: z 477 LEU cc_start: 0.8987 (mt) cc_final: 0.8768 (mt) REVERT: z 481 GLN cc_start: 0.8896 (pt0) cc_final: 0.8688 (pt0) REVERT: z 500 ASP cc_start: 0.8596 (t0) cc_final: 0.7938 (t0) REVERT: Z 40 LYS cc_start: 0.9180 (mmtt) cc_final: 0.8669 (mmmt) REVERT: Z 43 LEU cc_start: 0.7699 (tp) cc_final: 0.7462 (tp) REVERT: Z 111 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8410 (mm-30) REVERT: Z 122 PHE cc_start: 0.9011 (m-10) cc_final: 0.8391 (m-10) REVERT: Z 131 LYS cc_start: 0.8910 (mttt) cc_final: 0.8446 (ttpt) REVERT: Z 151 LEU cc_start: 0.9455 (mt) cc_final: 0.9055 (tt) REVERT: Z 192 HIS cc_start: 0.8570 (m90) cc_final: 0.8212 (m90) REVERT: Z 193 MET cc_start: 0.7910 (ppp) cc_final: 0.7017 (ppp) REVERT: Z 223 ASP cc_start: 0.7244 (m-30) cc_final: 0.7024 (t0) REVERT: Z 224 MET cc_start: 0.3045 (mmt) cc_final: 0.2780 (mmm) REVERT: Z 376 CYS cc_start: 0.6916 (m) cc_final: 0.6592 (m) REVERT: Z 384 THR cc_start: 0.8236 (p) cc_final: 0.7967 (p) REVERT: Z 408 ASP cc_start: 0.7925 (t70) cc_final: 0.7665 (t0) REVERT: Z 412 ILE cc_start: 0.9516 (mt) cc_final: 0.9312 (tp) REVERT: Z 431 MET cc_start: 0.7017 (mpp) cc_final: 0.6659 (mpp) REVERT: Z 442 THR cc_start: 0.8980 (p) cc_final: 0.8620 (t) REVERT: Z 482 ASP cc_start: 0.9008 (m-30) cc_final: 0.8116 (p0) REVERT: Z 532 GLU cc_start: 0.8192 (tp30) cc_final: 0.7796 (tp30) outliers start: 3 outliers final: 0 residues processed: 1630 average time/residue: 0.5549 time to fit residues: 1538.6453 Evaluate side-chains 1324 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1324 time to evaluate : 5.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 3.9990 chunk 441 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 579 optimal weight: 0.8980 chunk 321 optimal weight: 3.9990 chunk 664 optimal weight: 0.9990 chunk 537 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 5.9990 chunk 698 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 261 GLN b 420 GLN D 59 ASN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN D 473 HIS e 50 HIS ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 HIS g 24 ASN g 503 GLN g 535 HIS ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 HIS ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 567 GLN G 568 GLN h 90 GLN h 345 HIS ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 91 GLN ** q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 ASN q 392 ASN q 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 62697 Z= 0.164 Angle : 0.540 9.396 84560 Z= 0.276 Chirality : 0.042 0.238 10175 Planarity : 0.003 0.062 10863 Dihedral : 3.647 22.367 8578 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 0.06 % Allowed : 1.50 % Favored : 98.44 % 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: 0.00 (0.09), residues: 8076 helix: 0.67 (0.08), residues: 3775 sheet: -0.17 (0.20), residues: 661 loop : -0.59 (0.10), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP h 497 HIS 0.015 0.001 HIS b 155 PHE 0.015 0.001 PHE h 442 TYR 0.035 0.001 TYR h 427 ARG 0.012 0.001 ARG Q 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1610 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1606 time to evaluate : 5.377 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: H 33 CYS cc_start: 0.9041 (m) cc_final: 0.8835 (m) REVERT: H 113 LYS cc_start: 0.9539 (mtpt) cc_final: 0.8979 (mtpt) REVERT: H 150 GLU cc_start: 0.7759 (tm-30) cc_final: 0.6582 (mp0) REVERT: H 163 ARG cc_start: 0.6507 (mtt-85) cc_final: 0.5637 (ttp-110) REVERT: H 283 ARG cc_start: 0.5473 (mmp80) cc_final: 0.5018 (tpp-160) REVERT: H 355 MET cc_start: 0.5539 (pmm) cc_final: 0.4759 (ppp) REVERT: H 364 LEU cc_start: 0.8094 (pp) cc_final: 0.7779 (pp) REVERT: H 452 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8679 (mm-40) REVERT: H 467 LYS cc_start: 0.8742 (ptpp) cc_final: 0.8328 (ptpp) REVERT: H 485 THR cc_start: 0.7767 (p) cc_final: 0.6834 (p) REVERT: a 34 MET cc_start: 0.8574 (mmp) cc_final: 0.8056 (mmm) REVERT: a 121 HIS cc_start: 0.8110 (t-90) cc_final: 0.7505 (t70) REVERT: a 164 MET cc_start: 0.6080 (ttt) cc_final: 0.5130 (tpp) REVERT: a 176 PHE cc_start: 0.8745 (t80) cc_final: 0.8133 (m-10) REVERT: a 179 MET cc_start: 0.6476 (ptp) cc_final: 0.6260 (ptp) REVERT: a 326 LEU cc_start: 0.7757 (mp) cc_final: 0.7457 (mm) REVERT: a 341 MET cc_start: -0.1741 (mtp) cc_final: -0.3253 (ptt) REVERT: a 398 MET cc_start: 0.3130 (mmp) cc_final: 0.2743 (mmp) REVERT: a 403 HIS cc_start: 0.8084 (m-70) cc_final: 0.7560 (m-70) REVERT: a 450 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7438 (mm-30) REVERT: a 469 ASP cc_start: 0.8427 (t0) cc_final: 0.8055 (t0) REVERT: a 497 TYR cc_start: 0.7451 (m-80) cc_final: 0.6823 (m-10) REVERT: a 526 LYS cc_start: 0.9012 (mmpt) cc_final: 0.8727 (mmmt) REVERT: a 529 LYS cc_start: 0.9075 (tptp) cc_final: 0.8707 (tptp) REVERT: A 27 ASN cc_start: 0.8864 (m-40) cc_final: 0.8487 (p0) REVERT: A 108 LEU cc_start: 0.8507 (mt) cc_final: 0.8004 (mt) REVERT: A 111 ARG cc_start: 0.8150 (mmt-90) cc_final: 0.7855 (mmt90) REVERT: A 113 ASN cc_start: 0.8028 (t0) cc_final: 0.7604 (t0) REVERT: A 125 ILE cc_start: 0.9604 (mt) cc_final: 0.9249 (mt) REVERT: A 129 PHE cc_start: 0.9444 (m-10) cc_final: 0.9223 (m-80) REVERT: A 175 PHE cc_start: 0.8304 (m-80) cc_final: 0.7292 (t80) REVERT: A 176 PHE cc_start: 0.7780 (m-10) cc_final: 0.7508 (m-80) REVERT: A 233 MET cc_start: 0.3178 (ptp) cc_final: 0.2653 (ptm) REVERT: A 236 ARG cc_start: 0.6689 (ttp-110) cc_final: 0.6454 (tmt-80) REVERT: A 398 MET cc_start: 0.6915 (mmp) cc_final: 0.6677 (mmp) REVERT: A 411 ARG cc_start: 0.8379 (mtt180) cc_final: 0.7177 (mmm160) REVERT: A 526 LYS cc_start: 0.9135 (mttt) cc_final: 0.8583 (mmtm) REVERT: b 31 ASP cc_start: 0.8668 (m-30) cc_final: 0.8293 (m-30) REVERT: b 79 ASN cc_start: 0.7815 (p0) cc_final: 0.7549 (p0) REVERT: b 107 GLU cc_start: 0.8801 (tt0) cc_final: 0.8532 (pt0) REVERT: b 155 HIS cc_start: 0.5659 (p-80) cc_final: 0.5265 (p90) REVERT: b 347 MET cc_start: 0.6897 (tpp) cc_final: 0.6329 (ptp) REVERT: b 402 LEU cc_start: 0.9492 (mt) cc_final: 0.9246 (tp) REVERT: b 409 MET cc_start: 0.9292 (tpp) cc_final: 0.8712 (tpp) REVERT: b 413 LYS cc_start: 0.9460 (tttt) cc_final: 0.8864 (ttmm) REVERT: b 476 ASN cc_start: 0.9088 (t0) cc_final: 0.8842 (t0) REVERT: b 482 MET cc_start: 0.7500 (mmp) cc_final: 0.7232 (mmm) REVERT: b 503 GLU cc_start: 0.9470 (mt-10) cc_final: 0.8790 (mt-10) REVERT: b 506 GLU cc_start: 0.7760 (tt0) cc_final: 0.7469 (mt-10) REVERT: b 508 LEU cc_start: 0.9301 (mm) cc_final: 0.8922 (tt) REVERT: B 57 THR cc_start: 0.5872 (t) cc_final: 0.5321 (t) REVERT: B 81 SER cc_start: 0.9090 (m) cc_final: 0.8821 (p) REVERT: B 118 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8087 (tp-100) REVERT: B 269 MET cc_start: 0.3496 (ptm) cc_final: 0.3296 (ttp) REVERT: B 409 MET cc_start: 0.9063 (mmp) cc_final: 0.8149 (mmm) REVERT: B 416 ASP cc_start: 0.9388 (m-30) cc_final: 0.9063 (m-30) REVERT: B 443 ILE cc_start: 0.9057 (pt) cc_final: 0.8829 (pt) REVERT: B 446 ASP cc_start: 0.8292 (p0) cc_final: 0.8064 (p0) REVERT: B 447 ASN cc_start: 0.9045 (m-40) cc_final: 0.8560 (p0) REVERT: d 39 LEU cc_start: 0.8944 (tp) cc_final: 0.8711 (tp) REVERT: d 47 MET cc_start: 0.6684 (ppp) cc_final: 0.6418 (ppp) REVERT: d 65 LEU cc_start: 0.8798 (mt) cc_final: 0.8363 (mt) REVERT: d 68 MET cc_start: 0.6507 (pmm) cc_final: 0.5845 (pmm) REVERT: d 77 MET cc_start: 0.8003 (ppp) cc_final: 0.7358 (ppp) REVERT: d 91 ASP cc_start: 0.7137 (t0) cc_final: 0.6682 (t70) REVERT: d 116 HIS cc_start: 0.7596 (t-90) cc_final: 0.7234 (t-90) REVERT: d 120 ILE cc_start: 0.9142 (mp) cc_final: 0.8592 (mp) REVERT: d 124 PHE cc_start: 0.9364 (m-10) cc_final: 0.9023 (m-80) REVERT: d 125 GLN cc_start: 0.8274 (mm-40) cc_final: 0.8028 (mm-40) REVERT: d 130 ARG cc_start: 0.8586 (mtp-110) cc_final: 0.8355 (mtp-110) REVERT: d 166 TYR cc_start: 0.7680 (m-80) cc_final: 0.7363 (m-80) REVERT: d 305 LEU cc_start: 0.5961 (mt) cc_final: 0.5665 (pp) REVERT: d 394 LEU cc_start: 0.7678 (mm) cc_final: 0.7408 (mt) REVERT: d 445 SER cc_start: 0.8976 (m) cc_final: 0.8726 (p) REVERT: d 457 ASN cc_start: 0.8633 (p0) cc_final: 0.8422 (p0) REVERT: d 513 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8923 (mm-30) REVERT: D 38 SER cc_start: 0.9448 (m) cc_final: 0.8936 (t) REVERT: D 44 MET cc_start: 0.7281 (tpt) cc_final: 0.6940 (tpt) REVERT: D 91 ASP cc_start: 0.8181 (t0) cc_final: 0.7296 (t70) REVERT: D 209 MET cc_start: 0.3975 (tmm) cc_final: 0.3708 (tmm) REVERT: e 127 SER cc_start: 0.9527 (m) cc_final: 0.8987 (p) REVERT: e 132 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8629 (tp40) REVERT: e 135 GLU cc_start: 0.8868 (pm20) cc_final: 0.8612 (pm20) REVERT: e 161 LEU cc_start: 0.9040 (mt) cc_final: 0.8382 (mt) REVERT: e 203 MET cc_start: 0.6757 (ptp) cc_final: 0.6162 (ptp) REVERT: e 212 MET cc_start: 0.6076 (ppp) cc_final: 0.5623 (ppp) REVERT: e 229 ARG cc_start: 0.7711 (mmt-90) cc_final: 0.7091 (mtm110) REVERT: e 405 THR cc_start: 0.7952 (m) cc_final: 0.7645 (p) REVERT: e 481 MET cc_start: 0.8153 (mmp) cc_final: 0.7822 (mmp) REVERT: e 486 ASN cc_start: 0.8468 (m-40) cc_final: 0.8105 (t0) REVERT: e 537 GLN cc_start: 0.8819 (tt0) cc_final: 0.8618 (tt0) REVERT: e 544 LEU cc_start: 0.9072 (tp) cc_final: 0.8756 (tp) REVERT: e 548 ILE cc_start: 0.9447 (mm) cc_final: 0.8882 (mm) REVERT: e 549 LEU cc_start: 0.9407 (mm) cc_final: 0.9180 (mm) REVERT: e 550 LYS cc_start: 0.9362 (mmpt) cc_final: 0.9088 (mmmt) REVERT: e 552 ASP cc_start: 0.8791 (p0) cc_final: 0.8447 (p0) REVERT: E 428 CYS cc_start: 0.8906 (t) cc_final: 0.8583 (t) REVERT: E 432 ASN cc_start: 0.7990 (m-40) cc_final: 0.7572 (t0) REVERT: E 454 VAL cc_start: 0.9538 (t) cc_final: 0.9246 (p) REVERT: E 477 ASP cc_start: 0.8736 (t0) cc_final: 0.7326 (t0) REVERT: E 481 MET cc_start: 0.8053 (mtp) cc_final: 0.7117 (mtp) REVERT: E 485 GLU cc_start: 0.8604 (tp30) cc_final: 0.8011 (tm-30) REVERT: E 521 ASP cc_start: 0.7824 (t0) cc_final: 0.7460 (t0) REVERT: g 35 ILE cc_start: 0.9762 (pt) cc_final: 0.9489 (mp) REVERT: g 106 GLN cc_start: 0.7868 (pp30) cc_final: 0.7440 (pp30) REVERT: g 107 CYS cc_start: 0.7827 (p) cc_final: 0.7559 (p) REVERT: g 112 ILE cc_start: 0.9128 (mt) cc_final: 0.8804 (mt) REVERT: g 117 HIS cc_start: 0.8448 (t-90) cc_final: 0.8090 (t-90) REVERT: g 133 LEU cc_start: 0.9513 (mt) cc_final: 0.9099 (mt) REVERT: g 137 LYS cc_start: 0.9380 (mmtm) cc_final: 0.9135 (mmtm) REVERT: g 242 ARG cc_start: 0.6081 (mtm-85) cc_final: 0.5786 (tmm-80) REVERT: g 440 MET cc_start: 0.3766 (ppp) cc_final: 0.3271 (ppp) REVERT: g 510 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8601 (mm-30) REVERT: g 545 ASP cc_start: 0.7602 (p0) cc_final: 0.7334 (p0) REVERT: g 553 ASP cc_start: 0.8776 (p0) cc_final: 0.8494 (p0) REVERT: g 555 VAL cc_start: 0.9003 (t) cc_final: 0.8555 (m) REVERT: g 571 LYS cc_start: 0.9532 (tttt) cc_final: 0.9017 (pttt) REVERT: g 585 ASP cc_start: 0.6989 (m-30) cc_final: 0.6597 (m-30) REVERT: G 52 MET cc_start: 0.7083 (mmm) cc_final: 0.6762 (mmm) REVERT: G 78 MET cc_start: 0.8909 (mtt) cc_final: 0.8677 (mmm) REVERT: G 87 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8629 (tm-30) REVERT: G 97 ILE cc_start: 0.9144 (mm) cc_final: 0.8904 (mm) REVERT: G 99 LEU cc_start: 0.8688 (mm) cc_final: 0.8486 (mm) REVERT: G 120 ILE cc_start: 0.8957 (mm) cc_final: 0.7834 (mm) REVERT: G 172 CYS cc_start: 0.8413 (m) cc_final: 0.8013 (m) REVERT: G 202 ARG cc_start: 0.8376 (mtm180) cc_final: 0.7759 (mtm110) REVERT: G 481 MET cc_start: 0.8456 (ttt) cc_final: 0.8005 (ttt) REVERT: G 509 MET cc_start: 0.8991 (mmp) cc_final: 0.8744 (mmp) REVERT: G 512 ILE cc_start: 0.9131 (mm) cc_final: 0.8895 (mm) REVERT: G 517 ILE cc_start: 0.9310 (mm) cc_final: 0.9011 (mm) REVERT: G 572 THR cc_start: 0.9510 (p) cc_final: 0.9084 (p) REVERT: h 28 SER cc_start: 0.9402 (t) cc_final: 0.9120 (p) REVERT: h 216 ASN cc_start: 0.3771 (m110) cc_final: 0.3492 (t0) REVERT: h 322 ASP cc_start: 0.6063 (m-30) cc_final: 0.5747 (t0) REVERT: h 362 TYR cc_start: 0.1759 (m-80) cc_final: 0.1273 (m-80) REVERT: h 401 LYS cc_start: 0.6936 (mttt) cc_final: 0.6555 (mttt) REVERT: h 418 MET cc_start: 0.5574 (ttt) cc_final: 0.5322 (ttt) REVERT: h 434 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8741 (mtpt) REVERT: h 437 MET cc_start: 0.8727 (ppp) cc_final: 0.8158 (ppp) REVERT: h 438 ILE cc_start: 0.9110 (mt) cc_final: 0.8654 (mm) REVERT: h 449 ILE cc_start: 0.9331 (mt) cc_final: 0.9131 (mt) REVERT: h 460 ASP cc_start: 0.8539 (t0) cc_final: 0.8289 (t0) REVERT: h 514 THR cc_start: 0.9250 (t) cc_final: 0.8909 (m) REVERT: q 39 HIS cc_start: 0.7829 (t70) cc_final: 0.7487 (t-170) REVERT: q 71 MET cc_start: 0.8891 (ppp) cc_final: 0.8681 (ppp) REVERT: q 87 MET cc_start: 0.8925 (mtp) cc_final: 0.8013 (tpt) REVERT: q 90 GLU cc_start: 0.8288 (pp20) cc_final: 0.7641 (pp20) REVERT: q 106 LEU cc_start: 0.9180 (tp) cc_final: 0.8863 (tp) REVERT: q 133 MET cc_start: 0.9351 (ttp) cc_final: 0.8837 (tmm) REVERT: q 139 LEU cc_start: 0.8870 (mt) cc_final: 0.8152 (tt) REVERT: q 176 ASP cc_start: 0.8938 (p0) cc_final: 0.8662 (p0) REVERT: q 392 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7339 (t0) REVERT: q 393 ASN cc_start: 0.8312 (m-40) cc_final: 0.7749 (m-40) REVERT: q 451 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8673 (tp40) REVERT: q 470 ASP cc_start: 0.8262 (t0) cc_final: 0.7800 (t0) REVERT: Q 112 ASN cc_start: 0.8394 (t0) cc_final: 0.7783 (t0) REVERT: Q 122 LEU cc_start: 0.8747 (mp) cc_final: 0.8443 (mp) REVERT: Q 128 ILE cc_start: 0.9101 (mt) cc_final: 0.8890 (mm) REVERT: Q 140 LYS cc_start: 0.8772 (tppt) cc_final: 0.8427 (tppt) REVERT: Q 167 ILE cc_start: 0.9036 (pt) cc_final: 0.8456 (tp) REVERT: Q 227 VAL cc_start: 0.7566 (t) cc_final: 0.7349 (t) REVERT: Q 282 LYS cc_start: 0.4764 (mttt) cc_final: 0.4323 (tptp) REVERT: Q 311 HIS cc_start: 0.9119 (m-70) cc_final: 0.8661 (m-70) REVERT: Q 451 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8169 (mm110) REVERT: Q 540 SER cc_start: 0.9383 (m) cc_final: 0.8881 (p) REVERT: z 66 MET cc_start: 0.8354 (ppp) cc_final: 0.8060 (ppp) REVERT: z 127 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8790 (tptt) REVERT: z 155 ARG cc_start: 0.8849 (mtm-85) cc_final: 0.8514 (ttm110) REVERT: z 199 MET cc_start: 0.8219 (ppp) cc_final: 0.7630 (ppp) REVERT: z 268 LYS cc_start: 0.9159 (tttt) cc_final: 0.8838 (pttm) REVERT: z 283 GLU cc_start: 0.8272 (pt0) cc_final: 0.7947 (pt0) REVERT: z 376 CYS cc_start: 0.6430 (m) cc_final: 0.6175 (m) REVERT: z 399 LEU cc_start: 0.9738 (mt) cc_final: 0.9429 (pp) REVERT: z 431 MET cc_start: 0.7752 (mtt) cc_final: 0.7481 (ptp) REVERT: z 474 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8889 (mm-30) REVERT: z 481 GLN cc_start: 0.8973 (pt0) cc_final: 0.8685 (pt0) REVERT: z 500 ASP cc_start: 0.8795 (t0) cc_final: 0.8087 (t0) REVERT: Z 24 THR cc_start: 0.8938 (m) cc_final: 0.8565 (p) REVERT: Z 29 LEU cc_start: 0.9145 (tp) cc_final: 0.8931 (tp) REVERT: Z 33 LEU cc_start: 0.9402 (mp) cc_final: 0.9090 (mp) REVERT: Z 66 MET cc_start: 0.3487 (ppp) cc_final: 0.3263 (ppp) REVERT: Z 122 PHE cc_start: 0.8952 (m-10) cc_final: 0.8441 (m-10) REVERT: Z 131 LYS cc_start: 0.8835 (mttt) cc_final: 0.8359 (ttpt) REVERT: Z 151 LEU cc_start: 0.9458 (mt) cc_final: 0.9064 (tt) REVERT: Z 192 HIS cc_start: 0.8568 (m90) cc_final: 0.8276 (m90) REVERT: Z 193 MET cc_start: 0.7965 (ppp) cc_final: 0.6960 (ppp) REVERT: Z 223 ASP cc_start: 0.7266 (m-30) cc_final: 0.7016 (t0) REVERT: Z 224 MET cc_start: 0.3670 (mmt) cc_final: 0.3179 (mmm) REVERT: Z 376 CYS cc_start: 0.6885 (m) cc_final: 0.6561 (m) REVERT: Z 384 THR cc_start: 0.8391 (p) cc_final: 0.8113 (p) REVERT: Z 408 ASP cc_start: 0.8126 (t70) cc_final: 0.7863 (t0) REVERT: Z 431 MET cc_start: 0.7176 (mpp) cc_final: 0.6772 (mpp) REVERT: Z 442 THR cc_start: 0.9054 (p) cc_final: 0.8658 (t) REVERT: Z 478 ASP cc_start: 0.8673 (m-30) cc_final: 0.8433 (m-30) REVERT: Z 482 ASP cc_start: 0.9007 (m-30) cc_final: 0.8130 (p0) outliers start: 4 outliers final: 1 residues processed: 1608 average time/residue: 0.5533 time to fit residues: 1517.8065 Evaluate side-chains 1314 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1312 time to evaluate : 5.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 1.9990 chunk 700 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 456 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 778 optimal weight: 7.9990 chunk 646 optimal weight: 8.9990 chunk 360 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 257 optimal weight: 2.9990 chunk 408 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: ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 430 ASN ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN b 420 GLN B 304 ASN ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS D 217 GLN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 HIS e 138 GLN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 HIS ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 503 GLN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 567 GLN G 568 GLN ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN h 345 HIS ** h 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 515 ASN ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 ASN ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.7336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 62697 Z= 0.240 Angle : 0.621 11.812 84560 Z= 0.322 Chirality : 0.044 0.257 10175 Planarity : 0.004 0.066 10863 Dihedral : 4.090 22.826 8578 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 0.01 % Allowed : 1.97 % Favored : 98.02 % 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: -0.13 (0.09), residues: 8076 helix: 0.61 (0.08), residues: 3815 sheet: -0.33 (0.19), residues: 671 loop : -0.71 (0.10), residues: 3590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP h 497 HIS 0.010 0.001 HIS E 424 PHE 0.027 0.002 PHE Z 132 TYR 0.030 0.002 TYR Q 131 ARG 0.019 0.001 ARG G 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1599 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1598 time to evaluate : 5.383 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: H 44 LEU cc_start: 0.8601 (tp) cc_final: 0.8259 (tt) REVERT: H 118 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8658 (tm-30) REVERT: H 150 GLU cc_start: 0.7836 (tm-30) cc_final: 0.6594 (mp0) REVERT: H 163 ARG cc_start: 0.6830 (mtt-85) cc_final: 0.6063 (ttp-110) REVERT: H 355 MET cc_start: 0.5446 (pmm) cc_final: 0.4296 (ppp) REVERT: H 434 LYS cc_start: 0.9217 (mmtm) cc_final: 0.8897 (mmtm) REVERT: H 452 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8684 (mm-40) REVERT: H 459 PHE cc_start: 0.8000 (m-80) cc_final: 0.7617 (m-80) REVERT: H 467 LYS cc_start: 0.8883 (ptpp) cc_final: 0.8581 (ttmt) REVERT: a 34 MET cc_start: 0.8652 (mmp) cc_final: 0.8134 (mmm) REVERT: a 44 LEU cc_start: 0.9233 (tp) cc_final: 0.9009 (tp) REVERT: a 60 PHE cc_start: 0.6956 (p90) cc_final: 0.6584 (p90) REVERT: a 104 ILE cc_start: 0.9723 (mm) cc_final: 0.9518 (mm) REVERT: a 121 HIS cc_start: 0.8282 (t-90) cc_final: 0.7683 (t70) REVERT: a 123 THR cc_start: 0.8956 (m) cc_final: 0.8630 (m) REVERT: a 164 MET cc_start: 0.5986 (ttt) cc_final: 0.5611 (ttm) REVERT: a 176 PHE cc_start: 0.8781 (t80) cc_final: 0.8216 (m-10) REVERT: a 217 LEU cc_start: 0.6998 (mt) cc_final: 0.6761 (mt) REVERT: a 341 MET cc_start: -0.1354 (mtp) cc_final: -0.2722 (ptm) REVERT: a 398 MET cc_start: 0.3477 (mmp) cc_final: 0.3178 (mmp) REVERT: a 450 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7861 (mm-30) REVERT: a 526 LYS cc_start: 0.8993 (mmpt) cc_final: 0.8692 (mmmt) REVERT: a 529 LYS cc_start: 0.9087 (tptp) cc_final: 0.8650 (tptp) REVERT: a 542 ASP cc_start: 0.8870 (t0) cc_final: 0.8548 (t0) REVERT: A 27 ASN cc_start: 0.8949 (m-40) cc_final: 0.8591 (p0) REVERT: A 108 LEU cc_start: 0.8545 (mt) cc_final: 0.8047 (mt) REVERT: A 111 ARG cc_start: 0.8194 (mmt-90) cc_final: 0.7886 (mmt90) REVERT: A 113 ASN cc_start: 0.8156 (t0) cc_final: 0.7724 (t0) REVERT: A 125 ILE cc_start: 0.9605 (mt) cc_final: 0.9273 (mt) REVERT: A 129 PHE cc_start: 0.9472 (m-10) cc_final: 0.9181 (m-80) REVERT: A 206 LEU cc_start: 0.8810 (mp) cc_final: 0.8065 (tt) REVERT: A 233 MET cc_start: 0.3010 (ptp) cc_final: 0.1568 (ppp) REVERT: A 236 ARG cc_start: 0.6698 (ttp-110) cc_final: 0.6347 (tmt-80) REVERT: A 398 MET cc_start: 0.6905 (mmp) cc_final: 0.6184 (mpp) REVERT: A 411 ARG cc_start: 0.8461 (mtt180) cc_final: 0.7371 (mmm160) REVERT: A 450 GLU cc_start: 0.8862 (tp30) cc_final: 0.8564 (tp30) REVERT: A 472 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8207 (mm-30) REVERT: A 518 LEU cc_start: 0.9054 (tp) cc_final: 0.8843 (tp) REVERT: A 526 LYS cc_start: 0.9200 (mttt) cc_final: 0.8665 (mmtm) REVERT: b 31 ASP cc_start: 0.8777 (m-30) cc_final: 0.8425 (m-30) REVERT: b 79 ASN cc_start: 0.7925 (p0) cc_final: 0.7697 (p0) REVERT: b 107 GLU cc_start: 0.8880 (tt0) cc_final: 0.8660 (pt0) REVERT: b 347 MET cc_start: 0.6983 (tpp) cc_final: 0.6571 (ptp) REVERT: b 402 LEU cc_start: 0.9497 (mt) cc_final: 0.9275 (mp) REVERT: b 409 MET cc_start: 0.9284 (tpp) cc_final: 0.8657 (tpp) REVERT: b 413 LYS cc_start: 0.9518 (tttt) cc_final: 0.8908 (ttmm) REVERT: b 482 MET cc_start: 0.7885 (mmp) cc_final: 0.7593 (mmm) REVERT: b 508 LEU cc_start: 0.9358 (mm) cc_final: 0.8902 (tt) REVERT: B 57 THR cc_start: 0.7041 (t) cc_final: 0.6452 (t) REVERT: B 81 SER cc_start: 0.9037 (m) cc_final: 0.8797 (p) REVERT: B 116 HIS cc_start: 0.7621 (m-70) cc_final: 0.7314 (m-70) REVERT: B 133 ASP cc_start: 0.9231 (m-30) cc_final: 0.8978 (m-30) REVERT: B 269 MET cc_start: 0.3942 (ptm) cc_final: 0.3629 (ttp) REVERT: B 416 ASP cc_start: 0.9417 (m-30) cc_final: 0.9087 (m-30) REVERT: B 443 ILE cc_start: 0.9105 (pt) cc_final: 0.8886 (pt) REVERT: B 446 ASP cc_start: 0.8118 (p0) cc_final: 0.7910 (p0) REVERT: B 447 ASN cc_start: 0.9057 (m-40) cc_final: 0.8553 (p0) REVERT: d 39 LEU cc_start: 0.8901 (tp) cc_final: 0.8617 (tp) REVERT: d 65 LEU cc_start: 0.8732 (mt) cc_final: 0.8361 (mt) REVERT: d 68 MET cc_start: 0.6458 (pmm) cc_final: 0.5939 (pmm) REVERT: d 77 MET cc_start: 0.8343 (ppp) cc_final: 0.7518 (ppp) REVERT: d 116 HIS cc_start: 0.7915 (t-90) cc_final: 0.7407 (t-90) REVERT: d 124 PHE cc_start: 0.9471 (m-10) cc_final: 0.9043 (m-80) REVERT: d 130 ARG cc_start: 0.8600 (mtp-110) cc_final: 0.8376 (mtp-110) REVERT: d 305 LEU cc_start: 0.6047 (mt) cc_final: 0.5752 (pp) REVERT: d 389 GLU cc_start: 0.8132 (pp20) cc_final: 0.7337 (pm20) REVERT: d 394 LEU cc_start: 0.7642 (mm) cc_final: 0.7440 (mm) REVERT: d 445 SER cc_start: 0.9051 (m) cc_final: 0.8810 (p) REVERT: D 44 MET cc_start: 0.7098 (tpt) cc_final: 0.6822 (tpt) REVERT: D 91 ASP cc_start: 0.7728 (t0) cc_final: 0.7156 (t70) REVERT: D 183 ASP cc_start: 0.8148 (t70) cc_final: 0.7880 (t70) REVERT: D 432 MET cc_start: 0.8620 (ppp) cc_final: 0.7935 (ppp) REVERT: e 127 SER cc_start: 0.9456 (m) cc_final: 0.9008 (p) REVERT: e 132 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8033 (tp40) REVERT: e 161 LEU cc_start: 0.9070 (mt) cc_final: 0.8473 (mt) REVERT: e 229 ARG cc_start: 0.7813 (mmt-90) cc_final: 0.7116 (mtm110) REVERT: e 353 HIS cc_start: 0.7935 (m-70) cc_final: 0.7706 (m-70) REVERT: e 394 ILE cc_start: 0.6876 (mt) cc_final: 0.6327 (mp) REVERT: e 481 MET cc_start: 0.8248 (mmp) cc_final: 0.7956 (mmp) REVERT: e 544 LEU cc_start: 0.9131 (tp) cc_final: 0.8852 (tp) REVERT: e 550 LYS cc_start: 0.9411 (mmpt) cc_final: 0.9084 (mmmt) REVERT: e 552 ASP cc_start: 0.8927 (p0) cc_final: 0.8537 (p0) REVERT: E 71 ASP cc_start: 0.8422 (m-30) cc_final: 0.8177 (m-30) REVERT: E 428 CYS cc_start: 0.8977 (t) cc_final: 0.8630 (t) REVERT: E 432 ASN cc_start: 0.8090 (m-40) cc_final: 0.7569 (t0) REVERT: E 454 VAL cc_start: 0.9609 (t) cc_final: 0.9378 (p) REVERT: E 477 ASP cc_start: 0.8638 (t0) cc_final: 0.7121 (t0) REVERT: E 481 MET cc_start: 0.8086 (mtp) cc_final: 0.7176 (mtp) REVERT: E 485 GLU cc_start: 0.8690 (tp30) cc_final: 0.7933 (tm-30) REVERT: E 521 ASP cc_start: 0.7770 (t0) cc_final: 0.7391 (t0) REVERT: g 35 ILE cc_start: 0.9697 (pt) cc_final: 0.9451 (mp) REVERT: g 106 GLN cc_start: 0.8306 (pp30) cc_final: 0.8077 (pp30) REVERT: g 107 CYS cc_start: 0.8108 (p) cc_final: 0.7906 (p) REVERT: g 112 ILE cc_start: 0.9208 (mt) cc_final: 0.8865 (mt) REVERT: g 117 HIS cc_start: 0.8642 (t-90) cc_final: 0.8259 (t-90) REVERT: g 133 LEU cc_start: 0.9540 (mt) cc_final: 0.9173 (mt) REVERT: g 137 LYS cc_start: 0.9387 (mmtm) cc_final: 0.9123 (mmtm) REVERT: g 163 TYR cc_start: 0.6463 (t80) cc_final: 0.6102 (t80) REVERT: g 234 MET cc_start: 0.1984 (mmt) cc_final: 0.1694 (mmm) REVERT: g 242 ARG cc_start: 0.6050 (mtm-85) cc_final: 0.5605 (tmm-80) REVERT: g 364 TYR cc_start: 0.6770 (m-80) cc_final: 0.6394 (m-80) REVERT: g 440 MET cc_start: 0.3974 (ppp) cc_final: 0.3457 (ppp) REVERT: g 487 LEU cc_start: 0.8957 (mt) cc_final: 0.8643 (mt) REVERT: g 509 MET cc_start: 0.9486 (mmp) cc_final: 0.9067 (mmt) REVERT: g 553 ASP cc_start: 0.8977 (p0) cc_final: 0.8546 (p0) REVERT: g 555 VAL cc_start: 0.9078 (t) cc_final: 0.8565 (m) REVERT: g 571 LYS cc_start: 0.9537 (tttt) cc_final: 0.9275 (ttmt) REVERT: G 42 LYS cc_start: 0.9338 (mmtt) cc_final: 0.9078 (mmtp) REVERT: G 50 ASP cc_start: 0.8010 (t0) cc_final: 0.7721 (t0) REVERT: G 52 MET cc_start: 0.7165 (mmm) cc_final: 0.6825 (mmm) REVERT: G 120 ILE cc_start: 0.9007 (mm) cc_final: 0.8088 (mm) REVERT: G 172 CYS cc_start: 0.8529 (m) cc_final: 0.8205 (m) REVERT: G 234 MET cc_start: -0.2558 (mtt) cc_final: -0.2758 (mtm) REVERT: G 481 MET cc_start: 0.8975 (ttt) cc_final: 0.8658 (ttt) REVERT: G 509 MET cc_start: 0.9077 (mmp) cc_final: 0.8807 (mmp) REVERT: G 511 CYS cc_start: 0.9225 (p) cc_final: 0.8997 (p) REVERT: G 517 ILE cc_start: 0.9264 (mm) cc_final: 0.9000 (mm) REVERT: G 547 ASP cc_start: 0.9217 (t0) cc_final: 0.8612 (p0) REVERT: G 572 THR cc_start: 0.9557 (p) cc_final: 0.9216 (p) REVERT: h 28 SER cc_start: 0.9453 (t) cc_final: 0.9236 (m) REVERT: h 41 LYS cc_start: 0.9047 (tptt) cc_final: 0.8783 (tptm) REVERT: h 109 MET cc_start: 0.8462 (tpp) cc_final: 0.8036 (tpp) REVERT: h 216 ASN cc_start: 0.2913 (m110) cc_final: 0.2585 (t0) REVERT: h 243 SER cc_start: 0.2894 (t) cc_final: 0.2606 (p) REVERT: h 323 MET cc_start: -0.0609 (tmm) cc_final: -0.1164 (ttm) REVERT: h 362 TYR cc_start: 0.1746 (m-80) cc_final: 0.1114 (m-80) REVERT: h 418 MET cc_start: 0.5834 (ttt) cc_final: 0.5435 (ttt) REVERT: h 420 VAL cc_start: 0.9224 (t) cc_final: 0.8952 (t) REVERT: h 437 MET cc_start: 0.8798 (ppp) cc_final: 0.8587 (ppp) REVERT: h 438 ILE cc_start: 0.9210 (mt) cc_final: 0.8926 (mt) REVERT: h 449 ILE cc_start: 0.9468 (mt) cc_final: 0.9247 (mt) REVERT: h 460 ASP cc_start: 0.8666 (t0) cc_final: 0.8394 (t0) REVERT: h 518 LEU cc_start: 0.9092 (mp) cc_final: 0.8699 (mp) REVERT: q 39 HIS cc_start: 0.7755 (t70) cc_final: 0.7440 (t-90) REVERT: q 109 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8160 (mm-30) REVERT: q 133 MET cc_start: 0.9369 (ttp) cc_final: 0.9019 (tmm) REVERT: q 348 THR cc_start: 0.4550 (m) cc_final: 0.4251 (t) REVERT: q 393 ASN cc_start: 0.8205 (m-40) cc_final: 0.7593 (t0) REVERT: q 451 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8480 (tp40) REVERT: q 454 VAL cc_start: 0.9648 (t) cc_final: 0.9182 (p) REVERT: q 470 ASP cc_start: 0.8475 (t0) cc_final: 0.8157 (t0) REVERT: q 521 LEU cc_start: 0.9364 (tp) cc_final: 0.8968 (tp) REVERT: q 526 PHE cc_start: 0.9095 (t80) cc_final: 0.8721 (t80) REVERT: Q 42 CYS cc_start: 0.8962 (m) cc_final: 0.8754 (p) REVERT: Q 49 CYS cc_start: 0.9089 (m) cc_final: 0.8795 (m) REVERT: Q 94 ILE cc_start: 0.9192 (pt) cc_final: 0.8971 (mm) REVERT: Q 109 GLU cc_start: 0.8680 (mm-30) cc_final: 0.7835 (tm-30) REVERT: Q 112 ASN cc_start: 0.8549 (t0) cc_final: 0.8321 (t0) REVERT: Q 140 LYS cc_start: 0.8800 (tppt) cc_final: 0.8477 (tppt) REVERT: Q 146 VAL cc_start: 0.8818 (t) cc_final: 0.8454 (t) REVERT: Q 167 ILE cc_start: 0.9213 (pt) cc_final: 0.8677 (tp) REVERT: Q 282 LYS cc_start: 0.4760 (mttt) cc_final: 0.4248 (tptp) REVERT: Q 311 HIS cc_start: 0.9139 (m-70) cc_final: 0.8865 (p-80) REVERT: Q 403 ASP cc_start: 0.8022 (p0) cc_final: 0.7619 (m-30) REVERT: Q 451 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8419 (mm110) REVERT: Q 463 LEU cc_start: 0.9410 (tp) cc_final: 0.9160 (tt) REVERT: Q 472 ASN cc_start: 0.7561 (p0) cc_final: 0.7193 (p0) REVERT: Q 515 GLU cc_start: 0.9353 (mp0) cc_final: 0.8971 (mp0) REVERT: Q 516 ASN cc_start: 0.8417 (m-40) cc_final: 0.7154 (p0) REVERT: Q 540 SER cc_start: 0.9483 (m) cc_final: 0.8914 (p) REVERT: z 36 ASN cc_start: 0.9160 (m-40) cc_final: 0.8760 (m-40) REVERT: z 37 LEU cc_start: 0.7676 (tp) cc_final: 0.7061 (mp) REVERT: z 66 MET cc_start: 0.8635 (ppp) cc_final: 0.8342 (ppp) REVERT: z 117 ILE cc_start: 0.8204 (mt) cc_final: 0.7904 (mm) REVERT: z 123 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9102 (tp30) REVERT: z 127 LYS cc_start: 0.9322 (mtpp) cc_final: 0.9041 (tptt) REVERT: z 155 ARG cc_start: 0.8850 (mtm-85) cc_final: 0.8447 (ttm110) REVERT: z 193 MET cc_start: 0.7352 (ptp) cc_final: 0.7003 (ttt) REVERT: z 199 MET cc_start: 0.8167 (ppp) cc_final: 0.7611 (ppp) REVERT: z 268 LYS cc_start: 0.9128 (tttt) cc_final: 0.8854 (pttm) REVERT: z 283 GLU cc_start: 0.8278 (pt0) cc_final: 0.8032 (pt0) REVERT: z 364 PHE cc_start: 0.8391 (m-10) cc_final: 0.8026 (m-80) REVERT: z 431 MET cc_start: 0.7725 (mtt) cc_final: 0.7477 (ptm) REVERT: z 474 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8853 (mm-30) REVERT: z 481 GLN cc_start: 0.8945 (pt0) cc_final: 0.8715 (pm20) REVERT: z 500 ASP cc_start: 0.8613 (t0) cc_final: 0.8026 (t0) REVERT: z 503 ILE cc_start: 0.9424 (mt) cc_final: 0.9035 (mt) REVERT: Z 27 GLU cc_start: 0.9056 (tp30) cc_final: 0.8145 (tm-30) REVERT: Z 40 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8479 (mmmm) REVERT: Z 66 MET cc_start: 0.5293 (ppp) cc_final: 0.4776 (ppp) REVERT: Z 192 HIS cc_start: 0.8782 (m90) cc_final: 0.8453 (m90) REVERT: Z 193 MET cc_start: 0.8261 (ppp) cc_final: 0.7822 (ppp) REVERT: Z 384 THR cc_start: 0.8674 (p) cc_final: 0.8438 (p) REVERT: Z 425 TYR cc_start: 0.7505 (m-10) cc_final: 0.7296 (m-10) REVERT: Z 431 MET cc_start: 0.7282 (mpp) cc_final: 0.6981 (mtm) REVERT: Z 442 THR cc_start: 0.9204 (p) cc_final: 0.8494 (t) REVERT: Z 478 ASP cc_start: 0.8924 (m-30) cc_final: 0.8684 (m-30) REVERT: Z 527 LEU cc_start: 0.9690 (mt) cc_final: 0.9482 (mt) outliers start: 1 outliers final: 0 residues processed: 1598 average time/residue: 0.5551 time to fit residues: 1520.4732 Evaluate side-chains 1266 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1266 time to evaluate : 5.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 443 optimal weight: 0.0980 chunk 568 optimal weight: 0.9980 chunk 440 optimal weight: 0.9980 chunk 655 optimal weight: 0.9990 chunk 434 optimal weight: 10.0000 chunk 775 optimal weight: 3.9990 chunk 485 optimal weight: 0.1980 chunk 473 optimal weight: 5.9990 chunk 358 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN B 304 ASN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** g 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 567 GLN h 90 GLN h 345 HIS ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 314 ASN q 392 ASN q 482 HIS q 494 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.7455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 62697 Z= 0.154 Angle : 0.562 9.095 84560 Z= 0.284 Chirality : 0.043 0.277 10175 Planarity : 0.003 0.049 10863 Dihedral : 3.879 24.116 8578 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 0.01 % Allowed : 0.96 % Favored : 99.02 % 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: 0.00 (0.09), residues: 8076 helix: 0.74 (0.08), residues: 3815 sheet: -0.31 (0.19), residues: 693 loop : -0.65 (0.10), residues: 3568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP h 478 HIS 0.009 0.001 HIS E 424 PHE 0.030 0.001 PHE q 137 TYR 0.035 0.001 TYR h 427 ARG 0.012 0.000 ARG b 495 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1605 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1604 time to evaluate : 5.427 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: H 118 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8636 (tm-30) REVERT: H 150 GLU cc_start: 0.7736 (tm-30) cc_final: 0.6450 (mp0) REVERT: H 163 ARG cc_start: 0.6766 (mtt-85) cc_final: 0.5947 (ttp-110) REVERT: H 317 ARG cc_start: 0.6187 (mtm110) cc_final: 0.5979 (ptp90) REVERT: H 355 MET cc_start: 0.5472 (pmm) cc_final: 0.4361 (ppp) REVERT: H 434 LYS cc_start: 0.9242 (mmtm) cc_final: 0.8839 (mmtm) REVERT: H 452 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8639 (mm-40) REVERT: a 34 MET cc_start: 0.8621 (mmp) cc_final: 0.8085 (mmm) REVERT: a 117 LYS cc_start: 0.9248 (mmtt) cc_final: 0.8996 (mmtm) REVERT: a 118 ASN cc_start: 0.8975 (t0) cc_final: 0.8661 (t0) REVERT: a 121 HIS cc_start: 0.8329 (t-90) cc_final: 0.7743 (t70) REVERT: a 123 THR cc_start: 0.8982 (m) cc_final: 0.8730 (m) REVERT: a 179 MET cc_start: 0.6499 (ptp) cc_final: 0.6208 (ptp) REVERT: a 341 MET cc_start: -0.1428 (mtp) cc_final: -0.2889 (ptm) REVERT: a 398 MET cc_start: 0.3089 (mmp) cc_final: 0.2748 (mmp) REVERT: a 450 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7736 (mm-30) REVERT: a 469 ASP cc_start: 0.8284 (t70) cc_final: 0.7609 (t0) REVERT: a 473 LEU cc_start: 0.8996 (mt) cc_final: 0.8733 (mt) REVERT: a 526 LYS cc_start: 0.8962 (mmpt) cc_final: 0.8663 (mmmt) REVERT: a 529 LYS cc_start: 0.9100 (tptp) cc_final: 0.8698 (tptp) REVERT: A 26 ARG cc_start: 0.7391 (mmm-85) cc_final: 0.7103 (tpp80) REVERT: A 27 ASN cc_start: 0.8921 (m-40) cc_final: 0.8611 (p0) REVERT: A 82 ILE cc_start: 0.8900 (mm) cc_final: 0.8693 (mm) REVERT: A 111 ARG cc_start: 0.8345 (mmt-90) cc_final: 0.7902 (mmt90) REVERT: A 125 ILE cc_start: 0.9578 (mt) cc_final: 0.9263 (mt) REVERT: A 129 PHE cc_start: 0.9416 (m-10) cc_final: 0.9184 (m-80) REVERT: A 175 PHE cc_start: 0.8419 (m-10) cc_final: 0.7806 (t80) REVERT: A 205 VAL cc_start: 0.6241 (t) cc_final: 0.5918 (t) REVERT: A 206 LEU cc_start: 0.8691 (mp) cc_final: 0.7961 (tt) REVERT: A 233 MET cc_start: 0.2771 (ptp) cc_final: 0.2012 (ptm) REVERT: A 236 ARG cc_start: 0.6880 (ttp-110) cc_final: 0.6383 (tmt-80) REVERT: A 333 THR cc_start: 0.5961 (m) cc_final: 0.5659 (t) REVERT: A 398 MET cc_start: 0.6753 (mmp) cc_final: 0.6050 (mpp) REVERT: A 411 ARG cc_start: 0.8465 (mtt180) cc_final: 0.7354 (mmm160) REVERT: A 526 LYS cc_start: 0.9146 (mttt) cc_final: 0.8925 (tttt) REVERT: A 532 LEU cc_start: 0.9476 (mt) cc_final: 0.8527 (tp) REVERT: b 31 ASP cc_start: 0.8778 (m-30) cc_final: 0.8437 (m-30) REVERT: b 34 LYS cc_start: 0.9466 (tmtt) cc_final: 0.9259 (tttm) REVERT: b 79 ASN cc_start: 0.8197 (p0) cc_final: 0.7985 (p0) REVERT: b 107 GLU cc_start: 0.8810 (tt0) cc_final: 0.8566 (pt0) REVERT: b 120 ILE cc_start: 0.8561 (mt) cc_final: 0.6569 (mt) REVERT: b 124 TYR cc_start: 0.9180 (m-10) cc_final: 0.8397 (m-80) REVERT: b 135 LEU cc_start: 0.9002 (mt) cc_final: 0.8733 (mt) REVERT: b 347 MET cc_start: 0.7069 (tpp) cc_final: 0.6745 (ptp) REVERT: b 409 MET cc_start: 0.9419 (tpp) cc_final: 0.8839 (tpp) REVERT: b 413 LYS cc_start: 0.9471 (tttt) cc_final: 0.8837 (ttmm) REVERT: b 482 MET cc_start: 0.7557 (mmp) cc_final: 0.7193 (mmm) REVERT: b 491 TYR cc_start: 0.5417 (t80) cc_final: 0.4728 (t80) REVERT: b 508 LEU cc_start: 0.9324 (mm) cc_final: 0.8930 (tt) REVERT: B 57 THR cc_start: 0.6890 (t) cc_final: 0.6318 (t) REVERT: B 81 SER cc_start: 0.9041 (m) cc_final: 0.8814 (p) REVERT: B 118 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8037 (tp-100) REVERT: B 133 ASP cc_start: 0.9206 (m-30) cc_final: 0.8947 (m-30) REVERT: B 143 SER cc_start: 0.6163 (t) cc_final: 0.5926 (m) REVERT: B 269 MET cc_start: 0.3801 (ptm) cc_final: 0.3487 (ttp) REVERT: B 409 MET cc_start: 0.8992 (mmp) cc_final: 0.8598 (mmm) REVERT: B 416 ASP cc_start: 0.9394 (m-30) cc_final: 0.9084 (m-30) REVERT: B 443 ILE cc_start: 0.9021 (pt) cc_final: 0.8769 (pt) REVERT: B 446 ASP cc_start: 0.8065 (p0) cc_final: 0.7826 (p0) REVERT: B 447 ASN cc_start: 0.9023 (m-40) cc_final: 0.8433 (p0) REVERT: d 37 THR cc_start: 0.9097 (p) cc_final: 0.8848 (p) REVERT: d 39 LEU cc_start: 0.8941 (tp) cc_final: 0.8620 (tp) REVERT: d 44 MET cc_start: 0.8673 (tpt) cc_final: 0.8282 (tpp) REVERT: d 65 LEU cc_start: 0.8683 (mt) cc_final: 0.8259 (mt) REVERT: d 68 MET cc_start: 0.6031 (pmm) cc_final: 0.5349 (pmm) REVERT: d 77 MET cc_start: 0.8206 (ppp) cc_final: 0.7422 (ppp) REVERT: d 116 HIS cc_start: 0.7837 (t-90) cc_final: 0.7343 (t-90) REVERT: d 124 PHE cc_start: 0.9483 (m-10) cc_final: 0.9185 (m-80) REVERT: d 305 LEU cc_start: 0.5958 (mt) cc_final: 0.5654 (pp) REVERT: d 394 LEU cc_start: 0.7676 (mm) cc_final: 0.7392 (mt) REVERT: D 44 MET cc_start: 0.6962 (tpt) cc_final: 0.6603 (tpt) REVERT: D 91 ASP cc_start: 0.7826 (t0) cc_final: 0.7042 (t70) REVERT: D 108 GLU cc_start: 0.8658 (tp30) cc_final: 0.8262 (tp30) REVERT: D 116 HIS cc_start: 0.8641 (t-90) cc_final: 0.8330 (t-90) REVERT: D 118 THR cc_start: 0.9169 (m) cc_final: 0.8886 (m) REVERT: D 432 MET cc_start: 0.8622 (ppp) cc_final: 0.8081 (ppp) REVERT: D 461 ASN cc_start: 0.8577 (t0) cc_final: 0.8357 (t0) REVERT: e 127 SER cc_start: 0.9468 (m) cc_final: 0.8955 (p) REVERT: e 132 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8146 (tp40) REVERT: e 161 LEU cc_start: 0.9122 (mt) cc_final: 0.8476 (mt) REVERT: e 226 MET cc_start: 0.7745 (ppp) cc_final: 0.7292 (ppp) REVERT: e 229 ARG cc_start: 0.7749 (mmt-90) cc_final: 0.6877 (ttp-110) REVERT: e 394 ILE cc_start: 0.7102 (mt) cc_final: 0.6521 (mp) REVERT: e 481 MET cc_start: 0.8099 (mmp) cc_final: 0.7603 (mmp) REVERT: e 544 LEU cc_start: 0.9226 (tp) cc_final: 0.8849 (tp) REVERT: e 550 LYS cc_start: 0.9385 (mmpt) cc_final: 0.9081 (mmmt) REVERT: e 552 ASP cc_start: 0.8922 (p0) cc_final: 0.8499 (p0) REVERT: E 71 ASP cc_start: 0.8313 (m-30) cc_final: 0.8088 (m-30) REVERT: E 428 CYS cc_start: 0.8947 (t) cc_final: 0.8611 (t) REVERT: E 432 ASN cc_start: 0.7978 (m-40) cc_final: 0.7634 (t0) REVERT: E 454 VAL cc_start: 0.9601 (t) cc_final: 0.9321 (p) REVERT: E 481 MET cc_start: 0.8059 (mtp) cc_final: 0.7821 (mmm) REVERT: E 485 GLU cc_start: 0.8579 (tp30) cc_final: 0.8116 (tm-30) REVERT: E 521 ASP cc_start: 0.7854 (t0) cc_final: 0.7519 (t0) REVERT: E 550 LYS cc_start: 0.8270 (ptpp) cc_final: 0.7908 (mttp) REVERT: g 35 ILE cc_start: 0.9711 (pt) cc_final: 0.9466 (mp) REVERT: g 52 MET cc_start: 0.6879 (ppp) cc_final: 0.6652 (ppp) REVERT: g 76 LYS cc_start: 0.8134 (ptmt) cc_final: 0.7924 (mptt) REVERT: g 107 CYS cc_start: 0.8125 (p) cc_final: 0.7820 (p) REVERT: g 112 ILE cc_start: 0.9077 (mt) cc_final: 0.8710 (mt) REVERT: g 117 HIS cc_start: 0.8438 (t-90) cc_final: 0.8116 (t-90) REVERT: g 133 LEU cc_start: 0.9533 (mt) cc_final: 0.9077 (mt) REVERT: g 137 LYS cc_start: 0.9344 (mmtm) cc_final: 0.9091 (mmtm) REVERT: g 153 LYS cc_start: 0.9242 (mttt) cc_final: 0.8892 (mmtm) REVERT: g 163 TYR cc_start: 0.6498 (t80) cc_final: 0.6155 (t80) REVERT: g 234 MET cc_start: 0.1637 (mmt) cc_final: 0.1370 (mmm) REVERT: g 242 ARG cc_start: 0.6100 (mtm-85) cc_final: 0.5655 (tmm-80) REVERT: g 364 TYR cc_start: 0.6827 (m-80) cc_final: 0.6456 (m-80) REVERT: g 440 MET cc_start: 0.3709 (ppp) cc_final: 0.3209 (ppp) REVERT: g 487 LEU cc_start: 0.8773 (mt) cc_final: 0.8434 (mt) REVERT: g 510 GLU cc_start: 0.9272 (mm-30) cc_final: 0.9004 (mm-30) REVERT: g 568 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8430 (mm-40) REVERT: g 571 LYS cc_start: 0.9573 (tttt) cc_final: 0.9291 (ttmt) REVERT: g 580 LEU cc_start: 0.9267 (mt) cc_final: 0.9066 (mt) REVERT: g 585 ASP cc_start: 0.7790 (m-30) cc_final: 0.7347 (m-30) REVERT: G 52 MET cc_start: 0.7137 (mmm) cc_final: 0.6722 (mmm) REVERT: G 78 MET cc_start: 0.8976 (mtt) cc_final: 0.8708 (mmm) REVERT: G 93 THR cc_start: 0.8384 (p) cc_final: 0.8163 (p) REVERT: G 97 ILE cc_start: 0.9174 (mm) cc_final: 0.8889 (mm) REVERT: G 120 ILE cc_start: 0.9061 (mm) cc_final: 0.8016 (mm) REVERT: G 172 CYS cc_start: 0.8538 (m) cc_final: 0.7768 (m) REVERT: G 202 ARG cc_start: 0.8267 (mtm180) cc_final: 0.7664 (mtm110) REVERT: G 221 LYS cc_start: 0.3962 (tppt) cc_final: 0.2564 (pttm) REVERT: G 481 MET cc_start: 0.8903 (ttt) cc_final: 0.8459 (ttt) REVERT: G 511 CYS cc_start: 0.9215 (p) cc_final: 0.8986 (p) REVERT: G 517 ILE cc_start: 0.9271 (mm) cc_final: 0.8966 (mm) REVERT: G 531 LEU cc_start: 0.9525 (tp) cc_final: 0.9284 (tp) REVERT: G 547 ASP cc_start: 0.9173 (t0) cc_final: 0.8541 (p0) REVERT: G 567 GLN cc_start: 0.9433 (pt0) cc_final: 0.9227 (pp30) REVERT: G 572 THR cc_start: 0.9519 (p) cc_final: 0.9128 (p) REVERT: G 578 CYS cc_start: 0.8897 (p) cc_final: 0.8467 (p) REVERT: h 28 SER cc_start: 0.9448 (t) cc_final: 0.9205 (m) REVERT: h 38 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8383 (mt-10) REVERT: h 41 LYS cc_start: 0.9020 (tptt) cc_final: 0.8712 (tptm) REVERT: h 216 ASN cc_start: 0.3241 (m110) cc_final: 0.2989 (t0) REVERT: h 323 MET cc_start: -0.0792 (tmm) cc_final: -0.1131 (ttm) REVERT: h 362 TYR cc_start: 0.1817 (m-80) cc_final: 0.1345 (m-80) REVERT: h 401 LYS cc_start: 0.7026 (mttt) cc_final: 0.6601 (mttt) REVERT: h 434 LYS cc_start: 0.9067 (mtpt) cc_final: 0.8827 (mtpt) REVERT: h 438 ILE cc_start: 0.9163 (mt) cc_final: 0.8864 (mt) REVERT: h 449 ILE cc_start: 0.9471 (mt) cc_final: 0.9208 (mt) REVERT: h 467 LYS cc_start: 0.9247 (tttt) cc_final: 0.8676 (mptt) REVERT: q 71 MET cc_start: 0.8894 (ppp) cc_final: 0.8680 (ppp) REVERT: q 109 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8031 (mm-30) REVERT: q 139 LEU cc_start: 0.8932 (mt) cc_final: 0.8297 (tt) REVERT: q 348 THR cc_start: 0.4479 (m) cc_final: 0.4135 (t) REVERT: q 392 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7362 (p0) REVERT: q 393 ASN cc_start: 0.8184 (m-40) cc_final: 0.7390 (t0) REVERT: q 451 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8319 (tp40) REVERT: q 454 VAL cc_start: 0.9626 (t) cc_final: 0.9222 (p) REVERT: q 470 ASP cc_start: 0.8687 (t0) cc_final: 0.8390 (t70) REVERT: q 521 LEU cc_start: 0.9349 (tp) cc_final: 0.9019 (tp) REVERT: q 526 PHE cc_start: 0.9156 (t80) cc_final: 0.8719 (t80) REVERT: Q 39 HIS cc_start: 0.8206 (t-170) cc_final: 0.7909 (t-170) REVERT: Q 49 CYS cc_start: 0.9118 (m) cc_final: 0.8790 (m) REVERT: Q 53 LYS cc_start: 0.8561 (mppt) cc_final: 0.7806 (mptt) REVERT: Q 94 ILE cc_start: 0.9193 (pt) cc_final: 0.8976 (mm) REVERT: Q 109 GLU cc_start: 0.8786 (tp30) cc_final: 0.8399 (tp30) REVERT: Q 112 ASN cc_start: 0.8291 (t0) cc_final: 0.7960 (t0) REVERT: Q 140 LYS cc_start: 0.8788 (tppt) cc_final: 0.8505 (tppt) REVERT: Q 167 ILE cc_start: 0.9163 (pt) cc_final: 0.8726 (tp) REVERT: Q 282 LYS cc_start: 0.4787 (mttt) cc_final: 0.4352 (tptp) REVERT: Q 311 HIS cc_start: 0.9221 (m-70) cc_final: 0.8737 (m90) REVERT: Q 451 GLN cc_start: 0.8577 (mm-40) cc_final: 0.7890 (mm110) REVERT: Q 463 LEU cc_start: 0.9425 (tp) cc_final: 0.9184 (tt) REVERT: Q 515 GLU cc_start: 0.9332 (mp0) cc_final: 0.8908 (mp0) REVERT: Q 516 ASN cc_start: 0.8436 (m-40) cc_final: 0.7042 (p0) REVERT: Q 530 VAL cc_start: 0.9331 (m) cc_final: 0.9075 (p) REVERT: Q 540 SER cc_start: 0.9430 (m) cc_final: 0.8813 (p) REVERT: z 33 LEU cc_start: 0.9729 (mp) cc_final: 0.9379 (mp) REVERT: z 36 ASN cc_start: 0.9112 (m-40) cc_final: 0.8887 (m-40) REVERT: z 37 LEU cc_start: 0.7681 (tp) cc_final: 0.7117 (mp) REVERT: z 66 MET cc_start: 0.8623 (ppp) cc_final: 0.8367 (ppp) REVERT: z 92 THR cc_start: 0.6805 (t) cc_final: 0.6247 (t) REVERT: z 123 GLU cc_start: 0.9348 (mm-30) cc_final: 0.9088 (tp30) REVERT: z 155 ARG cc_start: 0.8803 (mtm-85) cc_final: 0.8503 (ttm110) REVERT: z 193 MET cc_start: 0.7544 (ptp) cc_final: 0.7061 (ttm) REVERT: z 199 MET cc_start: 0.8212 (ppp) cc_final: 0.7772 (ppp) REVERT: z 268 LYS cc_start: 0.9193 (tttt) cc_final: 0.8885 (pttm) REVERT: z 283 GLU cc_start: 0.8325 (pt0) cc_final: 0.8029 (pt0) REVERT: z 364 PHE cc_start: 0.8213 (m-10) cc_final: 0.7999 (m-80) REVERT: z 376 CYS cc_start: 0.7007 (m) cc_final: 0.6803 (m) REVERT: z 399 LEU cc_start: 0.9734 (mt) cc_final: 0.9462 (pp) REVERT: z 474 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8914 (mm-30) REVERT: z 500 ASP cc_start: 0.8729 (t0) cc_final: 0.8069 (t0) REVERT: z 503 ILE cc_start: 0.9354 (mt) cc_final: 0.9018 (mt) REVERT: Z 33 LEU cc_start: 0.9352 (mp) cc_final: 0.9111 (mp) REVERT: Z 40 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8646 (mmmt) REVERT: Z 66 MET cc_start: 0.5127 (ppp) cc_final: 0.4567 (ppp) REVERT: Z 102 LEU cc_start: 0.9065 (mt) cc_final: 0.8842 (mt) REVERT: Z 122 PHE cc_start: 0.8983 (m-10) cc_final: 0.8384 (m-10) REVERT: Z 151 LEU cc_start: 0.9503 (mt) cc_final: 0.9078 (tt) REVERT: Z 193 MET cc_start: 0.8061 (ppp) cc_final: 0.7435 (ppp) REVERT: Z 234 LEU cc_start: 0.8472 (tp) cc_final: 0.8223 (tp) REVERT: Z 296 ILE cc_start: 0.8544 (mp) cc_final: 0.8297 (pt) REVERT: Z 384 THR cc_start: 0.8584 (p) cc_final: 0.8313 (p) REVERT: Z 408 ASP cc_start: 0.8161 (t70) cc_final: 0.7875 (t0) REVERT: Z 425 TYR cc_start: 0.7501 (m-10) cc_final: 0.7288 (m-10) REVERT: Z 431 MET cc_start: 0.7235 (mpp) cc_final: 0.6769 (mpp) REVERT: Z 442 THR cc_start: 0.8887 (p) cc_final: 0.8451 (t) REVERT: Z 478 ASP cc_start: 0.8863 (m-30) cc_final: 0.8575 (m-30) REVERT: Z 527 LEU cc_start: 0.9662 (mt) cc_final: 0.9390 (mt) outliers start: 1 outliers final: 0 residues processed: 1604 average time/residue: 0.5490 time to fit residues: 1506.1710 Evaluate side-chains 1316 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1315 time to evaluate : 5.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 3.9990 chunk 309 optimal weight: 0.9990 chunk 463 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 493 optimal weight: 1.9990 chunk 528 optimal weight: 10.0000 chunk 383 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 609 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 90 GLN a 250 ASN a 481 HIS ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN E 424 HIS ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS h 345 HIS ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 472 HIS ** q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 ASN Z 370 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.8271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 62697 Z= 0.242 Angle : 0.669 10.846 84560 Z= 0.345 Chirality : 0.046 0.300 10175 Planarity : 0.004 0.064 10863 Dihedral : 4.396 29.418 8578 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 0.01 % Allowed : 0.90 % Favored : 99.08 % 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: -0.29 (0.09), residues: 8076 helix: 0.50 (0.08), residues: 3836 sheet: -0.64 (0.19), residues: 712 loop : -0.78 (0.10), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 440 HIS 0.010 0.002 HIS E 424 PHE 0.034 0.002 PHE E 150 TYR 0.020 0.002 TYR Q 131 ARG 0.016 0.001 ARG e 438 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1543 time to evaluate : 5.433 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: H 44 LEU cc_start: 0.8592 (tp) cc_final: 0.8291 (tt) REVERT: H 93 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8354 (mp0) REVERT: H 118 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8591 (tm-30) REVERT: H 150 GLU cc_start: 0.7769 (tm-30) cc_final: 0.6336 (mp0) REVERT: H 163 ARG cc_start: 0.6723 (mtt-85) cc_final: 0.5928 (ttp-110) REVERT: H 322 ASP cc_start: 0.4628 (m-30) cc_final: 0.4404 (t0) REVERT: H 388 GLU cc_start: 0.8193 (pm20) cc_final: 0.7945 (pm20) REVERT: a 34 MET cc_start: 0.8659 (mmp) cc_final: 0.8132 (mmm) REVERT: a 44 LEU cc_start: 0.9276 (tp) cc_final: 0.8911 (tp) REVERT: a 107 GLU cc_start: 0.8658 (tp30) cc_final: 0.8399 (tp30) REVERT: a 121 HIS cc_start: 0.8355 (t-90) cc_final: 0.7737 (t70) REVERT: a 123 THR cc_start: 0.9105 (m) cc_final: 0.8837 (m) REVERT: a 130 ARG cc_start: 0.8792 (ttm110) cc_final: 0.8157 (mmt180) REVERT: a 201 LYS cc_start: 0.6392 (pttt) cc_final: 0.5968 (tptt) REVERT: a 341 MET cc_start: -0.2096 (mtp) cc_final: -0.3313 (ptm) REVERT: a 450 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7800 (mm-30) REVERT: a 526 LYS cc_start: 0.9130 (mmpt) cc_final: 0.8770 (mmmt) REVERT: a 529 LYS cc_start: 0.9132 (tptp) cc_final: 0.8678 (tptp) REVERT: A 26 ARG cc_start: 0.7820 (mmm-85) cc_final: 0.7521 (tpp80) REVERT: A 27 ASN cc_start: 0.8996 (m-40) cc_final: 0.8754 (p0) REVERT: A 99 THR cc_start: 0.8979 (p) cc_final: 0.8726 (p) REVERT: A 125 ILE cc_start: 0.9555 (mt) cc_final: 0.9323 (mt) REVERT: A 129 PHE cc_start: 0.9368 (m-10) cc_final: 0.9052 (m-80) REVERT: A 175 PHE cc_start: 0.8430 (m-10) cc_final: 0.7566 (t80) REVERT: A 233 MET cc_start: 0.3291 (ptp) cc_final: 0.2343 (ptm) REVERT: A 236 ARG cc_start: 0.6973 (ttp-110) cc_final: 0.6643 (tmt-80) REVERT: A 333 THR cc_start: 0.5745 (m) cc_final: 0.5345 (t) REVERT: A 341 MET cc_start: 0.1597 (ttm) cc_final: 0.1336 (ttm) REVERT: A 398 MET cc_start: 0.6475 (mmp) cc_final: 0.5710 (mpp) REVERT: A 410 LYS cc_start: 0.8747 (tptt) cc_final: 0.8492 (tptp) REVERT: A 411 ARG cc_start: 0.8484 (mtt180) cc_final: 0.7308 (mmm160) REVERT: A 486 MET cc_start: 0.8020 (ppp) cc_final: 0.7631 (ppp) REVERT: A 533 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7613 (tm-30) REVERT: b 31 ASP cc_start: 0.8837 (m-30) cc_final: 0.8544 (m-30) REVERT: b 79 ASN cc_start: 0.8261 (p0) cc_final: 0.7925 (p0) REVERT: b 347 MET cc_start: 0.7289 (tpp) cc_final: 0.6690 (ptp) REVERT: b 409 MET cc_start: 0.9447 (tpp) cc_final: 0.8607 (tpp) REVERT: b 413 LYS cc_start: 0.9494 (tttt) cc_final: 0.8951 (ttmm) REVERT: b 443 ILE cc_start: 0.9611 (mp) cc_final: 0.9410 (mp) REVERT: b 446 ASP cc_start: 0.7683 (m-30) cc_final: 0.7477 (m-30) REVERT: b 482 MET cc_start: 0.7749 (mmp) cc_final: 0.7314 (mmm) REVERT: b 506 GLU cc_start: 0.7975 (tt0) cc_final: 0.7572 (mt-10) REVERT: b 508 LEU cc_start: 0.9386 (mm) cc_final: 0.9134 (tp) REVERT: B 79 ASN cc_start: 0.8825 (m-40) cc_final: 0.8598 (p0) REVERT: B 85 ASP cc_start: 0.8940 (m-30) cc_final: 0.8563 (m-30) REVERT: B 143 SER cc_start: 0.6200 (t) cc_final: 0.5980 (m) REVERT: B 269 MET cc_start: 0.3931 (ptm) cc_final: 0.3470 (ttm) REVERT: B 293 TYR cc_start: 0.6964 (t80) cc_final: 0.6518 (m-80) REVERT: B 416 ASP cc_start: 0.9440 (m-30) cc_final: 0.9099 (m-30) REVERT: B 447 ASN cc_start: 0.9039 (m-40) cc_final: 0.8597 (p0) REVERT: B 512 ASP cc_start: 0.7975 (m-30) cc_final: 0.7774 (m-30) REVERT: d 36 ARG cc_start: 0.9063 (ptm-80) cc_final: 0.8823 (ptm160) REVERT: d 39 LEU cc_start: 0.8996 (tp) cc_final: 0.8676 (tp) REVERT: d 44 MET cc_start: 0.8742 (tpt) cc_final: 0.8351 (tpp) REVERT: d 65 LEU cc_start: 0.8736 (mt) cc_final: 0.8277 (mt) REVERT: d 68 MET cc_start: 0.6341 (pmm) cc_final: 0.5507 (pmm) REVERT: d 77 MET cc_start: 0.8443 (ppp) cc_final: 0.7667 (ppp) REVERT: d 88 GLU cc_start: 0.9065 (mp0) cc_final: 0.8838 (mp0) REVERT: d 116 HIS cc_start: 0.8177 (t-90) cc_final: 0.7577 (t-90) REVERT: d 124 PHE cc_start: 0.9530 (m-10) cc_final: 0.9252 (m-80) REVERT: d 305 LEU cc_start: 0.6070 (mt) cc_final: 0.5707 (pp) REVERT: d 394 LEU cc_start: 0.7859 (mm) cc_final: 0.7576 (mt) REVERT: d 447 LEU cc_start: 0.9209 (mt) cc_final: 0.9007 (mt) REVERT: D 82 SER cc_start: 0.9349 (m) cc_final: 0.9122 (p) REVERT: D 85 GLN cc_start: 0.8964 (tp40) cc_final: 0.8619 (tp40) REVERT: D 91 ASP cc_start: 0.8060 (t0) cc_final: 0.7776 (t0) REVERT: D 135 LEU cc_start: 0.9360 (pp) cc_final: 0.9116 (pp) REVERT: D 183 ASP cc_start: 0.8267 (t70) cc_final: 0.8050 (t70) REVERT: D 399 CYS cc_start: 0.8371 (m) cc_final: 0.7907 (p) REVERT: D 432 MET cc_start: 0.8800 (ppp) cc_final: 0.8252 (ppp) REVERT: D 441 GLN cc_start: 0.8583 (mp10) cc_final: 0.8365 (pm20) REVERT: e 127 SER cc_start: 0.9401 (m) cc_final: 0.8549 (p) REVERT: e 132 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8098 (tp40) REVERT: e 161 LEU cc_start: 0.9228 (mt) cc_final: 0.8461 (mt) REVERT: e 212 MET cc_start: 0.6218 (ppp) cc_final: 0.5921 (ppp) REVERT: e 226 MET cc_start: 0.7797 (ppp) cc_final: 0.6353 (ttm) REVERT: e 229 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.6917 (mtm110) REVERT: e 425 ASP cc_start: 0.8562 (m-30) cc_final: 0.8286 (m-30) REVERT: e 479 ILE cc_start: 0.9068 (mm) cc_final: 0.8851 (mm) REVERT: e 481 MET cc_start: 0.8188 (mmp) cc_final: 0.7728 (mmp) REVERT: e 482 THR cc_start: 0.8475 (p) cc_final: 0.8235 (p) REVERT: e 544 LEU cc_start: 0.9268 (tp) cc_final: 0.9010 (tp) REVERT: e 549 LEU cc_start: 0.9421 (mm) cc_final: 0.9209 (mm) REVERT: e 550 LYS cc_start: 0.9462 (mmpt) cc_final: 0.9110 (mmmt) REVERT: E 71 ASP cc_start: 0.8541 (m-30) cc_final: 0.7879 (m-30) REVERT: E 80 GLU cc_start: 0.7110 (tt0) cc_final: 0.6110 (tp30) REVERT: E 82 THR cc_start: 0.8265 (p) cc_final: 0.8043 (p) REVERT: E 94 MET cc_start: 0.7253 (tpp) cc_final: 0.6550 (tmm) REVERT: E 212 MET cc_start: 0.3102 (ttp) cc_final: 0.2868 (tmm) REVERT: E 412 ASN cc_start: 0.7865 (t0) cc_final: 0.7207 (p0) REVERT: E 421 ARG cc_start: 0.9064 (mtp85) cc_final: 0.8152 (ptp-170) REVERT: E 425 ASP cc_start: 0.8737 (m-30) cc_final: 0.8501 (m-30) REVERT: E 428 CYS cc_start: 0.8989 (t) cc_final: 0.8576 (t) REVERT: E 432 ASN cc_start: 0.7951 (m-40) cc_final: 0.7566 (t0) REVERT: E 454 VAL cc_start: 0.9534 (t) cc_final: 0.9307 (p) REVERT: E 465 ASP cc_start: 0.9221 (p0) cc_final: 0.8966 (p0) REVERT: E 477 ASP cc_start: 0.9227 (t70) cc_final: 0.7708 (t0) REVERT: E 481 MET cc_start: 0.8348 (mtp) cc_final: 0.7597 (mtp) REVERT: E 485 GLU cc_start: 0.8803 (tp30) cc_final: 0.8178 (tm-30) REVERT: E 521 ASP cc_start: 0.7982 (t0) cc_final: 0.7569 (t0) REVERT: g 35 ILE cc_start: 0.9696 (pt) cc_final: 0.9461 (mp) REVERT: g 107 CYS cc_start: 0.8316 (p) cc_final: 0.8053 (p) REVERT: g 117 HIS cc_start: 0.8628 (t-90) cc_final: 0.8160 (t-90) REVERT: g 127 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8848 (tmtt) REVERT: g 133 LEU cc_start: 0.9554 (mt) cc_final: 0.9095 (mt) REVERT: g 137 LYS cc_start: 0.9392 (mmtm) cc_final: 0.9121 (mmtm) REVERT: g 153 LYS cc_start: 0.9220 (mttt) cc_final: 0.8925 (mmtm) REVERT: g 163 TYR cc_start: 0.6633 (t80) cc_final: 0.6196 (t80) REVERT: g 242 ARG cc_start: 0.6032 (mtm-85) cc_final: 0.5714 (tmm-80) REVERT: g 440 MET cc_start: 0.3876 (ppp) cc_final: 0.3326 (ppp) REVERT: g 509 MET cc_start: 0.9456 (mmp) cc_final: 0.9256 (mmm) REVERT: g 553 ASP cc_start: 0.9166 (p0) cc_final: 0.8724 (p0) REVERT: g 555 VAL cc_start: 0.9223 (t) cc_final: 0.8748 (m) REVERT: g 571 LYS cc_start: 0.9578 (tttt) cc_final: 0.9299 (ttmt) REVERT: g 585 ASP cc_start: 0.7680 (m-30) cc_final: 0.7367 (m-30) REVERT: G 50 ASP cc_start: 0.8371 (t0) cc_final: 0.8114 (t0) REVERT: G 52 MET cc_start: 0.7521 (mmm) cc_final: 0.7245 (mmm) REVERT: G 65 LEU cc_start: 0.9456 (mt) cc_final: 0.9218 (mt) REVERT: G 87 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8805 (mm-30) REVERT: G 110 TYR cc_start: 0.7739 (m-80) cc_final: 0.7531 (m-80) REVERT: G 120 ILE cc_start: 0.9016 (mm) cc_final: 0.8048 (mm) REVERT: G 172 CYS cc_start: 0.8360 (m) cc_final: 0.7991 (m) REVERT: G 481 MET cc_start: 0.8916 (ttt) cc_final: 0.8416 (ttt) REVERT: G 547 ASP cc_start: 0.9221 (t0) cc_final: 0.8637 (p0) REVERT: G 572 THR cc_start: 0.9554 (p) cc_final: 0.9316 (p) REVERT: h 38 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8327 (mt-10) REVERT: h 209 MET cc_start: -0.2398 (ttp) cc_final: -0.3807 (mpp) REVERT: h 216 ASN cc_start: 0.3507 (m110) cc_final: 0.3196 (t0) REVERT: h 323 MET cc_start: -0.0928 (tmm) cc_final: -0.1140 (ttm) REVERT: h 362 TYR cc_start: 0.1805 (m-80) cc_final: 0.1291 (m-80) REVERT: h 418 MET cc_start: 0.5921 (ttt) cc_final: 0.5565 (ttt) REVERT: h 420 VAL cc_start: 0.9290 (t) cc_final: 0.9055 (t) REVERT: h 425 ARG cc_start: 0.9215 (ptp-170) cc_final: 0.8737 (mtm-85) REVERT: h 437 MET cc_start: 0.8765 (ppp) cc_final: 0.8310 (ppp) REVERT: h 438 ILE cc_start: 0.9198 (mt) cc_final: 0.8803 (mm) REVERT: h 449 ILE cc_start: 0.9555 (mt) cc_final: 0.9320 (mt) REVERT: h 460 ASP cc_start: 0.8609 (t0) cc_final: 0.8289 (t0) REVERT: h 467 LYS cc_start: 0.9345 (tttt) cc_final: 0.8953 (mptt) REVERT: q 39 HIS cc_start: 0.8351 (t-90) cc_final: 0.7829 (t70) REVERT: q 105 ILE cc_start: 0.9356 (mt) cc_final: 0.9063 (mt) REVERT: q 109 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8687 (mm-30) REVERT: q 133 MET cc_start: 0.9402 (ttp) cc_final: 0.8978 (tmm) REVERT: q 139 LEU cc_start: 0.9060 (mt) cc_final: 0.8670 (tt) REVERT: q 348 THR cc_start: 0.5037 (m) cc_final: 0.4732 (t) REVERT: q 393 ASN cc_start: 0.8204 (m-40) cc_final: 0.7749 (t0) REVERT: q 451 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8557 (tp40) REVERT: q 470 ASP cc_start: 0.8404 (t0) cc_final: 0.7801 (t0) REVERT: q 472 ASN cc_start: 0.8676 (m-40) cc_final: 0.8368 (m-40) REVERT: q 521 LEU cc_start: 0.9388 (tp) cc_final: 0.9073 (tp) REVERT: Q 49 CYS cc_start: 0.9072 (m) cc_final: 0.8735 (m) REVERT: Q 109 GLU cc_start: 0.8973 (tp30) cc_final: 0.7651 (tm-30) REVERT: Q 112 ASN cc_start: 0.8229 (t0) cc_final: 0.7563 (t0) REVERT: Q 140 LYS cc_start: 0.8857 (tppt) cc_final: 0.8516 (tppt) REVERT: Q 167 ILE cc_start: 0.9345 (pt) cc_final: 0.8845 (tp) REVERT: Q 202 PHE cc_start: 0.8248 (t80) cc_final: 0.7925 (t80) REVERT: Q 282 LYS cc_start: 0.4819 (mttt) cc_final: 0.4328 (tptp) REVERT: Q 311 HIS cc_start: 0.9136 (m-70) cc_final: 0.8747 (m-70) REVERT: Q 451 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8315 (mm110) REVERT: Q 515 GLU cc_start: 0.9346 (mp0) cc_final: 0.9084 (mp0) REVERT: Q 516 ASN cc_start: 0.8734 (m-40) cc_final: 0.7510 (p0) REVERT: Q 533 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8467 (mm-30) REVERT: z 33 LEU cc_start: 0.9729 (mp) cc_final: 0.9500 (mp) REVERT: z 37 LEU cc_start: 0.7696 (tp) cc_final: 0.7090 (mp) REVERT: z 66 MET cc_start: 0.8802 (ppp) cc_final: 0.8454 (ppp) REVERT: z 123 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9104 (tp30) REVERT: z 155 ARG cc_start: 0.8817 (mtm-85) cc_final: 0.8616 (ttm110) REVERT: z 193 MET cc_start: 0.7687 (ptp) cc_final: 0.7338 (ttm) REVERT: z 199 MET cc_start: 0.8326 (ppp) cc_final: 0.7725 (ppp) REVERT: z 268 LYS cc_start: 0.9173 (tttt) cc_final: 0.8894 (pttm) REVERT: z 283 GLU cc_start: 0.8247 (pt0) cc_final: 0.8009 (pt0) REVERT: z 445 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8779 (tm-30) REVERT: z 449 GLU cc_start: 0.9165 (tp30) cc_final: 0.8946 (tp30) REVERT: z 460 LYS cc_start: 0.9024 (tttt) cc_final: 0.8787 (tmtt) REVERT: z 474 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8793 (mm-30) REVERT: z 500 ASP cc_start: 0.8738 (t0) cc_final: 0.8164 (t0) REVERT: z 503 ILE cc_start: 0.9406 (mt) cc_final: 0.9124 (mt) REVERT: Z 40 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8566 (mmmt) REVERT: Z 66 MET cc_start: 0.5589 (ppp) cc_final: 0.4725 (ppp) REVERT: Z 102 LEU cc_start: 0.9128 (mt) cc_final: 0.8886 (mt) REVERT: Z 151 LEU cc_start: 0.9572 (mt) cc_final: 0.8958 (tt) REVERT: Z 193 MET cc_start: 0.8270 (ppp) cc_final: 0.7467 (ppp) REVERT: Z 296 ILE cc_start: 0.8506 (mp) cc_final: 0.8283 (pt) REVERT: Z 376 CYS cc_start: 0.7412 (m) cc_final: 0.6953 (m) REVERT: Z 408 ASP cc_start: 0.8413 (t70) cc_final: 0.8173 (t70) REVERT: Z 425 TYR cc_start: 0.7696 (m-10) cc_final: 0.7258 (m-10) REVERT: Z 442 THR cc_start: 0.8990 (p) cc_final: 0.8627 (t) REVERT: Z 474 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7858 (tp30) REVERT: Z 478 ASP cc_start: 0.8898 (m-30) cc_final: 0.8072 (m-30) REVERT: Z 532 GLU cc_start: 0.8351 (tp30) cc_final: 0.7528 (tt0) REVERT: Z 533 LEU cc_start: 0.8316 (pt) cc_final: 0.7459 (pt) outliers start: 1 outliers final: 0 residues processed: 1544 average time/residue: 0.5658 time to fit residues: 1499.7163 Evaluate side-chains 1243 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1243 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 4.9990 chunk 743 optimal weight: 3.9990 chunk 678 optimal weight: 9.9990 chunk 723 optimal weight: 8.9990 chunk 435 optimal weight: 2.9990 chunk 314 optimal weight: 0.7980 chunk 567 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 653 optimal weight: 7.9990 chunk 683 optimal weight: 10.0000 chunk 720 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 250 ASN A 363 GLN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 486 ASN e 537 GLN E 424 HIS ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** g 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 291 ASN h 345 HIS ** h 466 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 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 258 ASN z 337 GLN z 430 ASN Z 337 GLN Z 430 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.8989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 62697 Z= 0.265 Angle : 0.693 12.135 84560 Z= 0.358 Chirality : 0.046 0.317 10175 Planarity : 0.004 0.058 10863 Dihedral : 4.732 28.396 8578 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 0.01 % Allowed : 0.60 % Favored : 99.39 % 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: -0.61 (0.09), residues: 8076 helix: 0.29 (0.08), residues: 3835 sheet: -0.91 (0.19), residues: 708 loop : -0.98 (0.10), residues: 3533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP h 478 HIS 0.013 0.002 HIS q 58 PHE 0.032 0.002 PHE B 433 TYR 0.023 0.002 TYR Q 131 ARG 0.019 0.001 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1550 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1549 time to evaluate : 5.512 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: H 44 LEU cc_start: 0.8670 (tp) cc_final: 0.8416 (tt) REVERT: H 118 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8503 (tm-30) REVERT: H 163 ARG cc_start: 0.6712 (mtt-85) cc_final: 0.6012 (ttp-110) REVERT: H 166 MET cc_start: 0.1686 (mtt) cc_final: -0.0131 (mtt) REVERT: H 355 MET cc_start: 0.5531 (pmm) cc_final: 0.5291 (pmm) REVERT: H 388 GLU cc_start: 0.8108 (pm20) cc_final: 0.7878 (pm20) REVERT: a 34 MET cc_start: 0.8776 (mmp) cc_final: 0.8163 (mmm) REVERT: a 42 SER cc_start: 0.9468 (m) cc_final: 0.9219 (p) REVERT: a 51 LYS cc_start: 0.8047 (mptt) cc_final: 0.7462 (mmtm) REVERT: a 118 ASN cc_start: 0.9151 (t0) cc_final: 0.8936 (t0) REVERT: a 121 HIS cc_start: 0.8395 (t-90) cc_final: 0.7834 (t70) REVERT: a 341 MET cc_start: -0.3346 (mtp) cc_final: -0.3995 (ptm) REVERT: a 450 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7792 (mm-30) REVERT: a 494 ARG cc_start: 0.6762 (mmt-90) cc_final: 0.6461 (mmt-90) REVERT: a 502 LEU cc_start: 0.8102 (mt) cc_final: 0.7887 (mt) REVERT: a 526 LYS cc_start: 0.9051 (mmpt) cc_final: 0.8723 (mmmt) REVERT: a 529 LYS cc_start: 0.9155 (tptp) cc_final: 0.8737 (tptp) REVERT: A 82 ILE cc_start: 0.9056 (mm) cc_final: 0.8686 (mp) REVERT: A 85 GLU cc_start: 0.8672 (pp20) cc_final: 0.8364 (pp20) REVERT: A 111 ARG cc_start: 0.8278 (mmt90) cc_final: 0.7859 (mmm-85) REVERT: A 125 ILE cc_start: 0.9565 (mt) cc_final: 0.9257 (mt) REVERT: A 129 PHE cc_start: 0.9410 (m-10) cc_final: 0.9064 (m-80) REVERT: A 164 MET cc_start: 0.7011 (mmt) cc_final: 0.6501 (mmt) REVERT: A 175 PHE cc_start: 0.8322 (m-10) cc_final: 0.7493 (t80) REVERT: A 206 LEU cc_start: 0.8561 (mp) cc_final: 0.8168 (tt) REVERT: A 233 MET cc_start: 0.3889 (ptp) cc_final: 0.2798 (ptm) REVERT: A 236 ARG cc_start: 0.6436 (ttp-110) cc_final: 0.6230 (tmt-80) REVERT: A 333 THR cc_start: 0.5731 (m) cc_final: 0.5388 (t) REVERT: A 410 LYS cc_start: 0.8638 (tptt) cc_final: 0.8352 (tptp) REVERT: A 411 ARG cc_start: 0.8562 (mtt180) cc_final: 0.7400 (mmm160) REVERT: A 486 MET cc_start: 0.7918 (ppp) cc_final: 0.7583 (ppp) REVERT: A 506 ARG cc_start: 0.8838 (tmt170) cc_final: 0.8498 (tmt-80) REVERT: A 533 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7777 (tm-30) REVERT: b 31 ASP cc_start: 0.8981 (m-30) cc_final: 0.8744 (m-30) REVERT: b 109 LEU cc_start: 0.9293 (mt) cc_final: 0.9055 (mt) REVERT: b 310 ASP cc_start: 0.6527 (m-30) cc_final: 0.6250 (p0) REVERT: b 347 MET cc_start: 0.7204 (tpp) cc_final: 0.6584 (ptp) REVERT: b 409 MET cc_start: 0.9457 (tpp) cc_final: 0.8791 (ttm) REVERT: b 413 LYS cc_start: 0.9510 (tttt) cc_final: 0.8984 (ttmm) REVERT: b 446 ASP cc_start: 0.7584 (m-30) cc_final: 0.7366 (m-30) REVERT: b 482 MET cc_start: 0.8257 (mmp) cc_final: 0.7736 (mmm) REVERT: b 508 LEU cc_start: 0.9399 (mm) cc_final: 0.9161 (tp) REVERT: B 56 VAL cc_start: 0.8211 (p) cc_final: 0.7629 (p) REVERT: B 79 ASN cc_start: 0.8915 (m-40) cc_final: 0.8588 (p0) REVERT: B 81 SER cc_start: 0.9200 (m) cc_final: 0.8878 (p) REVERT: B 85 ASP cc_start: 0.8924 (m-30) cc_final: 0.8602 (m-30) REVERT: B 116 HIS cc_start: 0.7691 (m-70) cc_final: 0.7104 (m-70) REVERT: B 133 ASP cc_start: 0.9190 (m-30) cc_final: 0.8940 (m-30) REVERT: B 269 MET cc_start: 0.3805 (ptm) cc_final: 0.3325 (ttm) REVERT: B 416 ASP cc_start: 0.9452 (m-30) cc_final: 0.9204 (m-30) REVERT: B 443 ILE cc_start: 0.9131 (pt) cc_final: 0.8833 (pt) REVERT: B 447 ASN cc_start: 0.8994 (m-40) cc_final: 0.8700 (m-40) REVERT: d 36 ARG cc_start: 0.9090 (ptm-80) cc_final: 0.8886 (ptm160) REVERT: d 39 LEU cc_start: 0.9024 (tp) cc_final: 0.8776 (tp) REVERT: d 65 LEU cc_start: 0.8751 (mt) cc_final: 0.8334 (mt) REVERT: d 68 MET cc_start: 0.6381 (pmm) cc_final: 0.5540 (pmm) REVERT: d 77 MET cc_start: 0.8373 (ppp) cc_final: 0.7462 (ppp) REVERT: d 116 HIS cc_start: 0.8444 (t-90) cc_final: 0.7720 (t-90) REVERT: d 124 PHE cc_start: 0.9553 (m-10) cc_final: 0.9258 (m-80) REVERT: d 305 LEU cc_start: 0.6281 (mt) cc_final: 0.5842 (pp) REVERT: d 394 LEU cc_start: 0.7752 (mm) cc_final: 0.7509 (mt) REVERT: d 457 ASN cc_start: 0.9065 (p0) cc_final: 0.8613 (p0) REVERT: D 82 SER cc_start: 0.9307 (m) cc_final: 0.9048 (p) REVERT: D 85 GLN cc_start: 0.8921 (tp40) cc_final: 0.8576 (tp40) REVERT: D 108 GLU cc_start: 0.8723 (tp30) cc_final: 0.8334 (tp30) REVERT: D 116 HIS cc_start: 0.8871 (t-90) cc_final: 0.8583 (t-90) REVERT: D 118 THR cc_start: 0.9332 (m) cc_final: 0.9130 (m) REVERT: D 183 ASP cc_start: 0.8350 (t70) cc_final: 0.8069 (t70) REVERT: D 399 CYS cc_start: 0.8241 (m) cc_final: 0.7770 (p) REVERT: D 432 MET cc_start: 0.8827 (ppp) cc_final: 0.8207 (ppp) REVERT: D 456 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6903 (tm-30) REVERT: D 457 ASN cc_start: 0.8880 (m-40) cc_final: 0.8411 (m-40) REVERT: D 461 ASN cc_start: 0.8442 (t0) cc_final: 0.8099 (t0) REVERT: e 132 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8121 (tp40) REVERT: e 156 LEU cc_start: 0.9183 (pp) cc_final: 0.8956 (pp) REVERT: e 161 LEU cc_start: 0.9188 (mt) cc_final: 0.8948 (mm) REVERT: e 167 ASP cc_start: 0.8463 (p0) cc_final: 0.8192 (p0) REVERT: e 212 MET cc_start: 0.6211 (ppp) cc_final: 0.5989 (ppp) REVERT: e 226 MET cc_start: 0.7895 (ppp) cc_final: 0.6434 (ttm) REVERT: e 425 ASP cc_start: 0.8634 (m-30) cc_final: 0.8334 (m-30) REVERT: e 481 MET cc_start: 0.8209 (mmp) cc_final: 0.7891 (mmp) REVERT: e 544 LEU cc_start: 0.9286 (tp) cc_final: 0.9011 (tp) REVERT: e 550 LYS cc_start: 0.9411 (mmpt) cc_final: 0.9065 (mmmt) REVERT: E 65 LEU cc_start: 0.8694 (tp) cc_final: 0.8464 (tp) REVERT: E 71 ASP cc_start: 0.8451 (m-30) cc_final: 0.7869 (m-30) REVERT: E 72 LYS cc_start: 0.9143 (mmtm) cc_final: 0.8941 (mmmm) REVERT: E 80 GLU cc_start: 0.7062 (tt0) cc_final: 0.6304 (tp30) REVERT: E 82 THR cc_start: 0.8396 (p) cc_final: 0.8105 (p) REVERT: E 94 MET cc_start: 0.7598 (tpp) cc_final: 0.6884 (tmm) REVERT: E 111 GLN cc_start: 0.8281 (mp10) cc_final: 0.7681 (mp10) REVERT: E 150 PHE cc_start: 0.7913 (m-80) cc_final: 0.7449 (m-80) REVERT: E 309 MET cc_start: -0.0422 (tmm) cc_final: -0.1493 (ttm) REVERT: E 362 ILE cc_start: 0.7273 (mp) cc_final: 0.6873 (mp) REVERT: E 421 ARG cc_start: 0.9141 (mtp85) cc_final: 0.8187 (ptp-170) REVERT: E 425 ASP cc_start: 0.8683 (m-30) cc_final: 0.8278 (m-30) REVERT: E 428 CYS cc_start: 0.9062 (t) cc_final: 0.8476 (p) REVERT: E 432 ASN cc_start: 0.8010 (m-40) cc_final: 0.7599 (t0) REVERT: E 454 VAL cc_start: 0.9551 (t) cc_final: 0.9326 (p) REVERT: E 477 ASP cc_start: 0.9071 (t70) cc_final: 0.7622 (t0) REVERT: E 481 MET cc_start: 0.8142 (mtp) cc_final: 0.7470 (mtp) REVERT: E 485 GLU cc_start: 0.8689 (tp30) cc_final: 0.7974 (tm-30) REVERT: E 550 LYS cc_start: 0.8381 (ptpp) cc_final: 0.8052 (mttp) REVERT: E 553 ASN cc_start: 0.6977 (m-40) cc_final: 0.6695 (m110) REVERT: g 35 ILE cc_start: 0.9683 (pt) cc_final: 0.9470 (mp) REVERT: g 48 LEU cc_start: 0.8764 (tp) cc_final: 0.8552 (tp) REVERT: g 117 HIS cc_start: 0.8653 (t-90) cc_final: 0.8105 (t-90) REVERT: g 133 LEU cc_start: 0.9594 (mt) cc_final: 0.9144 (mt) REVERT: g 137 LYS cc_start: 0.9389 (mmtm) cc_final: 0.9122 (mmtm) REVERT: g 153 LYS cc_start: 0.9320 (mttt) cc_final: 0.8921 (pttm) REVERT: g 163 TYR cc_start: 0.6311 (t80) cc_final: 0.5960 (t80) REVERT: g 242 ARG cc_start: 0.6041 (mtm-85) cc_final: 0.5629 (tmm-80) REVERT: g 480 GLU cc_start: 0.8919 (pm20) cc_final: 0.8248 (pm20) REVERT: g 555 VAL cc_start: 0.9325 (t) cc_final: 0.8998 (t) REVERT: g 571 LYS cc_start: 0.9580 (tttt) cc_final: 0.9336 (ttmt) REVERT: g 582 ARG cc_start: 0.9100 (mmm160) cc_final: 0.7843 (mmm-85) REVERT: g 585 ASP cc_start: 0.7610 (m-30) cc_final: 0.7226 (m-30) REVERT: G 47 MET cc_start: 0.7795 (mmp) cc_final: 0.7533 (mmp) REVERT: G 120 ILE cc_start: 0.9015 (mm) cc_final: 0.7999 (mm) REVERT: G 131 ASP cc_start: 0.9054 (p0) cc_final: 0.8799 (p0) REVERT: G 172 CYS cc_start: 0.8422 (m) cc_final: 0.8041 (m) REVERT: G 460 MET cc_start: 0.8270 (ppp) cc_final: 0.7992 (ppp) REVERT: G 480 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8164 (mm-30) REVERT: G 481 MET cc_start: 0.8913 (ttt) cc_final: 0.8603 (ttt) REVERT: G 487 LEU cc_start: 0.8794 (tp) cc_final: 0.8311 (tp) REVERT: G 509 MET cc_start: 0.9090 (mmp) cc_final: 0.8889 (mmp) REVERT: G 554 MET cc_start: 0.8838 (tpt) cc_final: 0.8388 (tpt) REVERT: h 38 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8420 (mt-10) REVERT: h 209 MET cc_start: -0.2043 (ttp) cc_final: -0.3459 (mpp) REVERT: h 216 ASN cc_start: 0.2586 (m110) cc_final: 0.2178 (t0) REVERT: h 437 MET cc_start: 0.8777 (ppp) cc_final: 0.8328 (ppp) REVERT: h 438 ILE cc_start: 0.9278 (mt) cc_final: 0.8984 (mm) REVERT: h 449 ILE cc_start: 0.9564 (mt) cc_final: 0.9341 (mt) REVERT: h 460 ASP cc_start: 0.8512 (t0) cc_final: 0.7969 (t0) REVERT: h 467 LYS cc_start: 0.9382 (tttt) cc_final: 0.8826 (tmtt) REVERT: h 488 ILE cc_start: 0.8722 (mm) cc_final: 0.7596 (mm) REVERT: h 504 ILE cc_start: 0.9499 (pt) cc_final: 0.9171 (tp) REVERT: q 39 HIS cc_start: 0.8496 (t-90) cc_final: 0.7424 (t70) REVERT: q 105 ILE cc_start: 0.9409 (mt) cc_final: 0.9087 (mt) REVERT: q 109 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8280 (mm-30) REVERT: q 431 ILE cc_start: 0.9556 (mt) cc_final: 0.9315 (mt) REVERT: q 451 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8774 (tp40) REVERT: q 470 ASP cc_start: 0.8475 (t0) cc_final: 0.7912 (t0) REVERT: q 472 ASN cc_start: 0.8706 (m-40) cc_final: 0.8415 (m-40) REVERT: q 521 LEU cc_start: 0.9422 (tp) cc_final: 0.9180 (tp) REVERT: Q 45 SER cc_start: 0.9249 (m) cc_final: 0.8481 (m) REVERT: Q 49 CYS cc_start: 0.9218 (m) cc_final: 0.8834 (m) REVERT: Q 140 LYS cc_start: 0.8903 (tppt) cc_final: 0.8549 (tppt) REVERT: Q 146 VAL cc_start: 0.9050 (t) cc_final: 0.8758 (p) REVERT: Q 167 ILE cc_start: 0.9350 (pt) cc_final: 0.8884 (tp) REVERT: Q 282 LYS cc_start: 0.4878 (mttt) cc_final: 0.4392 (tptp) REVERT: Q 311 HIS cc_start: 0.9112 (m-70) cc_final: 0.8736 (m90) REVERT: Q 451 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8269 (mm110) REVERT: Q 515 GLU cc_start: 0.9348 (mp0) cc_final: 0.9082 (mp0) REVERT: Q 516 ASN cc_start: 0.8798 (m-40) cc_final: 0.7602 (p0) REVERT: z 27 GLU cc_start: 0.8369 (mp0) cc_final: 0.7996 (tt0) REVERT: z 33 LEU cc_start: 0.9699 (mp) cc_final: 0.9454 (mp) REVERT: z 36 ASN cc_start: 0.9364 (m-40) cc_final: 0.8866 (m-40) REVERT: z 37 LEU cc_start: 0.7931 (tp) cc_final: 0.7260 (mp) REVERT: z 66 MET cc_start: 0.8870 (ppp) cc_final: 0.8295 (ppp) REVERT: z 104 GLN cc_start: 0.9088 (mm110) cc_final: 0.8868 (mm110) REVERT: z 123 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9150 (tp30) REVERT: z 155 ARG cc_start: 0.8829 (mtm-85) cc_final: 0.8522 (ttm110) REVERT: z 199 MET cc_start: 0.7182 (ppp) cc_final: 0.6653 (tmm) REVERT: z 268 LYS cc_start: 0.9153 (tttt) cc_final: 0.8878 (pttm) REVERT: z 283 GLU cc_start: 0.8411 (pt0) cc_final: 0.8163 (pt0) REVERT: z 376 CYS cc_start: 0.7478 (m) cc_final: 0.7270 (m) REVERT: z 399 LEU cc_start: 0.9753 (mt) cc_final: 0.9479 (pp) REVERT: z 460 LYS cc_start: 0.9114 (tttt) cc_final: 0.8898 (tmtt) REVERT: z 481 GLN cc_start: 0.9062 (pm20) cc_final: 0.8804 (pm20) REVERT: z 500 ASP cc_start: 0.8740 (t0) cc_final: 0.8393 (t0) REVERT: Z 40 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8396 (mmmt) REVERT: Z 45 MET cc_start: 0.8292 (pmm) cc_final: 0.7882 (pmm) REVERT: Z 102 LEU cc_start: 0.9166 (mt) cc_final: 0.8875 (mt) REVERT: Z 195 GLU cc_start: 0.7707 (tp30) cc_final: 0.7331 (tp30) REVERT: Z 408 ASP cc_start: 0.8425 (t70) cc_final: 0.8222 (t70) REVERT: Z 425 TYR cc_start: 0.7884 (m-10) cc_final: 0.7450 (m-10) REVERT: Z 431 MET cc_start: 0.7433 (mpp) cc_final: 0.6934 (mpp) REVERT: Z 442 THR cc_start: 0.8818 (p) cc_final: 0.7735 (t) REVERT: Z 445 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8061 (mp0) REVERT: Z 467 LEU cc_start: 0.9167 (mt) cc_final: 0.8830 (tp) REVERT: Z 474 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8191 (tp30) REVERT: Z 475 ASP cc_start: 0.8455 (m-30) cc_final: 0.7953 (t70) REVERT: Z 478 ASP cc_start: 0.8890 (m-30) cc_final: 0.8140 (m-30) REVERT: Z 495 ILE cc_start: 0.8787 (mt) cc_final: 0.8586 (mm) REVERT: Z 527 LEU cc_start: 0.9645 (mt) cc_final: 0.9419 (mt) REVERT: Z 532 GLU cc_start: 0.8325 (tp30) cc_final: 0.7623 (tt0) REVERT: Z 533 LEU cc_start: 0.8265 (pt) cc_final: 0.7603 (pt) outliers start: 1 outliers final: 0 residues processed: 1550 average time/residue: 0.5568 time to fit residues: 1484.0796 Evaluate side-chains 1259 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1259 time to evaluate : 5.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 0.6980 chunk 764 optimal weight: 0.7980 chunk 466 optimal weight: 2.9990 chunk 362 optimal weight: 6.9990 chunk 531 optimal weight: 0.7980 chunk 801 optimal weight: 0.5980 chunk 738 optimal weight: 5.9990 chunk 638 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 493 optimal weight: 0.8980 chunk 391 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 ASN ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 250 ASN ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 HIS d 62 HIS ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN G 72 HIS ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 351 ASN G 567 GLN G 568 GLN ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 345 HIS q 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 129 GLN z 52 ASN z 83 GLN Z 461 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.8992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 62697 Z= 0.176 Angle : 0.636 12.058 84560 Z= 0.320 Chirality : 0.045 0.260 10175 Planarity : 0.003 0.054 10863 Dihedral : 4.390 28.381 8578 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.64 % 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: -0.32 (0.09), residues: 8076 helix: 0.52 (0.08), residues: 3837 sheet: -0.73 (0.19), residues: 694 loop : -0.84 (0.10), residues: 3545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 497 HIS 0.007 0.001 HIS q 39 PHE 0.035 0.002 PHE A 451 TYR 0.019 0.001 TYR Q 131 ARG 0.009 0.001 ARG a 443 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1559 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1556 time to evaluate : 5.475 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: H 40 LEU cc_start: 0.9680 (mt) cc_final: 0.9460 (mt) REVERT: H 44 LEU cc_start: 0.8672 (tp) cc_final: 0.8305 (tt) REVERT: H 118 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8628 (tm-30) REVERT: H 150 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6070 (mp0) REVERT: H 163 ARG cc_start: 0.6823 (mtt-85) cc_final: 0.5994 (ttp-110) REVERT: H 355 MET cc_start: 0.5636 (pmm) cc_final: 0.5388 (pmm) REVERT: H 388 GLU cc_start: 0.8156 (pm20) cc_final: 0.7910 (pm20) REVERT: H 434 LYS cc_start: 0.9284 (mmtm) cc_final: 0.8870 (mmtm) REVERT: H 484 GLU cc_start: 0.8961 (pm20) cc_final: 0.8599 (pm20) REVERT: a 34 MET cc_start: 0.8720 (mmp) cc_final: 0.8148 (mmm) REVERT: a 121 HIS cc_start: 0.8406 (t-90) cc_final: 0.7996 (t70) REVERT: a 179 MET cc_start: 0.6036 (ptp) cc_final: 0.5808 (ptp) REVERT: a 341 MET cc_start: -0.2869 (mtp) cc_final: -0.4091 (ptp) REVERT: a 398 MET cc_start: 0.3633 (mmm) cc_final: 0.3313 (mmm) REVERT: a 403 HIS cc_start: 0.8432 (m-70) cc_final: 0.7773 (m-70) REVERT: a 450 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7762 (mm-30) REVERT: a 455 LEU cc_start: 0.9429 (mp) cc_final: 0.8721 (mp) REVERT: a 502 LEU cc_start: 0.8282 (mt) cc_final: 0.7996 (mt) REVERT: a 526 LYS cc_start: 0.9023 (mmpt) cc_final: 0.8662 (mmmt) REVERT: a 529 LYS cc_start: 0.9159 (tptp) cc_final: 0.8843 (tptp) REVERT: A 27 ASN cc_start: 0.8893 (m-40) cc_final: 0.8391 (p0) REVERT: A 73 LEU cc_start: 0.8467 (mt) cc_final: 0.8182 (mt) REVERT: A 86 LEU cc_start: 0.9113 (mt) cc_final: 0.8894 (mt) REVERT: A 125 ILE cc_start: 0.9629 (mt) cc_final: 0.9256 (mt) REVERT: A 129 PHE cc_start: 0.9429 (m-10) cc_final: 0.9076 (m-80) REVERT: A 164 MET cc_start: 0.6799 (mmt) cc_final: 0.6289 (mmt) REVERT: A 175 PHE cc_start: 0.8454 (m-10) cc_final: 0.7453 (t80) REVERT: A 206 LEU cc_start: 0.8467 (mp) cc_final: 0.8031 (tt) REVERT: A 233 MET cc_start: 0.4089 (ptp) cc_final: 0.3089 (ptm) REVERT: A 333 THR cc_start: 0.5826 (m) cc_final: 0.5490 (t) REVERT: A 398 MET cc_start: 0.6496 (mmp) cc_final: 0.5885 (mpp) REVERT: A 411 ARG cc_start: 0.8587 (mtt180) cc_final: 0.7461 (mmm160) REVERT: A 486 MET cc_start: 0.7963 (ppp) cc_final: 0.7616 (ppp) REVERT: A 506 ARG cc_start: 0.8818 (tmt170) cc_final: 0.8529 (tmt-80) REVERT: A 533 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7438 (tm-30) REVERT: b 31 ASP cc_start: 0.8956 (m-30) cc_final: 0.8694 (m-30) REVERT: b 79 ASN cc_start: 0.8016 (p0) cc_final: 0.7692 (p0) REVERT: b 109 LEU cc_start: 0.9253 (mt) cc_final: 0.9035 (mt) REVERT: b 347 MET cc_start: 0.7166 (tpp) cc_final: 0.6854 (ptp) REVERT: b 409 MET cc_start: 0.9471 (tpp) cc_final: 0.8653 (tpp) REVERT: b 413 LYS cc_start: 0.9429 (tttt) cc_final: 0.8798 (ttmm) REVERT: b 454 GLU cc_start: 0.8328 (tt0) cc_final: 0.7685 (tt0) REVERT: b 476 ASN cc_start: 0.9452 (t0) cc_final: 0.9200 (t0) REVERT: b 482 MET cc_start: 0.8054 (mmp) cc_final: 0.7427 (mmm) REVERT: b 506 GLU cc_start: 0.7724 (tt0) cc_final: 0.7364 (mt-10) REVERT: b 508 LEU cc_start: 0.9280 (mm) cc_final: 0.9012 (tp) REVERT: b 514 ILE cc_start: 0.7843 (tt) cc_final: 0.7617 (tt) REVERT: B 57 THR cc_start: 0.7411 (p) cc_final: 0.6508 (t) REVERT: B 85 ASP cc_start: 0.8899 (m-30) cc_final: 0.8522 (m-30) REVERT: B 116 HIS cc_start: 0.7535 (m-70) cc_final: 0.7088 (m-70) REVERT: B 293 TYR cc_start: 0.6912 (t80) cc_final: 0.6454 (m-80) REVERT: B 413 LYS cc_start: 0.9368 (pttt) cc_final: 0.9055 (tptm) REVERT: B 416 ASP cc_start: 0.9432 (m-30) cc_final: 0.9158 (m-30) REVERT: B 443 ILE cc_start: 0.9160 (pt) cc_final: 0.8871 (pt) REVERT: B 446 ASP cc_start: 0.8231 (p0) cc_final: 0.7978 (p0) REVERT: B 447 ASN cc_start: 0.8944 (m-40) cc_final: 0.8676 (m-40) REVERT: d 36 ARG cc_start: 0.9024 (ptm-80) cc_final: 0.8811 (ptm160) REVERT: d 65 LEU cc_start: 0.8686 (mt) cc_final: 0.8203 (mt) REVERT: d 68 MET cc_start: 0.6257 (pmm) cc_final: 0.5432 (pmm) REVERT: d 77 MET cc_start: 0.8200 (ppp) cc_final: 0.7627 (ppp) REVERT: d 116 HIS cc_start: 0.8337 (t-90) cc_final: 0.7804 (t-90) REVERT: d 124 PHE cc_start: 0.9505 (m-10) cc_final: 0.9244 (m-80) REVERT: d 305 LEU cc_start: 0.6005 (mt) cc_final: 0.5660 (pp) REVERT: d 394 LEU cc_start: 0.7721 (mm) cc_final: 0.7407 (mt) REVERT: d 457 ASN cc_start: 0.8989 (p0) cc_final: 0.8611 (p0) REVERT: D 82 SER cc_start: 0.9161 (m) cc_final: 0.8889 (p) REVERT: D 85 GLN cc_start: 0.8906 (tp40) cc_final: 0.8514 (tp40) REVERT: D 116 HIS cc_start: 0.8829 (t-90) cc_final: 0.8605 (t-90) REVERT: D 118 THR cc_start: 0.9265 (m) cc_final: 0.9042 (m) REVERT: D 399 CYS cc_start: 0.8246 (m) cc_final: 0.7788 (p) REVERT: D 432 MET cc_start: 0.6904 (ppp) cc_final: 0.6500 (ptt) REVERT: D 456 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6803 (tm-30) REVERT: D 461 ASN cc_start: 0.8363 (t0) cc_final: 0.8013 (t0) REVERT: e 72 LYS cc_start: 0.6576 (mttt) cc_final: 0.6133 (mmmt) REVERT: e 96 LEU cc_start: 0.6686 (pp) cc_final: 0.5587 (tp) REVERT: e 161 LEU cc_start: 0.9075 (mt) cc_final: 0.8831 (mm) REVERT: e 167 ASP cc_start: 0.8293 (p0) cc_final: 0.8075 (p0) REVERT: e 226 MET cc_start: 0.7810 (ppp) cc_final: 0.6389 (ttm) REVERT: e 229 ARG cc_start: 0.7325 (mmt-90) cc_final: 0.6977 (mtm110) REVERT: e 425 ASP cc_start: 0.8457 (m-30) cc_final: 0.8136 (m-30) REVERT: e 481 MET cc_start: 0.8146 (mmp) cc_final: 0.7788 (mmp) REVERT: e 529 ASP cc_start: 0.8930 (p0) cc_final: 0.8668 (p0) REVERT: e 549 LEU cc_start: 0.9432 (mm) cc_final: 0.9199 (mm) REVERT: e 550 LYS cc_start: 0.9410 (mmpt) cc_final: 0.9031 (mmmt) REVERT: E 71 ASP cc_start: 0.8243 (m-30) cc_final: 0.7946 (m-30) REVERT: E 80 GLU cc_start: 0.6951 (tt0) cc_final: 0.6184 (tp30) REVERT: E 82 THR cc_start: 0.8362 (p) cc_final: 0.8131 (p) REVERT: E 94 MET cc_start: 0.7744 (tpp) cc_final: 0.6634 (tmm) REVERT: E 150 PHE cc_start: 0.7936 (m-80) cc_final: 0.7383 (m-80) REVERT: E 212 MET cc_start: 0.2951 (ttp) cc_final: 0.2603 (tmm) REVERT: E 421 ARG cc_start: 0.9061 (mtp85) cc_final: 0.8106 (ptp-170) REVERT: E 428 CYS cc_start: 0.8993 (t) cc_final: 0.8649 (t) REVERT: E 432 ASN cc_start: 0.7999 (m-40) cc_final: 0.7604 (t0) REVERT: E 454 VAL cc_start: 0.9514 (t) cc_final: 0.9194 (p) REVERT: E 477 ASP cc_start: 0.9082 (t70) cc_final: 0.7546 (t0) REVERT: E 481 MET cc_start: 0.8291 (mtp) cc_final: 0.7555 (mtp) REVERT: E 485 GLU cc_start: 0.8654 (tp30) cc_final: 0.8063 (tm-30) REVERT: E 550 LYS cc_start: 0.8337 (ptpp) cc_final: 0.8048 (mttp) REVERT: g 48 LEU cc_start: 0.8728 (tp) cc_final: 0.8467 (tp) REVERT: g 78 MET cc_start: 0.7362 (tpp) cc_final: 0.6644 (tpp) REVERT: g 111 LEU cc_start: 0.9351 (tp) cc_final: 0.9150 (tp) REVERT: g 117 HIS cc_start: 0.8646 (t-90) cc_final: 0.8061 (t-90) REVERT: g 133 LEU cc_start: 0.9547 (mt) cc_final: 0.9115 (mt) REVERT: g 137 LYS cc_start: 0.9380 (mmtm) cc_final: 0.9151 (mmtm) REVERT: g 153 LYS cc_start: 0.9300 (mttt) cc_final: 0.8950 (mmtm) REVERT: g 163 TYR cc_start: 0.6170 (t80) cc_final: 0.5857 (t80) REVERT: g 242 ARG cc_start: 0.6076 (mtm-85) cc_final: 0.5648 (tmm-80) REVERT: g 480 GLU cc_start: 0.8761 (pm20) cc_final: 0.8305 (pm20) REVERT: g 553 ASP cc_start: 0.9043 (p0) cc_final: 0.8802 (p0) REVERT: g 555 VAL cc_start: 0.9255 (t) cc_final: 0.8834 (m) REVERT: g 571 LYS cc_start: 0.9586 (tttt) cc_final: 0.9289 (ttmt) REVERT: g 582 ARG cc_start: 0.8950 (mmm160) cc_final: 0.7728 (mmm-85) REVERT: g 585 ASP cc_start: 0.7622 (m-30) cc_final: 0.7386 (m-30) REVERT: G 47 MET cc_start: 0.7607 (mmp) cc_final: 0.7390 (mmp) REVERT: G 52 MET cc_start: 0.7149 (mtt) cc_final: 0.6693 (mtt) REVERT: G 87 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8742 (mm-30) REVERT: G 110 TYR cc_start: 0.7805 (m-80) cc_final: 0.7566 (m-80) REVERT: G 120 ILE cc_start: 0.9000 (mm) cc_final: 0.7883 (mm) REVERT: G 172 CYS cc_start: 0.8256 (m) cc_final: 0.7848 (m) REVERT: G 221 LYS cc_start: 0.3451 (tptt) cc_final: 0.1711 (pttm) REVERT: G 480 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8393 (mm-30) REVERT: G 481 MET cc_start: 0.8858 (ttt) cc_final: 0.8396 (ttt) REVERT: G 554 MET cc_start: 0.8477 (tpt) cc_final: 0.8140 (tpt) REVERT: G 564 VAL cc_start: 0.9188 (t) cc_final: 0.8969 (m) REVERT: h 38 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8358 (mt-10) REVERT: h 108 LEU cc_start: 0.9227 (tp) cc_final: 0.8034 (tp) REVERT: h 124 LEU cc_start: 0.9024 (pp) cc_final: 0.8700 (pp) REVERT: h 209 MET cc_start: -0.2207 (ttp) cc_final: -0.3524 (mpp) REVERT: h 216 ASN cc_start: 0.2909 (m110) cc_final: 0.2485 (t0) REVERT: h 449 ILE cc_start: 0.9533 (mt) cc_final: 0.9261 (mt) REVERT: h 466 ASN cc_start: 0.7799 (p0) cc_final: 0.7298 (p0) REVERT: h 467 LYS cc_start: 0.9093 (tttt) cc_final: 0.8417 (mptt) REVERT: h 504 ILE cc_start: 0.9452 (pt) cc_final: 0.9104 (tp) REVERT: q 39 HIS cc_start: 0.8505 (t-90) cc_final: 0.6559 (t-170) REVERT: q 105 ILE cc_start: 0.9365 (mt) cc_final: 0.8838 (mt) REVERT: q 109 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8464 (mm-30) REVERT: q 273 MET cc_start: 0.2810 (tmm) cc_final: 0.2382 (tpp) REVERT: q 451 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8687 (tp40) REVERT: q 461 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8202 (ttp-110) REVERT: q 470 ASP cc_start: 0.8552 (t0) cc_final: 0.7995 (t0) REVERT: q 472 ASN cc_start: 0.8708 (m-40) cc_final: 0.8400 (m-40) REVERT: q 521 LEU cc_start: 0.9375 (tp) cc_final: 0.9134 (tp) REVERT: Q 45 SER cc_start: 0.8534 (m) cc_final: 0.7956 (m) REVERT: Q 49 CYS cc_start: 0.9076 (m) cc_final: 0.8520 (m) REVERT: Q 101 ASN cc_start: 0.8569 (m110) cc_final: 0.8224 (m-40) REVERT: Q 109 GLU cc_start: 0.8519 (mm-30) cc_final: 0.7850 (tm-30) REVERT: Q 112 ASN cc_start: 0.8579 (t0) cc_final: 0.8093 (t0) REVERT: Q 122 LEU cc_start: 0.9124 (mm) cc_final: 0.8769 (mm) REVERT: Q 127 ILE cc_start: 0.9206 (mm) cc_final: 0.8828 (mm) REVERT: Q 140 LYS cc_start: 0.8841 (tppt) cc_final: 0.8568 (tppt) REVERT: Q 167 ILE cc_start: 0.9300 (pt) cc_final: 0.8745 (tp) REVERT: Q 282 LYS cc_start: 0.4712 (mttt) cc_final: 0.4231 (tptp) REVERT: Q 311 HIS cc_start: 0.9004 (m-70) cc_final: 0.8645 (m90) REVERT: Q 403 ASP cc_start: 0.8408 (m-30) cc_final: 0.7881 (p0) REVERT: Q 463 LEU cc_start: 0.9328 (tt) cc_final: 0.9046 (tt) REVERT: Q 515 GLU cc_start: 0.9293 (mp0) cc_final: 0.9070 (mp0) REVERT: Q 516 ASN cc_start: 0.8397 (m-40) cc_final: 0.7276 (p0) REVERT: Q 530 VAL cc_start: 0.9429 (m) cc_final: 0.9119 (m) REVERT: z 27 GLU cc_start: 0.8455 (mp0) cc_final: 0.7903 (tt0) REVERT: z 37 LEU cc_start: 0.7834 (tp) cc_final: 0.7114 (mp) REVERT: z 66 MET cc_start: 0.8879 (ppp) cc_final: 0.8331 (ppp) REVERT: z 92 THR cc_start: 0.6802 (t) cc_final: 0.6241 (t) REVERT: z 126 ARG cc_start: 0.9178 (ttp80) cc_final: 0.8900 (ttp80) REVERT: z 128 GLU cc_start: 0.8749 (tp30) cc_final: 0.8018 (tt0) REVERT: z 155 ARG cc_start: 0.8774 (mtm-85) cc_final: 0.8482 (ttm110) REVERT: z 193 MET cc_start: 0.7606 (ttp) cc_final: 0.6846 (tmm) REVERT: z 199 MET cc_start: 0.7104 (ppp) cc_final: 0.6618 (ppp) REVERT: z 268 LYS cc_start: 0.9180 (tttt) cc_final: 0.8881 (pttm) REVERT: z 283 GLU cc_start: 0.8352 (pt0) cc_final: 0.8099 (pt0) REVERT: z 376 CYS cc_start: 0.7297 (m) cc_final: 0.6807 (m) REVERT: z 399 LEU cc_start: 0.9729 (mt) cc_final: 0.9489 (pp) REVERT: z 408 ASP cc_start: 0.8878 (t0) cc_final: 0.8643 (t0) REVERT: z 445 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8786 (tm-30) REVERT: z 460 LYS cc_start: 0.9068 (tttt) cc_final: 0.8865 (tmtt) REVERT: z 481 GLN cc_start: 0.9090 (pm20) cc_final: 0.8827 (pm20) REVERT: z 500 ASP cc_start: 0.8878 (t0) cc_final: 0.8516 (t0) REVERT: Z 40 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8418 (mmtm) REVERT: Z 102 LEU cc_start: 0.9126 (mt) cc_final: 0.8848 (mt) REVERT: Z 118 ILE cc_start: 0.9540 (mm) cc_final: 0.8162 (mm) REVERT: Z 122 PHE cc_start: 0.8952 (m-10) cc_final: 0.8253 (m-10) REVERT: Z 193 MET cc_start: 0.7804 (ppp) cc_final: 0.6458 (ppp) REVERT: Z 195 GLU cc_start: 0.7182 (tp30) cc_final: 0.6823 (tp30) REVERT: Z 376 CYS cc_start: 0.7533 (m) cc_final: 0.6975 (m) REVERT: Z 408 ASP cc_start: 0.8315 (t70) cc_final: 0.8102 (t70) REVERT: Z 425 TYR cc_start: 0.7713 (m-10) cc_final: 0.7356 (m-10) REVERT: Z 431 MET cc_start: 0.7172 (mpp) cc_final: 0.6708 (mpp) REVERT: Z 442 THR cc_start: 0.8866 (p) cc_final: 0.7894 (t) REVERT: Z 445 GLU cc_start: 0.8634 (mt-10) cc_final: 0.7978 (mp0) REVERT: Z 467 LEU cc_start: 0.9071 (mt) cc_final: 0.8743 (tp) REVERT: Z 474 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7956 (tp30) REVERT: Z 478 ASP cc_start: 0.8856 (m-30) cc_final: 0.7939 (m-30) REVERT: Z 500 ASP cc_start: 0.8825 (t0) cc_final: 0.8475 (t70) REVERT: Z 527 LEU cc_start: 0.9650 (mt) cc_final: 0.9439 (mt) REVERT: Z 532 GLU cc_start: 0.8139 (tp30) cc_final: 0.7529 (tt0) REVERT: Z 533 LEU cc_start: 0.8279 (pt) cc_final: 0.7728 (pt) outliers start: 3 outliers final: 0 residues processed: 1557 average time/residue: 0.5717 time to fit residues: 1532.8958 Evaluate side-chains 1283 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1283 time to evaluate : 5.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 2.9990 chunk 680 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 588 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 639 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 chunk 656 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 ASN ** a 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 250 ASN a 380 HIS a 514 HIS ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 ASN ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** g 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 568 GLN ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 345 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.143645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.118717 restraints weight = 224220.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.121746 restraints weight = 150463.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.123324 restraints weight = 102705.928| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.9193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 62697 Z= 0.195 Angle : 0.634 15.030 84560 Z= 0.322 Chirality : 0.044 0.196 10175 Planarity : 0.003 0.054 10863 Dihedral : 4.369 24.118 8578 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.85 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % 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: -0.34 (0.09), residues: 8076 helix: 0.54 (0.08), residues: 3852 sheet: -0.74 (0.19), residues: 711 loop : -0.89 (0.10), residues: 3513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 497 HIS 0.007 0.001 HIS q 39 PHE 0.043 0.002 PHE a 436 TYR 0.031 0.001 TYR h 362 ARG 0.012 0.001 ARG z 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21593.29 seconds wall clock time: 375 minutes 59.22 seconds (22559.22 seconds total)