Starting phenix.real_space_refine on Sat Feb 17 08:10:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib8_35335/02_2024/8ib8_35335.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib8_35335/02_2024/8ib8_35335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib8_35335/02_2024/8ib8_35335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib8_35335/02_2024/8ib8_35335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib8_35335/02_2024/8ib8_35335.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib8_35335/02_2024/8ib8_35335.pdb" } resolution = 4.42 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= 0.001 sd= 0.027 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 418 5.16 5 C 43015 2.51 5 N 11916 2.21 5 O 13175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 437": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 456": "OE1" <-> "OE2" Residue "F GLU 415": "OE1" <-> "OE2" Residue "H GLU 117": "OE1" <-> "OE2" Residue "H GLU 263": "OE1" <-> "OE2" Residue "H GLU 418": "OE1" <-> "OE2" Residue "J GLU 19": "OE1" <-> "OE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K GLU 511": "OE1" <-> "OE2" Residue "L TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 93": "OE1" <-> "OE2" Residue "M GLU 207": "OE1" <-> "OE2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "P GLU 263": "OE1" <-> "OE2" Residue "Q GLU 32": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68524 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4051 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 519} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3925 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 9, 'TRANS': 511} Chain: "C" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4051 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 16, 'TRANS': 504} Chain: "D" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3935 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "E" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4063 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 18, 'TRANS': 508} Chain: "F" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4023 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "G" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4009 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 14, 'TRANS': 507} Chain: "H" Number of atoms: 4024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4024 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "I" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4054 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 14, 'TRANS': 519} Chain: "J" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3963 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 10, 'TRANS': 516} Chain: "K" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4048 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 16, 'TRANS': 504} Chain: "L" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3873 Classifications: {'peptide': 513} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 498} Chain: "M" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4038 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 18, 'TRANS': 505} Chain: "N" Number of atoms: 4024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4024 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "O" Number of atoms: 4002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4002 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "P" Number of atoms: 4024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4024 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "Q" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1647 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 193} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2770 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 335} Chain breaks: 1 Time building chain proxies: 25.33, per 1000 atoms: 0.37 Number of scatterers: 68524 At special positions: 0 Unit cell: (178.2, 176, 178.2, 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 418 16.00 O 13175 8.00 N 11916 7.00 C 43015 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: 21.86 Conformation dependent library (CDL) restraints added in 9.4 seconds 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16684 Finding SS restraints... Secondary structure from input PDB file: 342 helices and 107 sheets defined 54.9% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.63 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.584A pdb=" N ALA A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 25 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 removed outlier: 3.896A pdb=" N LEU A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 110 removed outlier: 4.268A pdb=" N ILE A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 135 Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 161 through 175 removed outlier: 4.182A pdb=" N ASP A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 259 through 281 removed outlier: 5.119A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.580A pdb=" N LEU A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.698A pdb=" N ALA A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 4.181A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 removed outlier: 4.332A pdb=" N ASN A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 478 through 485 removed outlier: 4.332A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.758A pdb=" N ALA A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 527 removed outlier: 4.070A pdb=" N ILE A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 4.113A pdb=" N ARG B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 66 through 73 removed outlier: 4.402A pdb=" N ILE B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 removed outlier: 3.658A pdb=" N LYS B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 118 Processing helix chain 'B' and resid 122 through 144 removed outlier: 4.179A pdb=" N ILE B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 169 removed outlier: 3.525A pdb=" N SER B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.964A pdb=" N THR B 173 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 removed outlier: 4.410A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU B 182 " --> pdb=" O HIS B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 286 removed outlier: 4.116A pdb=" N VAL B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.834A pdb=" N GLY B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 430 through 455 removed outlier: 4.322A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 457 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'C' and resid 19 through 35 removed outlier: 4.348A pdb=" N GLN C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.885A pdb=" N ILE C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 91 removed outlier: 3.822A pdb=" N LYS C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 115 removed outlier: 3.509A pdb=" N ILE C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.592A pdb=" N VAL C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 161 Processing helix chain 'C' and resid 162 through 167 removed outlier: 6.747A pdb=" N ILE C 165 " --> pdb=" O THR C 162 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG C 167 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 183 removed outlier: 4.749A pdb=" N ASN C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 285 removed outlier: 4.334A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 308 removed outlier: 3.974A pdb=" N GLN C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 306 " --> pdb=" O HIS C 302 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C 307 " --> pdb=" O TYR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 380 through 404 Processing helix chain 'C' and resid 412 through 429 removed outlier: 3.825A pdb=" N MET C 416 " --> pdb=" O GLY C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 445 removed outlier: 4.033A pdb=" N GLU C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 456 removed outlier: 3.914A pdb=" N ARG C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 471 Processing helix chain 'C' and resid 489 through 494 removed outlier: 3.883A pdb=" N LEU C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 494 " --> pdb=" O MET C 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 494' Processing helix chain 'C' and resid 498 through 517 removed outlier: 3.689A pdb=" N LYS C 502 " --> pdb=" O PRO C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 48 removed outlier: 3.686A pdb=" N ILE D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 127 removed outlier: 4.386A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 151 removed outlier: 3.790A pdb=" N GLU D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET D 151 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 4.089A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 removed outlier: 6.103A pdb=" N VAL D 175 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL D 176 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN D 178 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 195 Proline residue: D 185 - end of helix removed outlier: 3.716A pdb=" N VAL D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 292 removed outlier: 4.149A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 441 Processing helix chain 'D' and resid 445 through 458 Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 472 through 486 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.566A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA E 43 " --> pdb=" O MET E 39 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 73 through 81 removed outlier: 3.843A pdb=" N ILE E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 105 through 125 removed outlier: 3.685A pdb=" N ASP E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 152 Processing helix chain 'E' and resid 162 through 173 Processing helix chain 'E' and resid 176 through 181 removed outlier: 3.733A pdb=" N ASN E 179 " --> pdb=" O LYS E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.512A pdb=" N GLU E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 270 through 295 Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 391 through 412 Processing helix chain 'E' and resid 424 through 439 Processing helix chain 'E' and resid 444 through 456 removed outlier: 3.956A pdb=" N MET E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 465 removed outlier: 3.666A pdb=" N MET E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 484 removed outlier: 3.841A pdb=" N THR E 473 " --> pdb=" O ASN E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 510 through 530 removed outlier: 3.882A pdb=" N ILE E 530 " --> pdb=" O MET E 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 8 Processing helix chain 'F' and resid 15 through 35 Processing helix chain 'F' and resid 59 through 65 Processing helix chain 'F' and resid 71 through 88 Processing helix chain 'F' and resid 91 through 111 removed outlier: 3.814A pdb=" N ASN F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 138 removed outlier: 4.434A pdb=" N ILE F 119 " --> pdb=" O HIS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 157 removed outlier: 4.313A pdb=" N ARG F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 176 Processing helix chain 'F' and resid 200 through 204 removed outlier: 3.552A pdb=" N ASP F 203 " --> pdb=" O SER F 200 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR F 204 " --> pdb=" O GLU F 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 200 through 204' Processing helix chain 'F' and resid 252 through 282 removed outlier: 4.744A pdb=" N PHE F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.199A pdb=" N GLU F 322 " --> pdb=" O ARG F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 344 Processing helix chain 'F' and resid 380 through 404 removed outlier: 3.833A pdb=" N ASP F 404 " --> pdb=" O ASN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 426 removed outlier: 3.728A pdb=" N VAL F 416 " --> pdb=" O GLY F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 429 No H-bonds generated for 'chain 'F' and resid 427 through 429' Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.644A pdb=" N GLY F 436 " --> pdb=" O ARG F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.709A pdb=" N LYS F 449 " --> pdb=" O LEU F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 473 removed outlier: 3.687A pdb=" N THR F 462 " --> pdb=" O ASP F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 493 removed outlier: 3.540A pdb=" N GLY F 493 " --> pdb=" O ALA F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 517 Processing helix chain 'G' and resid 18 through 35 removed outlier: 3.787A pdb=" N ALA G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 73 through 90 Processing helix chain 'G' and resid 93 through 109 Processing helix chain 'G' and resid 110 through 113 Processing helix chain 'G' and resid 117 through 140 removed outlier: 3.693A pdb=" N ILE G 121 " --> pdb=" O HIS G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 164 Processing helix chain 'G' and resid 171 through 185 Processing helix chain 'G' and resid 204 through 208 Processing helix chain 'G' and resid 259 through 285 removed outlier: 3.736A pdb=" N GLY G 285 " --> pdb=" O ILE G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 Processing helix chain 'G' and resid 315 through 327 Processing helix chain 'G' and resid 378 through 402 removed outlier: 4.142A pdb=" N LYS G 401 " --> pdb=" O ARG G 397 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN G 402 " --> pdb=" O ARG G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 424 Processing helix chain 'G' and resid 428 through 442 Processing helix chain 'G' and resid 444 through 453 Processing helix chain 'G' and resid 456 through 471 removed outlier: 4.069A pdb=" N GLN G 470 " --> pdb=" O ALA G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 515 Processing helix chain 'H' and resid 10 through 14 Processing helix chain 'H' and resid 24 through 43 removed outlier: 3.663A pdb=" N VAL H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR H 30 " --> pdb=" O GLU H 26 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 76 removed outlier: 4.250A pdb=" N ILE H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 97 Processing helix chain 'H' and resid 100 through 122 removed outlier: 4.025A pdb=" N VAL H 104 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU H 105 " --> pdb=" O THR H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 143 Processing helix chain 'H' and resid 144 through 147 removed outlier: 3.834A pdb=" N VAL H 147 " --> pdb=" O PRO H 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 144 through 147' Processing helix chain 'H' and resid 156 through 169 removed outlier: 4.169A pdb=" N THR H 166 " --> pdb=" O SER H 162 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER H 167 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 191 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'H' and resid 261 through 267 removed outlier: 3.947A pdb=" N LEU H 265 " --> pdb=" O THR H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 286 Processing helix chain 'H' and resid 298 through 309 Processing helix chain 'H' and resid 317 through 329 Processing helix chain 'H' and resid 340 through 344 removed outlier: 3.602A pdb=" N MET H 344 " --> pdb=" O LEU H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 404 removed outlier: 4.247A pdb=" N ARG H 404 " --> pdb=" O LYS H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 428 Processing helix chain 'H' and resid 434 through 444 Processing helix chain 'H' and resid 446 through 456 removed outlier: 3.787A pdb=" N SER H 456 " --> pdb=" O LEU H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 472 removed outlier: 3.780A pdb=" N VAL H 463 " --> pdb=" O LYS H 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 501 through 520 Processing helix chain 'I' and resid 14 through 34 removed outlier: 4.596A pdb=" N ARG I 18 " --> pdb=" O GLY I 14 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA I 29 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER I 34 " --> pdb=" O ASN I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 64 removed outlier: 4.406A pdb=" N LEU I 64 " --> pdb=" O THR I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 86 Processing helix chain 'I' and resid 91 through 110 removed outlier: 3.823A pdb=" N ILE I 95 " --> pdb=" O THR I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 135 removed outlier: 3.643A pdb=" N VAL I 117 " --> pdb=" O HIS I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 157 Processing helix chain 'I' and resid 164 through 179 removed outlier: 3.786A pdb=" N PHE I 168 " --> pdb=" O ASN I 164 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE I 179 " --> pdb=" O ALA I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 208 Processing helix chain 'I' and resid 256 through 281 removed outlier: 4.294A pdb=" N LEU I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP I 261 " --> pdb=" O PRO I 257 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN I 262 " --> pdb=" O GLU I 258 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER I 268 " --> pdb=" O ARG I 264 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR I 271 " --> pdb=" O GLU I 267 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR I 281 " --> pdb=" O LYS I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 304 Processing helix chain 'I' and resid 313 through 324 Processing helix chain 'I' and resid 381 through 405 removed outlier: 3.646A pdb=" N CYS I 385 " --> pdb=" O ASN I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 413 through 426 Processing helix chain 'I' and resid 434 through 445 removed outlier: 3.613A pdb=" N LEU I 445 " --> pdb=" O PHE I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 457 Processing helix chain 'I' and resid 459 through 477 Processing helix chain 'I' and resid 478 through 486 removed outlier: 3.664A pdb=" N LYS I 481 " --> pdb=" O PRO I 478 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN I 482 " --> pdb=" O GLU I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 506 through 526 removed outlier: 3.749A pdb=" N LYS I 510 " --> pdb=" O PRO I 506 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 41 removed outlier: 4.027A pdb=" N ARG J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 74 Processing helix chain 'J' and resid 78 through 95 Processing helix chain 'J' and resid 98 through 119 Processing helix chain 'J' and resid 122 through 145 removed outlier: 3.552A pdb=" N ILE J 126 " --> pdb=" O HIS J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 170 removed outlier: 3.673A pdb=" N SER J 169 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS J 170 " --> pdb=" O THR J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 174 Processing helix chain 'J' and resid 175 through 189 removed outlier: 3.888A pdb=" N LYS J 181 " --> pdb=" O ASP J 177 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU J 182 " --> pdb=" O HIS J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 260 through 284 removed outlier: 3.916A pdb=" N VAL J 264 " --> pdb=" O SER J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 308 Processing helix chain 'J' and resid 316 through 328 removed outlier: 3.744A pdb=" N VAL J 320 " --> pdb=" O ASP J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 403 Processing helix chain 'J' and resid 411 through 428 Processing helix chain 'J' and resid 431 through 455 removed outlier: 3.625A pdb=" N ALA J 435 " --> pdb=" O LYS J 431 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU J 446 " --> pdb=" O ALA J 442 " (cutoff:3.500A) Proline residue: J 447 - end of helix Processing helix chain 'J' and resid 458 through 471 Processing helix chain 'J' and resid 488 through 492 Processing helix chain 'J' and resid 497 through 516 Processing helix chain 'K' and resid 19 through 35 removed outlier: 3.722A pdb=" N GLN K 23 " --> pdb=" O GLY K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 69 removed outlier: 3.920A pdb=" N GLU K 69 " --> pdb=" O ALA K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 91 Processing helix chain 'K' and resid 94 through 114 removed outlier: 3.643A pdb=" N PHE K 112 " --> pdb=" O VAL K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 141 removed outlier: 3.702A pdb=" N VAL K 122 " --> pdb=" O HIS K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 161 Processing helix chain 'K' and resid 162 through 167 removed outlier: 6.982A pdb=" N ILE K 165 " --> pdb=" O THR K 162 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG K 167 " --> pdb=" O ALA K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 182 removed outlier: 3.870A pdb=" N ALA K 179 " --> pdb=" O ILE K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 212 Processing helix chain 'K' and resid 263 through 284 removed outlier: 3.845A pdb=" N ILE K 282 " --> pdb=" O LEU K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 307 Processing helix chain 'K' and resid 316 through 328 Processing helix chain 'K' and resid 334 through 338 Processing helix chain 'K' and resid 339 through 343 removed outlier: 4.017A pdb=" N ASP K 342 " --> pdb=" O ARG K 339 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL K 343 " --> pdb=" O GLU K 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 339 through 343' Processing helix chain 'K' and resid 380 through 403 Processing helix chain 'K' and resid 412 through 427 removed outlier: 3.648A pdb=" N MET K 416 " --> pdb=" O GLY K 412 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS K 427 " --> pdb=" O THR K 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 445 removed outlier: 3.902A pdb=" N ALA K 441 " --> pdb=" O TYR K 437 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 454 removed outlier: 4.223A pdb=" N ARG K 449 " --> pdb=" O GLU K 445 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR K 450 " --> pdb=" O VAL K 446 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU K 451 " --> pdb=" O ILE K 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 458 through 470 removed outlier: 3.555A pdb=" N LEU K 462 " --> pdb=" O SER K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 471 through 475 removed outlier: 3.725A pdb=" N ASN K 474 " --> pdb=" O THR K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 490 through 494 removed outlier: 3.648A pdb=" N GLY K 494 " --> pdb=" O MET K 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 490 through 494' Processing helix chain 'K' and resid 499 through 517 removed outlier: 3.589A pdb=" N LEU K 517 " --> pdb=" O ALA K 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 47 Processing helix chain 'L' and resid 73 through 81 Processing helix chain 'L' and resid 85 through 102 Processing helix chain 'L' and resid 106 through 126 removed outlier: 3.941A pdb=" N VAL L 110 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE L 111 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS L 122 " --> pdb=" O ASP L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 152 removed outlier: 3.759A pdb=" N GLU L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 172 removed outlier: 3.595A pdb=" N LEU L 163 " --> pdb=" O ASP L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 174 No H-bonds generated for 'chain 'L' and resid 173 through 174' Processing helix chain 'L' and resid 175 through 178 removed outlier: 4.538A pdb=" N GLN L 178 " --> pdb=" O VAL L 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 175 through 178' Processing helix chain 'L' and resid 179 through 195 Proline residue: L 185 - end of helix removed outlier: 4.165A pdb=" N ILE L 195 " --> pdb=" O VAL L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 206 No H-bonds generated for 'chain 'L' and resid 204 through 206' Processing helix chain 'L' and resid 268 through 293 Processing helix chain 'L' and resid 310 through 320 Processing helix chain 'L' and resid 332 through 341 Processing helix chain 'L' and resid 352 through 356 Processing helix chain 'L' and resid 394 through 418 removed outlier: 3.937A pdb=" N ILE L 398 " --> pdb=" O ASN L 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 442 Processing helix chain 'L' and resid 446 through 458 removed outlier: 3.729A pdb=" N CYS L 450 " --> pdb=" O MET L 446 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET L 458 " --> pdb=" O PHE L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 469 Processing helix chain 'L' and resid 472 through 487 removed outlier: 3.552A pdb=" N THR L 476 " --> pdb=" O ASN L 472 " (cutoff:3.500A) Processing helix chain 'L' and resid 512 through 532 Processing helix chain 'M' and resid 30 through 48 removed outlier: 3.554A pdb=" N LEU M 34 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 80 removed outlier: 3.787A pdb=" N ILE M 77 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 102 Processing helix chain 'M' and resid 107 through 125 Processing helix chain 'M' and resid 129 through 152 removed outlier: 3.794A pdb=" N ILE M 133 " --> pdb=" O HIS M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 173 Processing helix chain 'M' and resid 176 through 181 removed outlier: 3.802A pdb=" N CYS M 181 " --> pdb=" O VAL M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 197 removed outlier: 3.517A pdb=" N GLU M 187 " --> pdb=" O ARG M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 209 Processing helix chain 'M' and resid 218 through 222 Processing helix chain 'M' and resid 270 through 296 removed outlier: 4.108A pdb=" N LYS M 282 " --> pdb=" O GLN M 278 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR M 295 " --> pdb=" O GLN M 291 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY M 296 " --> pdb=" O ILE M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 318 removed outlier: 3.623A pdb=" N ASN M 311 " --> pdb=" O ASP M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 326 through 338 Processing helix chain 'M' and resid 391 through 412 Processing helix chain 'M' and resid 423 through 439 removed outlier: 3.948A pdb=" N LYS M 439 " --> pdb=" O GLN M 435 " (cutoff:3.500A) Processing helix chain 'M' and resid 444 through 467 removed outlier: 4.154A pdb=" N ILE M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) Proline residue: M 459 - end of helix Processing helix chain 'M' and resid 469 through 484 removed outlier: 3.557A pdb=" N GLU M 484 " --> pdb=" O ARG M 480 " (cutoff:3.500A) Processing helix chain 'M' and resid 500 through 505 removed outlier: 3.750A pdb=" N GLN M 504 " --> pdb=" O ASP M 500 " (cutoff:3.500A) Processing helix chain 'M' and resid 510 through 528 Processing helix chain 'N' and resid 15 through 35 Processing helix chain 'N' and resid 59 through 67 Processing helix chain 'N' and resid 71 through 88 Processing helix chain 'N' and resid 92 through 111 removed outlier: 3.786A pdb=" N VAL N 96 " --> pdb=" O THR N 92 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU N 108 " --> pdb=" O LYS N 104 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR N 109 " --> pdb=" O GLN N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 138 removed outlier: 4.158A pdb=" N ILE N 119 " --> pdb=" O HIS N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 160 Processing helix chain 'N' and resid 161 through 178 removed outlier: 4.108A pdb=" N GLU N 170 " --> pdb=" O ASP N 166 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA N 178 " --> pdb=" O ASP N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 191 removed outlier: 3.758A pdb=" N MET N 190 " --> pdb=" O ASP N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 204 removed outlier: 4.158A pdb=" N THR N 204 " --> pdb=" O GLU N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 264 removed outlier: 3.841A pdb=" N ARG N 264 " --> pdb=" O VAL N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 282 Processing helix chain 'N' and resid 298 through 308 removed outlier: 3.817A pdb=" N GLU N 308 " --> pdb=" O ALA N 304 " (cutoff:3.500A) Processing helix chain 'N' and resid 317 through 328 removed outlier: 3.781A pdb=" N MET N 321 " --> pdb=" O LYS N 317 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU N 322 " --> pdb=" O ARG N 318 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU N 326 " --> pdb=" O GLU N 322 " (cutoff:3.500A) Processing helix chain 'N' and resid 340 through 344 Processing helix chain 'N' and resid 380 through 403 Processing helix chain 'N' and resid 412 through 426 Processing helix chain 'N' and resid 432 through 454 removed outlier: 3.696A pdb=" N GLY N 436 " --> pdb=" O ARG N 432 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU N 444 " --> pdb=" O PHE N 440 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE N 447 " --> pdb=" O ALA N 443 " (cutoff:3.500A) Proline residue: N 448 - end of helix removed outlier: 3.959A pdb=" N LEU N 451 " --> pdb=" O ILE N 447 " (cutoff:3.500A) Processing helix chain 'N' and resid 458 through 469 Processing helix chain 'N' and resid 489 through 493 Processing helix chain 'N' and resid 498 through 517 Processing helix chain 'O' and resid 17 through 36 removed outlier: 3.529A pdb=" N GLN O 21 " --> pdb=" O GLN O 17 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA O 28 " --> pdb=" O SER O 24 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL O 36 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 69 removed outlier: 4.100A pdb=" N ILE O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 90 Processing helix chain 'O' and resid 93 through 108 Processing helix chain 'O' and resid 109 through 114 Processing helix chain 'O' and resid 117 through 139 Processing helix chain 'O' and resid 147 through 164 Processing helix chain 'O' and resid 168 through 170 No H-bonds generated for 'chain 'O' and resid 168 through 170' Processing helix chain 'O' and resid 171 through 185 Processing helix chain 'O' and resid 259 through 284 removed outlier: 3.516A pdb=" N SER O 284 " --> pdb=" O LYS O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 296 through 307 removed outlier: 3.549A pdb=" N THR O 300 " --> pdb=" O GLY O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 315 through 327 Processing helix chain 'O' and resid 333 through 337 removed outlier: 3.830A pdb=" N ALA O 336 " --> pdb=" O SER O 333 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU O 337 " --> pdb=" O VAL O 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 333 through 337' Processing helix chain 'O' and resid 378 through 402 removed outlier: 4.151A pdb=" N LYS O 401 " --> pdb=" O ARG O 397 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN O 402 " --> pdb=" O ARG O 398 " (cutoff:3.500A) Processing helix chain 'O' and resid 410 through 424 removed outlier: 4.055A pdb=" N MET O 414 " --> pdb=" O GLY O 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 428 through 453 removed outlier: 3.816A pdb=" N GLN O 432 " --> pdb=" O PRO O 428 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU O 433 " --> pdb=" O GLY O 429 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE O 445 " --> pdb=" O ALA O 441 " (cutoff:3.500A) Proline residue: O 446 - end of helix removed outlier: 3.755A pdb=" N ASN O 452 " --> pdb=" O GLN O 448 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 469 Processing helix chain 'O' and resid 487 through 491 Processing helix chain 'O' and resid 496 through 515 Processing helix chain 'P' and resid 10 through 14 Processing helix chain 'P' and resid 28 through 44 removed outlier: 3.763A pdb=" N ASN P 32 " --> pdb=" O ALA P 28 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR P 43 " --> pdb=" O LEU P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 51 removed outlier: 3.632A pdb=" N ASN P 50 " --> pdb=" O TYR P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 76 Processing helix chain 'P' and resid 80 through 97 Processing helix chain 'P' and resid 100 through 122 removed outlier: 4.202A pdb=" N VAL P 104 " --> pdb=" O GLY P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 146 removed outlier: 3.841A pdb=" N VAL P 128 " --> pdb=" O SER P 124 " (cutoff:3.500A) Proline residue: P 144 - end of helix Processing helix chain 'P' and resid 156 through 170 removed outlier: 3.719A pdb=" N THR P 166 " --> pdb=" O SER P 162 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER P 167 " --> pdb=" O LEU P 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER P 170 " --> pdb=" O THR P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 190 removed outlier: 4.591A pdb=" N LEU P 179 " --> pdb=" O ASN P 175 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER P 189 " --> pdb=" O GLN P 185 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 200 No H-bonds generated for 'chain 'P' and resid 198 through 200' Processing helix chain 'P' and resid 211 through 215 Processing helix chain 'P' and resid 261 through 285 removed outlier: 3.829A pdb=" N LEU P 265 " --> pdb=" O THR P 261 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS P 270 " --> pdb=" O MET P 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 309 removed outlier: 3.540A pdb=" N LEU P 302 " --> pdb=" O ALA P 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 329 Processing helix chain 'P' and resid 340 through 344 removed outlier: 3.729A pdb=" N MET P 344 " --> pdb=" O LEU P 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 381 through 405 Processing helix chain 'P' and resid 413 through 428 Processing helix chain 'P' and resid 434 through 445 removed outlier: 4.288A pdb=" N PHE P 445 " --> pdb=" O PHE P 441 " (cutoff:3.500A) Processing helix chain 'P' and resid 446 through 456 Processing helix chain 'P' and resid 459 through 474 removed outlier: 4.255A pdb=" N VAL P 463 " --> pdb=" O LYS P 459 " (cutoff:3.500A) Processing helix chain 'P' and resid 493 through 496 removed outlier: 3.709A pdb=" N GLY P 496 " --> pdb=" O LEU P 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 493 through 496' Processing helix chain 'P' and resid 501 through 520 Processing helix chain 'Q' and resid 10 through 18 Processing helix chain 'Q' and resid 28 through 40 Processing helix chain 'Q' and resid 42 through 47 removed outlier: 3.807A pdb=" N THR Q 47 " --> pdb=" O SER Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 52 removed outlier: 4.445A pdb=" N THR Q 52 " --> pdb=" O TYR Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 87 Processing helix chain 'Q' and resid 101 through 107 removed outlier: 3.737A pdb=" N GLU Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 141 removed outlier: 3.522A pdb=" N ARG Q 139 " --> pdb=" O SER Q 135 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS Q 140 " --> pdb=" O GLY Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 155 Processing helix chain 'Q' and resid 179 through 184 removed outlier: 4.026A pdb=" N LEU Q 182 " --> pdb=" O ILE Q 179 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL Q 183 " --> pdb=" O GLY Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 201 Processing helix chain 'S' and resid 55 through 67 removed outlier: 3.751A pdb=" N GLN S 59 " --> pdb=" O GLY S 55 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER S 60 " --> pdb=" O ASP S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 92 removed outlier: 3.763A pdb=" N HIS S 88 " --> pdb=" O LYS S 84 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE S 90 " --> pdb=" O TRP S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 101 Processing helix chain 'S' and resid 112 through 128 removed outlier: 3.989A pdb=" N ARG S 116 " --> pdb=" O PRO S 112 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN S 121 " --> pdb=" O GLU S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 145 Processing helix chain 'S' and resid 181 through 193 Processing helix chain 'S' and resid 202 through 216 Processing helix chain 'S' and resid 222 through 232 Processing helix chain 'S' and resid 251 through 263 removed outlier: 4.049A pdb=" N PHE S 255 " --> pdb=" O GLY S 251 " (cutoff:3.500A) Proline residue: S 258 - end of helix removed outlier: 3.698A pdb=" N LEU S 261 " --> pdb=" O CYS S 257 " (cutoff:3.500A) Processing helix chain 'S' and resid 264 through 267 Processing helix chain 'S' and resid 273 through 284 Processing helix chain 'S' and resid 286 through 296 removed outlier: 3.873A pdb=" N ASP S 292 " --> pdb=" O ASP S 288 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN S 296 " --> pdb=" O ASP S 292 " (cutoff:3.500A) Processing helix chain 'S' and resid 308 through 321 removed outlier: 3.737A pdb=" N LEU S 320 " --> pdb=" O GLU S 316 " (cutoff:3.500A) Processing helix chain 'S' and resid 337 through 348 Processing helix chain 'S' and resid 351 through 356 Processing helix chain 'S' and resid 359 through 366 removed outlier: 4.250A pdb=" N GLU S 364 " --> pdb=" O GLN S 360 " (cutoff:3.500A) Processing helix chain 'S' and resid 368 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.555A pdb=" N THR A 55 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.268A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.201A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.201A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 348 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 232 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LYS A 233 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU A 287 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA A 235 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA8, first strand: chain 'B' and resid 17 through 19 removed outlier: 6.501A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 64 removed outlier: 3.585A pdb=" N MET B 62 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 64 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP B 49 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL D 535 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 51 " --> pdb=" O VAL D 535 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASN D 537 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU B 53 " --> pdb=" O ASN D 537 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.439A pdb=" N HIS B 200 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU B 375 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 202 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL B 374 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR B 213 " --> pdb=" O VAL B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 217 through 220 removed outlier: 6.901A pdb=" N SER B 345 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LYS B 236 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS B 347 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N CYS B 289 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LYS B 236 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE B 291 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 238 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 217 through 220 removed outlier: 6.901A pdb=" N SER B 345 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LYS B 236 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS B 347 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ALA B 332 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 239 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 257 through 258 removed outlier: 3.552A pdb=" N PHE F 249 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE F 248 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU H 258 " --> pdb=" O PHE F 248 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TYR F 250 " --> pdb=" O LEU H 258 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS E 263 " --> pdb=" O ALA G 253 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 257 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 51 Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 143 removed outlier: 3.773A pdb=" N ILE C 142 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 185 through 187 removed outlier: 3.625A pdb=" N GLU C 187 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 200 through 201 removed outlier: 7.458A pdb=" N ARG C 200 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR C 373 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 217 through 220 removed outlier: 3.772A pdb=" N ILE C 363 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 220 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 312 through 313 removed outlier: 5.626A pdb=" N VAL C 290 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 239 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N VAL C 332 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 240 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 479 through 481 Processing sheet with id=AC5, first strand: chain 'D' and resid 59 through 62 Processing sheet with id=AC6, first strand: chain 'D' and resid 152 through 153 Processing sheet with id=AC7, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.863A pdb=" N ILE D 388 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 390 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 227 through 229 removed outlier: 4.132A pdb=" N ALA D 362 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL D 241 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 323 through 328 removed outlier: 5.942A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE D 246 " --> pdb=" O GLY D 357 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 357 " --> pdb=" O ILE D 246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 491 through 494 Processing sheet with id=AD2, first strand: chain 'E' and resid 25 through 28 Processing sheet with id=AD3, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.538A pdb=" N LYS E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE E 387 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLU E 212 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLY E 389 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS E 214 " --> pdb=" O GLY E 389 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE E 386 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS E 223 " --> pdb=" O PHE E 386 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 228 through 230 removed outlier: 3.538A pdb=" N ALA E 246 " --> pdb=" O ALA E 356 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 301 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 228 through 230 removed outlier: 3.538A pdb=" N ALA E 246 " --> pdb=" O ALA E 356 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE E 250 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 418 through 420 removed outlier: 3.631A pdb=" N VAL E 419 " --> pdb=" O GLU E 508 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU E 508 " --> pdb=" O VAL E 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AD8, first strand: chain 'F' and resid 54 through 57 removed outlier: 3.576A pdb=" N THR F 57 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N MET F 44 " --> pdb=" O VAL H 521 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN H 523 " --> pdb=" O MET F 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 139 through 140 removed outlier: 3.673A pdb=" N VAL F 139 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 192 through 195 removed outlier: 3.515A pdb=" N SER F 205 " --> pdb=" O LEU F 375 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 210 through 212 removed outlier: 3.595A pdb=" N LEU F 349 " --> pdb=" O GLU F 364 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 311 through 313 removed outlier: 5.975A pdb=" N PHE F 289 " --> pdb=" O VAL F 311 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU F 313 " --> pdb=" O PHE F 289 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL F 291 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR F 229 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE F 292 " --> pdb=" O TYR F 229 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU F 231 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 14 through 17 removed outlier: 3.631A pdb=" N ASP G 14 " --> pdb=" O LYS G 521 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER G 16 " --> pdb=" O THR G 519 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU G 518 " --> pdb=" O MET H 55 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE H 57 " --> pdb=" O GLU G 518 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE G 520 " --> pdb=" O ILE H 57 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 47 through 49 removed outlier: 3.942A pdb=" N LYS G 47 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER G 59 " --> pdb=" O LYS G 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AE7, first strand: chain 'G' and resid 195 through 201 removed outlier: 3.935A pdb=" N THR G 371 " --> pdb=" O VAL G 211 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL G 211 " --> pdb=" O THR G 371 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 214 through 217 removed outlier: 3.517A pdb=" N PHE G 348 " --> pdb=" O TYR G 232 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR G 232 " --> pdb=" O PHE G 348 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 309 through 310 removed outlier: 8.889A pdb=" N GLN G 331 " --> pdb=" O ILE G 237 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU G 239 " --> pdb=" O GLN G 331 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 476 through 477 Processing sheet with id=AF2, first strand: chain 'H' and resid 202 through 208 removed outlier: 3.692A pdb=" N ARG H 203 " --> pdb=" O SER H 373 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 222 through 223 Processing sheet with id=AF4, first strand: chain 'H' and resid 311 through 314 Processing sheet with id=AF5, first strand: chain 'H' and resid 408 through 410 Processing sheet with id=AF6, first strand: chain 'H' and resid 478 through 480 Processing sheet with id=AF7, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.548A pdb=" N SER I 12 " --> pdb=" O LEU I 530 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU I 530 " --> pdb=" O SER I 12 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE I 527 " --> pdb=" O ASP L 58 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N MET L 60 " --> pdb=" O ILE I 527 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP I 529 " --> pdb=" O MET L 60 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLN L 62 " --> pdb=" O ASP I 529 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE I 531 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR L 71 " --> pdb=" O LYS L 59 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 52 through 55 removed outlier: 3.683A pdb=" N THR I 55 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP I 42 " --> pdb=" O ILE K 519 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP K 521 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY K 525 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 181 through 182 Processing sheet with id=AG1, first strand: chain 'I' and resid 197 through 200 removed outlier: 3.714A pdb=" N SER I 374 " --> pdb=" O ILE I 211 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET I 209 " --> pdb=" O ILE I 376 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 213 through 215 removed outlier: 3.930A pdb=" N GLU I 350 " --> pdb=" O LYS I 365 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL I 351 " --> pdb=" O ILE I 229 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE I 229 " --> pdb=" O VAL I 351 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 306 through 308 removed outlier: 6.841A pdb=" N LYS I 233 " --> pdb=" O VAL I 285 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU I 287 " --> pdb=" O LYS I 233 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA I 235 " --> pdb=" O LEU I 287 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 250 through 252 removed outlier: 6.668A pdb=" N GLN I 251 " --> pdb=" O VAL L 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'I' and resid 409 through 410 Processing sheet with id=AG6, first strand: chain 'I' and resid 487 through 489 Processing sheet with id=AG7, first strand: chain 'J' and resid 61 through 64 removed outlier: 4.044A pdb=" N MET J 62 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU J 52 " --> pdb=" O MET J 62 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR J 64 " --> pdb=" O LYS J 50 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS J 50 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE J 51 " --> pdb=" O VAL L 536 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'J' and resid 146 through 147 Processing sheet with id=AG9, first strand: chain 'J' and resid 199 through 205 removed outlier: 3.835A pdb=" N GLY J 377 " --> pdb=" O LYS J 204 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 218 through 220 removed outlier: 3.920A pdb=" N LEU J 220 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE J 360 " --> pdb=" O LEU J 220 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 310 through 312 removed outlier: 6.569A pdb=" N PHE J 290 " --> pdb=" O ILE J 312 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS J 236 " --> pdb=" O CYS J 289 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE J 291 " --> pdb=" O LYS J 236 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU J 238 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ALA J 332 " --> pdb=" O ILE J 237 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE J 239 " --> pdb=" O ALA J 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'J' and resid 310 through 312 removed outlier: 6.569A pdb=" N PHE J 290 " --> pdb=" O ILE J 312 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS J 236 " --> pdb=" O CYS J 289 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE J 291 " --> pdb=" O LYS J 236 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU J 238 " --> pdb=" O ILE J 291 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 255 through 256 removed outlier: 6.941A pdb=" N ARG J 255 " --> pdb=" O VAL M 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'J' and resid 476 through 478 Processing sheet with id=AH6, first strand: chain 'J' and resid 517 through 520 removed outlier: 3.973A pdb=" N VAL J 517 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET M 60 " --> pdb=" O VAL J 517 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASN J 519 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL M 62 " --> pdb=" O ASN J 519 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS M 59 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR M 71 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET M 61 " --> pdb=" O THR M 69 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 57 through 60 removed outlier: 3.713A pdb=" N LYS K 48 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N MET K 47 " --> pdb=" O VAL N 518 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU N 520 " --> pdb=" O MET K 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET K 49 " --> pdb=" O GLU N 520 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET N 522 " --> pdb=" O MET K 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU K 51 " --> pdb=" O MET N 522 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 142 through 143 removed outlier: 3.734A pdb=" N ILE K 142 " --> pdb=" O LEU K 407 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL K 408 " --> pdb=" O GLU K 497 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 185 through 187 removed outlier: 3.804A pdb=" N GLU K 187 " --> pdb=" O LYS K 191 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 200 through 201 removed outlier: 8.065A pdb=" N ARG K 200 " --> pdb=" O ILE K 374 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 217 through 220 Processing sheet with id=AI3, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AI4, first strand: chain 'K' and resid 256 through 258 removed outlier: 3.713A pdb=" N GLY N 247 " --> pdb=" O ILE K 256 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 478 through 480 Processing sheet with id=AI6, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.529A pdb=" N ARG L 153 " --> pdb=" O LEU L 421 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 208 through 212 removed outlier: 3.673A pdb=" N THR L 387 " --> pdb=" O VAL L 224 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 228 through 229 removed outlier: 3.605A pdb=" N GLU L 363 " --> pdb=" O LYS L 375 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N CYS L 379 " --> pdb=" O ALA L 359 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA L 359 " --> pdb=" O CYS L 379 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER L 358 " --> pdb=" O LYS L 245 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LYS L 245 " --> pdb=" O SER L 358 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU L 360 " --> pdb=" O LYS L 243 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 297 through 299 Processing sheet with id=AJ1, first strand: chain 'L' and resid 491 through 493 Processing sheet with id=AJ2, first strand: chain 'M' and resid 26 through 29 removed outlier: 7.702A pdb=" N LEU O 48 " --> pdb=" O ASP M 531 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE M 533 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL O 50 " --> pdb=" O ILE M 533 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS M 535 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP O 51 " --> pdb=" O LYS O 55 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS O 55 " --> pdb=" O ASP O 51 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'M' and resid 210 through 211 removed outlier: 3.698A pdb=" N ILE M 385 " --> pdb=" O LYS M 210 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M 223 " --> pdb=" O PHE M 386 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'M' and resid 214 through 215 removed outlier: 8.027A pdb=" N LYS M 214 " --> pdb=" O GLY M 389 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'M' and resid 227 through 230 removed outlier: 4.999A pdb=" N LEU M 358 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU M 244 " --> pdb=" O LEU M 358 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N LEU M 299 " --> pdb=" O ASP M 245 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS M 247 " --> pdb=" O LEU M 299 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE M 301 " --> pdb=" O LYS M 247 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA M 249 " --> pdb=" O ILE M 301 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA M 300 " --> pdb=" O VAL M 322 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 418 through 420 removed outlier: 3.703A pdb=" N GLU M 508 " --> pdb=" O VAL M 419 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'N' and resid 54 through 57 removed outlier: 6.639A pdb=" N MET N 44 " --> pdb=" O ASP P 522 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE P 524 " --> pdb=" O MET N 44 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET N 46 " --> pdb=" O ILE P 524 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N MET P 526 " --> pdb=" O MET N 46 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL N 48 " --> pdb=" O MET P 526 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'N' and resid 139 through 140 Processing sheet with id=AJ9, first strand: chain 'N' and resid 192 through 195 removed outlier: 6.160A pdb=" N GLU N 192 " --> pdb=" O LEU N 374 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE N 376 " --> pdb=" O GLU N 192 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET N 194 " --> pdb=" O ILE N 376 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'N' and resid 210 through 212 removed outlier: 3.640A pdb=" N LEU N 349 " --> pdb=" O GLU N 364 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N HIS N 346 " --> pdb=" O TYR N 229 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR N 229 " --> pdb=" O HIS N 346 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY N 348 " --> pdb=" O ASP N 227 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLY N 288 " --> pdb=" O VAL N 225 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP N 227 " --> pdb=" O GLY N 288 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL N 290 " --> pdb=" O ASP N 227 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR N 229 " --> pdb=" O VAL N 290 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE N 292 " --> pdb=" O TYR N 229 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU N 231 " --> pdb=" O ILE N 292 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL N 311 " --> pdb=" O PHE N 289 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'N' and resid 477 through 479 Processing sheet with id=AK3, first strand: chain 'O' and resid 197 through 201 Processing sheet with id=AK4, first strand: chain 'O' and resid 215 through 217 removed outlier: 3.644A pdb=" N PHE O 216 " --> pdb=" O ASN O 359 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'O' and resid 288 through 291 Processing sheet with id=AK6, first strand: chain 'O' and resid 405 through 407 Processing sheet with id=AK7, first strand: chain 'O' and resid 475 through 477 Processing sheet with id=AK8, first strand: chain 'O' and resid 516 through 520 removed outlier: 7.438A pdb=" N MET P 55 " --> pdb=" O ASP O 517 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR O 519 " --> pdb=" O MET P 55 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE P 57 " --> pdb=" O THR O 519 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'P' and resid 149 through 150 removed outlier: 3.833A pdb=" N CYS P 149 " --> pdb=" O LEU P 408 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'P' and resid 202 through 208 removed outlier: 3.538A pdb=" N SER P 216 " --> pdb=" O VAL P 376 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL P 360 " --> pdb=" O SER P 353 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'P' and resid 311 through 314 removed outlier: 5.952A pdb=" N VAL P 291 " --> pdb=" O VAL P 313 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA P 240 " --> pdb=" O VAL P 290 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY P 345 " --> pdb=" O ILE P 239 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'P' and resid 478 through 480 Processing sheet with id=AL4, first strand: chain 'Q' and resid 145 through 147 removed outlier: 3.546A pdb=" N LEU Q 119 " --> pdb=" O THR Q 165 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA Q 176 " --> pdb=" O VAL Q 168 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU Q 170 " --> pdb=" O ILE Q 174 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE Q 174 " --> pdb=" O LEU Q 170 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'S' and resid 71 through 72 removed outlier: 3.580A pdb=" N GLU S 72 " --> pdb=" O ILE S 75 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'S' and resid 131 through 132 Processing sheet with id=AL7, first strand: chain 'S' and resid 152 through 154 removed outlier: 3.511A pdb=" N VAL S 152 " --> pdb=" O VAL S 163 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL S 163 " --> pdb=" O VAL S 152 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'S' and resid 165 through 166 removed outlier: 3.993A pdb=" N TYR S 166 " --> pdb=" O TYR S 169 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR S 169 " --> pdb=" O TYR S 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL8 3879 hydrogen bonds defined for protein. 11115 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: 29.87 Time building geometry restraints manager: 24.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23074 1.34 - 1.46: 11055 1.46 - 1.58: 34531 1.58 - 1.70: 0 1.70 - 1.82: 692 Bond restraints: 69352 Sorted by residual: bond pdb=" N VAL B 9 " pdb=" CA VAL B 9 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.86e+00 bond pdb=" CA LEU I 525 " pdb=" C LEU I 525 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.38e-02 5.25e+03 9.60e+00 bond pdb=" CG GLU G 103 " pdb=" CD GLU G 103 " ideal model delta sigma weight residual 1.516 1.443 0.073 2.50e-02 1.60e+03 8.42e+00 bond pdb=" N ASN B 10 " pdb=" CA ASN B 10 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.72e+00 bond pdb=" CA ASP D 332 " pdb=" C ASP D 332 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.34e-02 5.57e+03 3.50e+00 ... (remaining 69347 not shown) Histogram of bond angle deviations from ideal: 95.25 - 103.02: 463 103.02 - 110.79: 23445 110.79 - 118.56: 33387 118.56 - 126.33: 35719 126.33 - 134.10: 566 Bond angle restraints: 93580 Sorted by residual: angle pdb=" N VAL K 183 " pdb=" CA VAL K 183 " pdb=" C VAL K 183 " ideal model delta sigma weight residual 113.47 107.15 6.32 1.01e+00 9.80e-01 3.91e+01 angle pdb=" N VAL F 244 " pdb=" CA VAL F 244 " pdb=" C VAL F 244 " ideal model delta sigma weight residual 112.43 107.24 5.19 9.20e-01 1.18e+00 3.18e+01 angle pdb=" N VAL G 72 " pdb=" CA VAL G 72 " pdb=" C VAL G 72 " ideal model delta sigma weight residual 113.20 108.09 5.11 9.60e-01 1.09e+00 2.83e+01 angle pdb=" N GLY F 431 " pdb=" CA GLY F 431 " pdb=" C GLY F 431 " ideal model delta sigma weight residual 110.60 118.01 -7.41 1.46e+00 4.69e-01 2.57e+01 angle pdb=" N GLU G 103 " pdb=" CA GLU G 103 " pdb=" CB GLU G 103 " ideal model delta sigma weight residual 110.30 117.47 -7.17 1.54e+00 4.22e-01 2.17e+01 ... (remaining 93575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 39114 18.04 - 36.08: 3208 36.08 - 54.12: 450 54.12 - 72.16: 142 72.16 - 90.20: 93 Dihedral angle restraints: 43007 sinusoidal: 17243 harmonic: 25764 Sorted by residual: dihedral pdb=" CA MET S 132 " pdb=" C MET S 132 " pdb=" N TYR S 133 " pdb=" CA TYR S 133 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA MET C 46 " pdb=" C MET C 46 " pdb=" N MET C 47 " pdb=" CA MET C 47 " ideal model delta harmonic sigma weight residual 180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA MET G 45 " pdb=" C MET G 45 " pdb=" N ASP G 46 " pdb=" CA ASP G 46 " ideal model delta harmonic sigma weight residual -180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 43004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 9955 0.074 - 0.148: 1167 0.148 - 0.223: 25 0.223 - 0.297: 3 0.297 - 0.371: 1 Chirality restraints: 11151 Sorted by residual: chirality pdb=" CB ILE P 497 " pdb=" CA ILE P 497 " pdb=" CG1 ILE P 497 " pdb=" CG2 ILE P 497 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB ILE Q 116 " pdb=" CA ILE Q 116 " pdb=" CG1 ILE Q 116 " pdb=" CG2 ILE Q 116 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CG LEU E 519 " pdb=" CB LEU E 519 " pdb=" CD1 LEU E 519 " pdb=" CD2 LEU E 519 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 11148 not shown) Planarity restraints: 12026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 15 " -0.287 9.50e-02 1.11e+02 1.29e-01 1.08e+01 pdb=" NE ARG Q 15 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG Q 15 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 15 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 15 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 104 " 0.012 2.00e-02 2.50e+03 2.39e-02 1.00e+01 pdb=" CG PHE G 104 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE G 104 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE G 104 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE G 104 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE G 104 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 104 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO Q 21 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C PRO Q 21 " 0.052 2.00e-02 2.50e+03 pdb=" O PRO Q 21 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO Q 22 " -0.018 2.00e-02 2.50e+03 ... (remaining 12023 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1289 2.63 - 3.20: 70465 3.20 - 3.76: 114583 3.76 - 4.33: 152132 4.33 - 4.90: 235540 Nonbonded interactions: 574009 Sorted by model distance: nonbonded pdb=" OE1 GLN D 32 " pdb=" OG SER J 3 " model vdw 2.062 2.440 nonbonded pdb=" O ASN I 193 " pdb=" NH2 ARG I 318 " model vdw 2.091 2.520 nonbonded pdb=" O ASP L 118 " pdb=" OG1 THR L 121 " model vdw 2.106 2.440 nonbonded pdb=" OE1 GLU N 263 " pdb=" OG1 THR P 251 " model vdw 2.109 2.440 nonbonded pdb=" OG1 THR A 367 " pdb=" O ARG A 370 " model vdw 2.112 2.440 ... (remaining 574004 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'I' and (resid 3 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 536)) } ncs_group { reference = chain 'B' selection = (chain 'J' and resid 8 through 528) } ncs_group { reference = (chain 'C' and resid 9 through 527) selection = (chain 'K' and resid 9 through 527) } ncs_group { reference = (chain 'D' and resid 27 through 539) selection = chain 'L' } ncs_group { reference = (chain 'E' and resid 13 through 536) selection = chain 'M' } ncs_group { reference = (chain 'F' and resid 4 through 527) selection = (chain 'N' and resid 4 through 527) } ncs_group { reference = (chain 'G' and resid 6 through 525) selection = (chain 'O' and resid 6 through 525) } ncs_group { reference = (chain 'H' and resid 3 through 529) selection = (chain 'P' and resid 3 through 529) } 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=0.00 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 10.220 Check model and map are aligned: 0.760 Set scattering table: 0.490 Process input model: 143.000 Find NCS groups from input model: 5.960 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 : 0.003 0.073 69352 Z= 0.229 Angle : 0.710 12.339 93580 Z= 0.402 Chirality : 0.044 0.371 11151 Planarity : 0.004 0.129 12026 Dihedral : 14.130 90.205 26323 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.01 % Allowed : 0.27 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: -1.11 (0.09), residues: 8910 helix: 0.27 (0.08), residues: 4381 sheet: -1.22 (0.16), residues: 977 loop : -1.83 (0.10), residues: 3552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 474 HIS 0.010 0.001 HIS H 21 PHE 0.052 0.002 PHE G 104 TYR 0.034 0.002 TYR P 132 ARG 0.017 0.001 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 807 time to evaluate : 5.970 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: A 306 MET cc_start: 0.6649 (mtm) cc_final: 0.5494 (mtt) REVERT: A 312 LEU cc_start: 0.8786 (tt) cc_final: 0.8361 (mm) REVERT: A 430 MET cc_start: 0.5902 (pmm) cc_final: 0.5467 (pmm) REVERT: B 89 ARG cc_start: 0.8547 (mmp80) cc_final: 0.8150 (mmp-170) REVERT: B 110 LEU cc_start: 0.8698 (mm) cc_final: 0.8422 (mm) REVERT: B 310 MET cc_start: 0.5655 (tpt) cc_final: 0.5219 (tpt) REVERT: B 387 GLU cc_start: 0.8333 (pp20) cc_final: 0.7740 (pp20) REVERT: C 134 ILE cc_start: 0.8926 (mm) cc_final: 0.8631 (pt) REVERT: C 219 MET cc_start: 0.7384 (mmp) cc_final: 0.6811 (tpp) REVERT: C 490 MET cc_start: 0.8814 (mmt) cc_final: 0.7834 (mmm) REVERT: D 78 LEU cc_start: 0.9607 (mt) cc_final: 0.9396 (mt) REVERT: D 81 MET cc_start: 0.9019 (mpp) cc_final: 0.8815 (mpp) REVERT: E 12 TYR cc_start: 0.7460 (t80) cc_final: 0.6884 (t80) REVERT: E 39 MET cc_start: 0.7494 (mtp) cc_final: 0.7291 (mtp) REVERT: E 239 MET cc_start: 0.8875 (ptp) cc_final: 0.8410 (ptp) REVERT: E 448 MET cc_start: 0.8128 (mpp) cc_final: 0.7859 (mpp) REVERT: F 63 LEU cc_start: 0.9456 (tp) cc_final: 0.9248 (tp) REVERT: F 177 LEU cc_start: 0.8838 (mt) cc_final: 0.8520 (mt) REVERT: F 389 ASP cc_start: 0.8538 (m-30) cc_final: 0.7788 (t0) REVERT: F 526 MET cc_start: 0.5827 (pmm) cc_final: 0.5622 (pmm) REVERT: G 227 MET cc_start: 0.7937 (mpp) cc_final: 0.7646 (mpp) REVERT: H 14 MET cc_start: 0.8289 (ptp) cc_final: 0.7073 (tmm) REVERT: H 249 MET cc_start: 0.5546 (mmt) cc_final: 0.5311 (mmt) REVERT: I 161 ILE cc_start: 0.6970 (pt) cc_final: 0.6613 (tp) REVERT: I 295 MET cc_start: 0.8330 (tpp) cc_final: 0.8128 (mmt) REVERT: I 384 MET cc_start: 0.7903 (ppp) cc_final: 0.7558 (ppp) REVERT: I 388 MET cc_start: 0.8117 (mpp) cc_final: 0.7525 (mpp) REVERT: J 436 MET cc_start: 0.6827 (ppp) cc_final: 0.6594 (ppp) REVERT: K 502 LYS cc_start: 0.8490 (ptpt) cc_final: 0.8172 (mmmt) REVERT: L 57 MET cc_start: 0.5704 (mpp) cc_final: 0.5414 (mpp) REVERT: L 137 PHE cc_start: 0.7862 (m-80) cc_final: 0.7319 (m-80) REVERT: L 307 ASP cc_start: 0.8953 (p0) cc_final: 0.8406 (m-30) REVERT: M 16 PHE cc_start: 0.6113 (p90) cc_final: 0.5764 (p90) REVERT: M 28 LEU cc_start: 0.8806 (mt) cc_final: 0.8578 (mt) REVERT: M 456 GLU cc_start: 0.8280 (pm20) cc_final: 0.8018 (pm20) REVERT: M 460 MET cc_start: 0.8243 (mtm) cc_final: 0.7639 (mtp) REVERT: M 474 MET cc_start: 0.8362 (mpp) cc_final: 0.8152 (mpp) REVERT: N 127 LYS cc_start: 0.8938 (tttt) cc_final: 0.8730 (tttt) REVERT: N 190 MET cc_start: 0.8797 (mpp) cc_final: 0.8432 (mpp) REVERT: O 46 ASP cc_start: 0.8293 (m-30) cc_final: 0.7971 (m-30) REVERT: O 193 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8672 (mmmm) REVERT: O 323 MET cc_start: 0.8775 (tmm) cc_final: 0.8367 (tmm) REVERT: O 358 TYR cc_start: 0.7728 (m-10) cc_final: 0.7296 (m-10) REVERT: O 380 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8313 (mm-40) REVERT: P 38 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8455 (mm-30) REVERT: P 92 MET cc_start: 0.9046 (mpp) cc_final: 0.8694 (mpp) REVERT: P 249 MET cc_start: 0.7792 (ptp) cc_final: 0.7583 (ptp) REVERT: P 324 LEU cc_start: 0.9029 (tp) cc_final: 0.8779 (tp) REVERT: P 492 MET cc_start: 0.7408 (mmt) cc_final: 0.7195 (mmt) outliers start: 1 outliers final: 0 residues processed: 808 average time/residue: 0.5922 time to fit residues: 838.7311 Evaluate side-chains 630 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 630 time to evaluate : 5.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 20.0000 chunk 673 optimal weight: 0.1980 chunk 373 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 454 optimal weight: 6.9990 chunk 359 optimal weight: 8.9990 chunk 696 optimal weight: 3.9990 chunk 269 optimal weight: 20.0000 chunk 423 optimal weight: 7.9990 chunk 518 optimal weight: 0.0870 chunk 806 optimal weight: 6.9990 overall best weight: 3.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 80 GLN ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 HIS ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN ** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 GLN G 380 GLN ** G 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 365 HIS ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 HIS ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 217 ASN ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN O 272 ASN ** O 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 69352 Z= 0.193 Angle : 0.596 11.038 93580 Z= 0.319 Chirality : 0.043 0.212 11151 Planarity : 0.004 0.103 12026 Dihedral : 5.085 52.704 9514 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.07 % Allowed : 5.21 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: -0.76 (0.09), residues: 8910 helix: 0.61 (0.08), residues: 4506 sheet: -1.04 (0.16), residues: 976 loop : -1.84 (0.10), residues: 3428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 114 HIS 0.014 0.001 HIS Q 133 PHE 0.030 0.002 PHE D 137 TYR 0.028 0.001 TYR P 132 ARG 0.015 0.000 ARG Q 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 815 time to evaluate : 6.148 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: A 312 LEU cc_start: 0.8839 (tt) cc_final: 0.8546 (tt) REVERT: A 430 MET cc_start: 0.5781 (pmm) cc_final: 0.5311 (pmm) REVERT: A 526 ARG cc_start: 0.7988 (tpm170) cc_final: 0.7776 (tpm170) REVERT: B 89 ARG cc_start: 0.8491 (mmp80) cc_final: 0.8149 (mmp-170) REVERT: B 110 LEU cc_start: 0.8563 (mm) cc_final: 0.8213 (mm) REVERT: B 310 MET cc_start: 0.4960 (tpt) cc_final: 0.4754 (tpt) REVERT: B 387 GLU cc_start: 0.8462 (pp20) cc_final: 0.7803 (pp20) REVERT: B 445 MET cc_start: 0.9185 (tpp) cc_final: 0.8959 (tpp) REVERT: C 134 ILE cc_start: 0.8867 (mm) cc_final: 0.8554 (pt) REVERT: C 195 ILE cc_start: 0.8515 (mt) cc_final: 0.8161 (mm) REVERT: C 219 MET cc_start: 0.7265 (mmp) cc_final: 0.6771 (tpp) REVERT: C 490 MET cc_start: 0.8727 (mmt) cc_final: 0.7650 (mmp) REVERT: D 58 ASP cc_start: 0.5645 (p0) cc_final: 0.5102 (p0) REVERT: E 12 TYR cc_start: 0.7349 (t80) cc_final: 0.6878 (t80) REVERT: E 39 MET cc_start: 0.7743 (mtp) cc_final: 0.7508 (mtp) REVERT: E 80 MET cc_start: 0.8090 (ptm) cc_final: 0.7833 (ptm) REVERT: E 239 MET cc_start: 0.8938 (ptp) cc_final: 0.8434 (ptp) REVERT: E 429 CYS cc_start: 0.8752 (m) cc_final: 0.8548 (m) REVERT: F 63 LEU cc_start: 0.9531 (tp) cc_final: 0.9272 (tp) REVERT: F 177 LEU cc_start: 0.8810 (mt) cc_final: 0.8502 (mt) REVERT: G 45 MET cc_start: 0.7063 (tpt) cc_final: 0.6698 (tpt) REVERT: H 14 MET cc_start: 0.8206 (ptp) cc_final: 0.7291 (tmm) REVERT: H 207 ILE cc_start: 0.9108 (mt) cc_final: 0.8902 (mp) REVERT: H 249 MET cc_start: 0.5662 (mmt) cc_final: 0.5255 (mmt) REVERT: I 384 MET cc_start: 0.8000 (ppp) cc_final: 0.7516 (ppp) REVERT: I 388 MET cc_start: 0.8127 (mpp) cc_final: 0.7430 (mpp) REVERT: J 436 MET cc_start: 0.6813 (ppp) cc_final: 0.6503 (ppp) REVERT: K 59 MET cc_start: 0.7373 (mmp) cc_final: 0.7170 (mmp) REVERT: K 101 LEU cc_start: 0.8922 (mt) cc_final: 0.8713 (mt) REVERT: L 28 ASP cc_start: 0.9058 (t0) cc_final: 0.8618 (p0) REVERT: L 57 MET cc_start: 0.5313 (mpp) cc_final: 0.5038 (mpp) REVERT: L 60 MET cc_start: 0.6958 (mmp) cc_final: 0.6594 (mmp) REVERT: L 137 PHE cc_start: 0.8018 (m-80) cc_final: 0.7572 (m-80) REVERT: L 307 ASP cc_start: 0.8997 (p0) cc_final: 0.8462 (m-30) REVERT: L 365 VAL cc_start: 0.8151 (p) cc_final: 0.7843 (m) REVERT: M 16 PHE cc_start: 0.6107 (p90) cc_final: 0.5762 (p90) REVERT: M 185 MET cc_start: 0.8302 (mpp) cc_final: 0.8063 (mpp) REVERT: M 460 MET cc_start: 0.8280 (mtm) cc_final: 0.7909 (mtp) REVERT: M 474 MET cc_start: 0.8461 (mpp) cc_final: 0.8240 (mpp) REVERT: N 67 MET cc_start: 0.6988 (mmp) cc_final: 0.6683 (mmp) REVERT: N 190 MET cc_start: 0.8730 (mpp) cc_final: 0.8363 (mpp) REVERT: N 321 MET cc_start: 0.7445 (ppp) cc_final: 0.7056 (ppp) REVERT: O 46 ASP cc_start: 0.8490 (m-30) cc_final: 0.8148 (m-30) REVERT: O 193 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8793 (mmmm) REVERT: O 227 MET cc_start: 0.8268 (mmm) cc_final: 0.7868 (mmm) REVERT: O 323 MET cc_start: 0.8478 (tmm) cc_final: 0.8256 (tmm) REVERT: O 358 TYR cc_start: 0.7797 (m-10) cc_final: 0.7393 (m-10) REVERT: O 389 LEU cc_start: 0.9168 (tp) cc_final: 0.8804 (pp) REVERT: P 38 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8452 (mm-30) REVERT: P 88 MET cc_start: 0.9114 (mtm) cc_final: 0.8853 (mtp) REVERT: P 169 MET cc_start: 0.7410 (ppp) cc_final: 0.7199 (ppp) REVERT: S 294 TYR cc_start: 0.8780 (m-10) cc_final: 0.8570 (m-10) outliers start: 5 outliers final: 1 residues processed: 819 average time/residue: 0.6550 time to fit residues: 944.3762 Evaluate side-chains 635 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 634 time to evaluate : 5.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 448 optimal weight: 7.9990 chunk 250 optimal weight: 30.0000 chunk 671 optimal weight: 20.0000 chunk 549 optimal weight: 0.0070 chunk 222 optimal weight: 7.9990 chunk 807 optimal weight: 9.9990 chunk 872 optimal weight: 50.0000 chunk 719 optimal weight: 0.1980 chunk 801 optimal weight: 7.9990 chunk 275 optimal weight: 8.9990 chunk 648 optimal weight: 10.0000 overall best weight: 4.8404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 320 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 522 ASN H 303 HIS ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 390 ASN ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN ** M 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 71 HIS ** N 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 475 GLN O 452 ASN ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 133 HIS ** S 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 69352 Z= 0.214 Angle : 0.592 10.221 93580 Z= 0.317 Chirality : 0.043 0.175 11151 Planarity : 0.004 0.066 12026 Dihedral : 5.047 41.303 9514 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: -0.70 (0.09), residues: 8910 helix: 0.69 (0.08), residues: 4496 sheet: -0.99 (0.16), residues: 954 loop : -1.85 (0.10), residues: 3460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 495 HIS 0.009 0.001 HIS L 484 PHE 0.023 0.002 PHE I 8 TYR 0.032 0.002 TYR E 137 ARG 0.007 0.000 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 821 time to evaluate : 6.025 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: A 306 MET cc_start: 0.6688 (mtm) cc_final: 0.5944 (mtt) REVERT: A 312 LEU cc_start: 0.8729 (tt) cc_final: 0.8478 (tp) REVERT: A 430 MET cc_start: 0.5811 (pmm) cc_final: 0.5372 (pmm) REVERT: A 526 ARG cc_start: 0.8063 (tpm170) cc_final: 0.7717 (tpm170) REVERT: B 89 ARG cc_start: 0.8498 (mmp80) cc_final: 0.8158 (mmp-170) REVERT: B 110 LEU cc_start: 0.8774 (mm) cc_final: 0.8411 (mm) REVERT: B 310 MET cc_start: 0.5164 (tpt) cc_final: 0.4909 (tpt) REVERT: B 387 GLU cc_start: 0.8689 (pp20) cc_final: 0.8224 (pp20) REVERT: B 445 MET cc_start: 0.9285 (tpp) cc_final: 0.8995 (tpp) REVERT: C 59 MET cc_start: 0.9031 (pmm) cc_final: 0.8772 (pmm) REVERT: C 134 ILE cc_start: 0.8829 (mm) cc_final: 0.8514 (pt) REVERT: C 195 ILE cc_start: 0.8558 (mt) cc_final: 0.8194 (mm) REVERT: C 219 MET cc_start: 0.7193 (mmp) cc_final: 0.6758 (mmm) REVERT: C 490 MET cc_start: 0.8681 (mmt) cc_final: 0.7814 (mmp) REVERT: D 58 ASP cc_start: 0.5468 (p0) cc_final: 0.4981 (p0) REVERT: E 12 TYR cc_start: 0.7481 (t80) cc_final: 0.6832 (t80) REVERT: E 37 HIS cc_start: 0.9138 (m90) cc_final: 0.8907 (m90) REVERT: E 239 MET cc_start: 0.9015 (ptp) cc_final: 0.8658 (ptp) REVERT: E 429 CYS cc_start: 0.8761 (m) cc_final: 0.8547 (m) REVERT: F 63 LEU cc_start: 0.9527 (tp) cc_final: 0.9168 (tp) REVERT: F 177 LEU cc_start: 0.8831 (mt) cc_final: 0.8501 (mt) REVERT: G 227 MET cc_start: 0.8171 (mpp) cc_final: 0.7839 (mpp) REVERT: I 384 MET cc_start: 0.7960 (ppp) cc_final: 0.7449 (ppp) REVERT: I 388 MET cc_start: 0.8278 (mpp) cc_final: 0.7773 (mpp) REVERT: J 275 MET cc_start: 0.7799 (mmp) cc_final: 0.6940 (mmm) REVERT: J 436 MET cc_start: 0.6838 (ppp) cc_final: 0.6559 (ppp) REVERT: K 101 LEU cc_start: 0.9010 (mt) cc_final: 0.8753 (mt) REVERT: L 28 ASP cc_start: 0.9076 (t0) cc_final: 0.8625 (p0) REVERT: L 57 MET cc_start: 0.5011 (mpp) cc_final: 0.4728 (mpp) REVERT: L 137 PHE cc_start: 0.7742 (m-80) cc_final: 0.7419 (m-80) REVERT: L 307 ASP cc_start: 0.9001 (p0) cc_final: 0.8444 (m-30) REVERT: M 16 PHE cc_start: 0.6112 (p90) cc_final: 0.5768 (p90) REVERT: M 185 MET cc_start: 0.8419 (mpp) cc_final: 0.8129 (mpp) REVERT: N 67 MET cc_start: 0.7047 (mmp) cc_final: 0.6716 (mmp) REVERT: N 190 MET cc_start: 0.8756 (mpp) cc_final: 0.8413 (mpp) REVERT: N 221 MET cc_start: 0.1770 (mtt) cc_final: 0.1542 (mtt) REVERT: N 321 MET cc_start: 0.7295 (ppp) cc_final: 0.6992 (ppp) REVERT: O 46 ASP cc_start: 0.8525 (m-30) cc_final: 0.8072 (m-30) REVERT: O 125 PHE cc_start: 0.8592 (m-10) cc_final: 0.8289 (m-80) REVERT: O 160 MET cc_start: 0.7068 (pmm) cc_final: 0.6697 (pmm) REVERT: O 193 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8697 (mmmm) REVERT: O 323 MET cc_start: 0.8507 (tmm) cc_final: 0.8272 (tmm) REVERT: O 358 TYR cc_start: 0.7896 (m-10) cc_final: 0.7483 (m-10) REVERT: O 389 LEU cc_start: 0.9178 (tp) cc_final: 0.8798 (pp) REVERT: P 38 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8500 (mm-30) REVERT: P 88 MET cc_start: 0.9087 (mtm) cc_final: 0.8774 (mtp) REVERT: P 169 MET cc_start: 0.7435 (ppp) cc_final: 0.7200 (ppp) REVERT: P 249 MET cc_start: 0.7670 (ptp) cc_final: 0.7196 (ptp) REVERT: P 385 MET cc_start: 0.7501 (mmm) cc_final: 0.7229 (mmt) REVERT: S 16 MET cc_start: 0.8770 (mmt) cc_final: 0.8552 (mmp) outliers start: 2 outliers final: 0 residues processed: 822 average time/residue: 0.5926 time to fit residues: 857.4285 Evaluate side-chains 640 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 640 time to evaluate : 5.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 798 optimal weight: 8.9990 chunk 607 optimal weight: 50.0000 chunk 419 optimal weight: 6.9990 chunk 89 optimal weight: 50.0000 chunk 385 optimal weight: 10.0000 chunk 542 optimal weight: 30.0000 chunk 810 optimal weight: 20.0000 chunk 858 optimal weight: 6.9990 chunk 423 optimal weight: 1.9990 chunk 768 optimal weight: 4.9990 chunk 231 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 GLN B 337 HIS ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 390 ASN ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN ** M 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 475 GLN O 130 GLN O 359 ASN ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 69352 Z= 0.246 Angle : 0.622 11.710 93580 Z= 0.331 Chirality : 0.044 0.318 11151 Planarity : 0.004 0.120 12026 Dihedral : 5.116 39.727 9514 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.04 % Allowed : 4.46 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: -0.77 (0.09), residues: 8910 helix: 0.63 (0.08), residues: 4504 sheet: -1.00 (0.16), residues: 916 loop : -1.89 (0.10), residues: 3490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP S 356 HIS 0.010 0.001 HIS L 484 PHE 0.023 0.002 PHE D 137 TYR 0.042 0.002 TYR E 137 ARG 0.025 0.001 ARG Q 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 821 time to evaluate : 6.027 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: A 306 MET cc_start: 0.7925 (mpp) cc_final: 0.7011 (mpp) REVERT: A 312 LEU cc_start: 0.8780 (tt) cc_final: 0.8441 (tt) REVERT: A 430 MET cc_start: 0.5904 (pmm) cc_final: 0.5456 (pmm) REVERT: A 526 ARG cc_start: 0.7483 (tpm170) cc_final: 0.7258 (tpm170) REVERT: B 89 ARG cc_start: 0.8475 (mmp80) cc_final: 0.8184 (mmp-170) REVERT: B 105 LEU cc_start: 0.9498 (tt) cc_final: 0.9214 (mt) REVERT: B 110 LEU cc_start: 0.8777 (mm) cc_final: 0.8438 (mm) REVERT: B 445 MET cc_start: 0.9274 (tpp) cc_final: 0.8989 (tpp) REVERT: B 502 GLN cc_start: 0.9353 (pp30) cc_final: 0.9114 (pp30) REVERT: C 59 MET cc_start: 0.9083 (pmm) cc_final: 0.8859 (pmm) REVERT: C 134 ILE cc_start: 0.8830 (mm) cc_final: 0.8515 (pt) REVERT: C 195 ILE cc_start: 0.8595 (mt) cc_final: 0.8273 (mm) REVERT: C 490 MET cc_start: 0.8648 (mmt) cc_final: 0.7712 (mmp) REVERT: D 33 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7028 (tt) REVERT: D 58 ASP cc_start: 0.5608 (p0) cc_final: 0.5004 (p0) REVERT: E 12 TYR cc_start: 0.7648 (t80) cc_final: 0.6886 (t80) REVERT: E 37 HIS cc_start: 0.9142 (m90) cc_final: 0.8888 (m90) REVERT: E 239 MET cc_start: 0.9072 (ptp) cc_final: 0.8742 (ptp) REVERT: E 429 CYS cc_start: 0.8795 (m) cc_final: 0.8574 (m) REVERT: F 63 LEU cc_start: 0.9511 (tp) cc_final: 0.9237 (tp) REVERT: F 177 LEU cc_start: 0.8845 (mt) cc_final: 0.8512 (mt) REVERT: I 81 LEU cc_start: 0.7349 (pp) cc_final: 0.7077 (pp) REVERT: I 171 MET cc_start: 0.6980 (ttp) cc_final: 0.6761 (ttp) REVERT: I 384 MET cc_start: 0.8144 (ppp) cc_final: 0.7653 (ppp) REVERT: I 388 MET cc_start: 0.8268 (mpp) cc_final: 0.7558 (mpp) REVERT: J 160 MET cc_start: 0.8508 (mpp) cc_final: 0.7985 (mpp) REVERT: J 275 MET cc_start: 0.7869 (mmp) cc_final: 0.7016 (mmm) REVERT: J 436 MET cc_start: 0.6844 (ppp) cc_final: 0.6551 (ppp) REVERT: K 101 LEU cc_start: 0.9015 (mt) cc_final: 0.8746 (mt) REVERT: L 57 MET cc_start: 0.5001 (mpp) cc_final: 0.4698 (mpp) REVERT: L 307 ASP cc_start: 0.8986 (p0) cc_final: 0.8428 (m-30) REVERT: L 365 VAL cc_start: 0.8195 (p) cc_final: 0.7881 (m) REVERT: M 28 LEU cc_start: 0.8589 (tp) cc_final: 0.8363 (tp) REVERT: M 61 MET cc_start: 0.7311 (pmm) cc_final: 0.6768 (pmm) REVERT: M 185 MET cc_start: 0.8510 (mpp) cc_final: 0.8267 (mpp) REVERT: N 67 MET cc_start: 0.7089 (mmp) cc_final: 0.6725 (mmp) REVERT: N 190 MET cc_start: 0.8795 (mpp) cc_final: 0.8449 (mpp) REVERT: N 221 MET cc_start: 0.1988 (mtt) cc_final: 0.1742 (mtt) REVERT: N 321 MET cc_start: 0.7336 (ppp) cc_final: 0.7073 (ppp) REVERT: O 46 ASP cc_start: 0.8583 (m-30) cc_final: 0.8027 (m-30) REVERT: O 125 PHE cc_start: 0.8635 (m-10) cc_final: 0.8417 (m-80) REVERT: O 193 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8702 (mmmm) REVERT: O 227 MET cc_start: 0.8256 (mmm) cc_final: 0.7699 (mmm) REVERT: O 323 MET cc_start: 0.8507 (tmm) cc_final: 0.8289 (tmm) REVERT: O 358 TYR cc_start: 0.8009 (m-10) cc_final: 0.7588 (m-10) REVERT: O 389 LEU cc_start: 0.9163 (tp) cc_final: 0.8792 (pp) REVERT: P 92 MET cc_start: 0.8766 (mmp) cc_final: 0.8472 (mmm) REVERT: P 221 MET cc_start: 0.7598 (mtp) cc_final: 0.6907 (mtt) REVERT: P 249 MET cc_start: 0.7613 (ptp) cc_final: 0.7078 (ptp) REVERT: P 385 MET cc_start: 0.7536 (mmm) cc_final: 0.7197 (mmt) REVERT: P 492 MET cc_start: 0.7826 (mmt) cc_final: 0.7570 (mmt) REVERT: S 294 TYR cc_start: 0.8963 (m-80) cc_final: 0.8717 (m-10) outliers start: 3 outliers final: 1 residues processed: 823 average time/residue: 0.5895 time to fit residues: 854.1553 Evaluate side-chains 637 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 635 time to evaluate : 5.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 714 optimal weight: 8.9990 chunk 487 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 639 optimal weight: 30.0000 chunk 354 optimal weight: 8.9990 chunk 732 optimal weight: 0.0670 chunk 593 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 438 optimal weight: 20.0000 chunk 770 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 502 GLN K 28 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 390 ASN ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN M 184 GLN ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 HIS ** N 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 69352 Z= 0.175 Angle : 0.581 11.102 93580 Z= 0.306 Chirality : 0.043 0.238 11151 Planarity : 0.004 0.065 12026 Dihedral : 4.952 35.230 9514 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: -0.51 (0.09), residues: 8910 helix: 0.88 (0.08), residues: 4505 sheet: -0.94 (0.16), residues: 933 loop : -1.79 (0.10), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 114 HIS 0.010 0.001 HIS E 505 PHE 0.037 0.001 PHE B 29 TYR 0.037 0.001 TYR E 137 ARG 0.014 0.000 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 846 time to evaluate : 6.055 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: A 239 PHE cc_start: 0.7552 (t80) cc_final: 0.7152 (t80) REVERT: A 306 MET cc_start: 0.7809 (mpp) cc_final: 0.7360 (mpp) REVERT: A 430 MET cc_start: 0.5751 (pmm) cc_final: 0.5276 (pmm) REVERT: A 526 ARG cc_start: 0.7558 (tpm170) cc_final: 0.7048 (tpm170) REVERT: B 29 PHE cc_start: 0.7894 (m-80) cc_final: 0.7658 (m-80) REVERT: B 89 ARG cc_start: 0.8473 (mmp80) cc_final: 0.8182 (mmp-170) REVERT: B 110 LEU cc_start: 0.8670 (mm) cc_final: 0.8363 (mm) REVERT: B 387 GLU cc_start: 0.8501 (pp20) cc_final: 0.7917 (pp20) REVERT: B 445 MET cc_start: 0.9243 (tpp) cc_final: 0.8960 (tpp) REVERT: C 59 MET cc_start: 0.9074 (pmm) cc_final: 0.8809 (pmm) REVERT: C 105 MET cc_start: 0.7912 (tmm) cc_final: 0.7681 (ppp) REVERT: C 134 ILE cc_start: 0.8925 (mm) cc_final: 0.8634 (pt) REVERT: C 195 ILE cc_start: 0.8595 (mt) cc_final: 0.8247 (mm) REVERT: C 490 MET cc_start: 0.8569 (mmt) cc_final: 0.7551 (mmp) REVERT: D 58 ASP cc_start: 0.5464 (p0) cc_final: 0.4911 (p0) REVERT: D 320 MET cc_start: 0.8307 (mtm) cc_final: 0.8058 (mmm) REVERT: E 12 TYR cc_start: 0.7602 (t80) cc_final: 0.6734 (t80) REVERT: E 37 HIS cc_start: 0.9054 (m90) cc_final: 0.8785 (m90) REVERT: E 39 MET cc_start: 0.7928 (mtp) cc_final: 0.7603 (mtp) REVERT: E 61 MET cc_start: 0.7466 (ppp) cc_final: 0.7141 (ppp) REVERT: E 239 MET cc_start: 0.9111 (ptp) cc_final: 0.8774 (ptp) REVERT: E 371 MET cc_start: 0.4773 (mtm) cc_final: 0.4427 (mtm) REVERT: E 429 CYS cc_start: 0.8825 (m) cc_final: 0.8593 (m) REVERT: F 63 LEU cc_start: 0.9487 (tp) cc_final: 0.9138 (tp) REVERT: F 177 LEU cc_start: 0.8773 (mt) cc_final: 0.8457 (mt) REVERT: H 14 MET cc_start: 0.7968 (ptp) cc_final: 0.7471 (tmm) REVERT: I 44 MET cc_start: 0.8687 (mmp) cc_final: 0.8382 (mmm) REVERT: I 384 MET cc_start: 0.8145 (ppp) cc_final: 0.7595 (ppp) REVERT: I 388 MET cc_start: 0.8259 (mpp) cc_final: 0.7567 (mpp) REVERT: I 396 LEU cc_start: 0.8810 (tt) cc_final: 0.8270 (pp) REVERT: J 275 MET cc_start: 0.7807 (mmp) cc_final: 0.6971 (mmm) REVERT: J 436 MET cc_start: 0.6744 (ppp) cc_final: 0.6476 (ppp) REVERT: K 59 MET cc_start: 0.7947 (mmp) cc_final: 0.7717 (mmp) REVERT: K 101 LEU cc_start: 0.9026 (mt) cc_final: 0.8705 (mt) REVERT: L 28 ASP cc_start: 0.9080 (t0) cc_final: 0.8533 (p0) REVERT: L 57 MET cc_start: 0.5002 (mpp) cc_final: 0.4717 (mpp) REVERT: L 99 ASP cc_start: 0.8283 (m-30) cc_final: 0.7926 (m-30) REVERT: L 137 PHE cc_start: 0.7581 (m-80) cc_final: 0.7137 (m-80) REVERT: L 307 ASP cc_start: 0.9019 (p0) cc_final: 0.8418 (m-30) REVERT: L 365 VAL cc_start: 0.8149 (p) cc_final: 0.7843 (m) REVERT: L 446 MET cc_start: 0.5400 (tmm) cc_final: 0.5140 (tmm) REVERT: M 474 MET cc_start: 0.8434 (mpp) cc_final: 0.8086 (mpp) REVERT: N 67 MET cc_start: 0.7137 (mmp) cc_final: 0.6760 (mmp) REVERT: N 190 MET cc_start: 0.8715 (mpp) cc_final: 0.8374 (mpp) REVERT: N 221 MET cc_start: 0.1858 (mtt) cc_final: 0.1648 (mtt) REVERT: O 46 ASP cc_start: 0.8612 (m-30) cc_final: 0.8010 (m-30) REVERT: O 125 PHE cc_start: 0.8590 (m-10) cc_final: 0.8355 (m-80) REVERT: O 194 MET cc_start: 0.6969 (tpp) cc_final: 0.6034 (tpp) REVERT: O 358 TYR cc_start: 0.7797 (m-10) cc_final: 0.7421 (m-10) REVERT: O 380 GLN cc_start: 0.8616 (mm110) cc_final: 0.8197 (mm-40) REVERT: O 389 LEU cc_start: 0.9108 (tp) cc_final: 0.8746 (pp) REVERT: P 249 MET cc_start: 0.7715 (ptp) cc_final: 0.7151 (ptp) REVERT: P 299 ASP cc_start: 0.8889 (t0) cc_final: 0.8640 (t0) REVERT: P 385 MET cc_start: 0.7634 (mmm) cc_final: 0.7294 (mmt) REVERT: P 492 MET cc_start: 0.7672 (mmt) cc_final: 0.7423 (mmt) REVERT: S 103 VAL cc_start: 0.7097 (t) cc_final: 0.6496 (t) REVERT: S 132 MET cc_start: 0.7755 (mmt) cc_final: 0.7476 (mmt) REVERT: S 294 TYR cc_start: 0.8955 (m-80) cc_final: 0.8727 (m-10) outliers start: 3 outliers final: 0 residues processed: 848 average time/residue: 0.5862 time to fit residues: 873.1951 Evaluate side-chains 652 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 5.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 288 optimal weight: 5.9990 chunk 772 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 503 optimal weight: 0.9990 chunk 211 optimal weight: 9.9990 chunk 859 optimal weight: 8.9990 chunk 713 optimal weight: 6.9990 chunk 397 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 451 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN B 426 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 184 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 442 GLN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN M 184 GLN ** M 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 GLN O 191 GLN O 470 GLN ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 69352 Z= 0.239 Angle : 0.626 13.477 93580 Z= 0.331 Chirality : 0.044 0.302 11151 Planarity : 0.004 0.066 12026 Dihedral : 5.057 33.055 9514 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.01 % Allowed : 2.73 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: -0.62 (0.09), residues: 8910 helix: 0.80 (0.08), residues: 4503 sheet: -1.07 (0.16), residues: 955 loop : -1.84 (0.10), residues: 3452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 114 HIS 0.013 0.001 HIS E 182 PHE 0.025 0.002 PHE B 29 TYR 0.035 0.002 TYR E 137 ARG 0.010 0.001 ARG D 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 805 time to evaluate : 5.955 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: A 239 PHE cc_start: 0.7623 (t80) cc_final: 0.7297 (t80) REVERT: A 306 MET cc_start: 0.7711 (mpp) cc_final: 0.7055 (mpp) REVERT: A 430 MET cc_start: 0.5874 (pmm) cc_final: 0.5417 (pmm) REVERT: A 526 ARG cc_start: 0.7760 (tpm170) cc_final: 0.7103 (tpm170) REVERT: B 89 ARG cc_start: 0.8507 (mmp80) cc_final: 0.8237 (mmp-170) REVERT: B 110 LEU cc_start: 0.8628 (mm) cc_final: 0.8290 (mm) REVERT: B 220 LEU cc_start: 0.7987 (pp) cc_final: 0.7710 (mm) REVERT: C 59 MET cc_start: 0.9093 (pmm) cc_final: 0.8831 (pmm) REVERT: C 134 ILE cc_start: 0.8950 (mm) cc_final: 0.8646 (pt) REVERT: C 151 MET cc_start: 0.5313 (ttp) cc_final: 0.4881 (ttt) REVERT: C 152 MET cc_start: 0.8890 (mtm) cc_final: 0.7655 (mmt) REVERT: C 195 ILE cc_start: 0.8639 (mt) cc_final: 0.8329 (mm) REVERT: C 490 MET cc_start: 0.8622 (mmt) cc_final: 0.7607 (mmp) REVERT: D 58 ASP cc_start: 0.5790 (p0) cc_final: 0.4963 (p0) REVERT: E 12 TYR cc_start: 0.7822 (t80) cc_final: 0.6796 (t80) REVERT: E 37 HIS cc_start: 0.9092 (m90) cc_final: 0.8833 (m90) REVERT: E 39 MET cc_start: 0.7939 (mtp) cc_final: 0.7644 (mtp) REVERT: E 48 MET cc_start: 0.8923 (mtp) cc_final: 0.8357 (ttm) REVERT: E 239 MET cc_start: 0.9198 (ptp) cc_final: 0.8893 (ptp) REVERT: E 429 CYS cc_start: 0.8788 (m) cc_final: 0.8559 (m) REVERT: E 448 MET cc_start: 0.8201 (mpp) cc_final: 0.7982 (mpp) REVERT: F 177 LEU cc_start: 0.8723 (mt) cc_final: 0.8425 (mt) REVERT: H 14 MET cc_start: 0.8066 (ptp) cc_final: 0.7411 (tmm) REVERT: I 384 MET cc_start: 0.8172 (ppp) cc_final: 0.7672 (ppp) REVERT: I 388 MET cc_start: 0.8442 (mpp) cc_final: 0.7714 (mpp) REVERT: I 396 LEU cc_start: 0.8873 (tt) cc_final: 0.8306 (pp) REVERT: J 275 MET cc_start: 0.7850 (mmp) cc_final: 0.7045 (mmm) REVERT: J 436 MET cc_start: 0.6782 (ppp) cc_final: 0.6566 (ppp) REVERT: K 101 LEU cc_start: 0.9021 (mt) cc_final: 0.8683 (mt) REVERT: K 518 ARG cc_start: 0.7683 (mtp85) cc_final: 0.6897 (tpt90) REVERT: L 28 ASP cc_start: 0.9103 (t0) cc_final: 0.8619 (p0) REVERT: L 57 MET cc_start: 0.4620 (mpp) cc_final: 0.4377 (mpp) REVERT: L 99 ASP cc_start: 0.8185 (m-30) cc_final: 0.7756 (m-30) REVERT: L 137 PHE cc_start: 0.7713 (m-80) cc_final: 0.7272 (m-80) REVERT: L 307 ASP cc_start: 0.9015 (p0) cc_final: 0.8403 (m-30) REVERT: L 365 VAL cc_start: 0.8191 (p) cc_final: 0.7878 (m) REVERT: L 446 MET cc_start: 0.5383 (tmm) cc_final: 0.5121 (tmm) REVERT: M 39 MET cc_start: 0.8709 (ptm) cc_final: 0.8490 (ptp) REVERT: M 61 MET cc_start: 0.7108 (pmm) cc_final: 0.6661 (pmm) REVERT: M 185 MET cc_start: 0.8484 (mpp) cc_final: 0.8223 (mpp) REVERT: M 526 MET cc_start: 0.7853 (tmm) cc_final: 0.7604 (ttt) REVERT: N 46 MET cc_start: 0.7673 (tmm) cc_final: 0.7472 (tmm) REVERT: N 67 MET cc_start: 0.7133 (mmp) cc_final: 0.6646 (mmp) REVERT: N 190 MET cc_start: 0.8740 (mpp) cc_final: 0.8442 (mpp) REVERT: O 46 ASP cc_start: 0.8654 (m-30) cc_final: 0.7999 (m-30) REVERT: O 125 PHE cc_start: 0.8647 (m-10) cc_final: 0.8370 (m-80) REVERT: O 227 MET cc_start: 0.8327 (mmm) cc_final: 0.7731 (mmm) REVERT: O 358 TYR cc_start: 0.7929 (m-10) cc_final: 0.7503 (m-10) REVERT: O 389 LEU cc_start: 0.9148 (tp) cc_final: 0.8790 (pp) REVERT: P 92 MET cc_start: 0.8816 (mmp) cc_final: 0.8386 (mmm) REVERT: P 169 MET cc_start: 0.7296 (ppp) cc_final: 0.7062 (ppp) REVERT: P 300 MET cc_start: 0.8665 (mpp) cc_final: 0.8427 (mpp) REVERT: P 324 LEU cc_start: 0.9029 (mt) cc_final: 0.8774 (mt) REVERT: P 385 MET cc_start: 0.7649 (mmm) cc_final: 0.7324 (mmt) REVERT: P 492 MET cc_start: 0.7678 (mmt) cc_final: 0.7440 (mmt) REVERT: S 103 VAL cc_start: 0.7402 (t) cc_final: 0.6616 (t) REVERT: S 132 MET cc_start: 0.7140 (mmt) cc_final: 0.6877 (mmt) REVERT: S 294 TYR cc_start: 0.8979 (m-80) cc_final: 0.8756 (m-10) outliers start: 1 outliers final: 0 residues processed: 806 average time/residue: 0.5982 time to fit residues: 847.3221 Evaluate side-chains 638 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 638 time to evaluate : 5.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 828 optimal weight: 0.1980 chunk 96 optimal weight: 5.9990 chunk 489 optimal weight: 20.0000 chunk 627 optimal weight: 0.7980 chunk 486 optimal weight: 20.0000 chunk 723 optimal weight: 6.9990 chunk 479 optimal weight: 5.9990 chunk 855 optimal weight: 20.0000 chunk 535 optimal weight: 9.9990 chunk 521 optimal weight: 0.0370 chunk 395 optimal weight: 20.0000 overall best weight: 2.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN B 361 HIS ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 184 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 HIS ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 514 ASN ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 GLN ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN M 184 GLN ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 386 GLN ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN P 79 GLN ** P 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 69352 Z= 0.171 Angle : 0.592 11.785 93580 Z= 0.308 Chirality : 0.043 0.313 11151 Planarity : 0.004 0.065 12026 Dihedral : 4.926 33.634 9514 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.01 % Allowed : 1.71 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: -0.41 (0.09), residues: 8910 helix: 0.98 (0.08), residues: 4500 sheet: -0.90 (0.17), residues: 937 loop : -1.78 (0.10), residues: 3473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 304 HIS 0.007 0.001 HIS L 484 PHE 0.030 0.001 PHE L 35 TYR 0.039 0.001 TYR C 126 ARG 0.019 0.000 ARG Q 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 845 time to evaluate : 5.953 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: A 306 MET cc_start: 0.7876 (mpp) cc_final: 0.7114 (mpp) REVERT: A 430 MET cc_start: 0.5835 (pmm) cc_final: 0.5373 (pmm) REVERT: A 526 ARG cc_start: 0.7728 (tpm170) cc_final: 0.6978 (tpm170) REVERT: B 89 ARG cc_start: 0.8497 (mmp80) cc_final: 0.8237 (mmp-170) REVERT: B 110 LEU cc_start: 0.8722 (mm) cc_final: 0.8383 (mm) REVERT: B 387 GLU cc_start: 0.8414 (pp20) cc_final: 0.7823 (pp20) REVERT: C 59 MET cc_start: 0.9122 (pmm) cc_final: 0.8833 (pmm) REVERT: C 134 ILE cc_start: 0.8910 (mm) cc_final: 0.8601 (pt) REVERT: C 195 ILE cc_start: 0.8573 (mt) cc_final: 0.8229 (mm) REVERT: C 490 MET cc_start: 0.8550 (mmt) cc_final: 0.7540 (mmp) REVERT: D 58 ASP cc_start: 0.5802 (p0) cc_final: 0.4708 (p0) REVERT: D 205 LEU cc_start: 0.9348 (tt) cc_final: 0.9130 (mm) REVERT: D 320 MET cc_start: 0.8283 (mtm) cc_final: 0.8025 (mmm) REVERT: E 12 TYR cc_start: 0.7804 (t80) cc_final: 0.6816 (t80) REVERT: E 37 HIS cc_start: 0.9079 (m90) cc_final: 0.8808 (m90) REVERT: E 39 MET cc_start: 0.7919 (mtp) cc_final: 0.7708 (mtp) REVERT: E 48 MET cc_start: 0.8972 (mtp) cc_final: 0.8452 (ttm) REVERT: E 239 MET cc_start: 0.9161 (ptp) cc_final: 0.8887 (ptp) REVERT: E 429 CYS cc_start: 0.8834 (m) cc_final: 0.8611 (m) REVERT: F 63 LEU cc_start: 0.9552 (tp) cc_final: 0.9218 (tp) REVERT: F 177 LEU cc_start: 0.8742 (mt) cc_final: 0.8420 (mt) REVERT: F 196 MET cc_start: 0.6972 (ttp) cc_final: 0.6727 (ttp) REVERT: H 14 MET cc_start: 0.8007 (ptp) cc_final: 0.7438 (tmm) REVERT: H 169 MET cc_start: 0.7761 (mmt) cc_final: 0.7559 (mmt) REVERT: I 95 ILE cc_start: 0.8706 (mm) cc_final: 0.8429 (pt) REVERT: I 171 MET cc_start: 0.6979 (ptm) cc_final: 0.6694 (ptm) REVERT: I 384 MET cc_start: 0.8189 (ppp) cc_final: 0.7694 (ppp) REVERT: I 388 MET cc_start: 0.8327 (mpp) cc_final: 0.7717 (mpp) REVERT: I 396 LEU cc_start: 0.8807 (tt) cc_final: 0.8272 (pp) REVERT: J 275 MET cc_start: 0.7988 (mmp) cc_final: 0.7175 (mmm) REVERT: J 436 MET cc_start: 0.6693 (ppp) cc_final: 0.6439 (ppp) REVERT: K 49 MET cc_start: 0.6931 (ttt) cc_final: 0.6658 (ttp) REVERT: K 101 LEU cc_start: 0.9027 (mt) cc_final: 0.8673 (mt) REVERT: L 28 ASP cc_start: 0.8941 (t0) cc_final: 0.8399 (p0) REVERT: L 57 MET cc_start: 0.4770 (mpp) cc_final: 0.4514 (mpp) REVERT: L 99 ASP cc_start: 0.8194 (m-30) cc_final: 0.7786 (m-30) REVERT: L 137 PHE cc_start: 0.7798 (m-80) cc_final: 0.7525 (m-80) REVERT: L 307 ASP cc_start: 0.9037 (p0) cc_final: 0.8413 (m-30) REVERT: L 446 MET cc_start: 0.5175 (tmm) cc_final: 0.4929 (tmm) REVERT: M 39 MET cc_start: 0.8750 (ptm) cc_final: 0.8534 (ptt) REVERT: M 61 MET cc_start: 0.7106 (pmm) cc_final: 0.6885 (pmm) REVERT: N 67 MET cc_start: 0.7150 (mmp) cc_final: 0.6780 (mmp) REVERT: N 190 MET cc_start: 0.8724 (mpp) cc_final: 0.8418 (mpp) REVERT: O 14 ASP cc_start: 0.9477 (t70) cc_final: 0.9098 (p0) REVERT: O 46 ASP cc_start: 0.8647 (m-30) cc_final: 0.8008 (m-30) REVERT: O 125 PHE cc_start: 0.8607 (m-10) cc_final: 0.8325 (m-80) REVERT: O 194 MET cc_start: 0.6821 (tpp) cc_final: 0.6110 (tpp) REVERT: O 227 MET cc_start: 0.8275 (mmm) cc_final: 0.7693 (mmm) REVERT: O 358 TYR cc_start: 0.7745 (m-10) cc_final: 0.7332 (m-10) REVERT: O 380 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8003 (mm-40) REVERT: O 389 LEU cc_start: 0.9104 (tp) cc_final: 0.8761 (pp) REVERT: P 324 LEU cc_start: 0.8864 (mt) cc_final: 0.8633 (mt) REVERT: P 385 MET cc_start: 0.7638 (mmm) cc_final: 0.7318 (mmt) REVERT: P 492 MET cc_start: 0.7567 (mmt) cc_final: 0.7280 (mmt) REVERT: Q 187 MET cc_start: 0.0589 (mmp) cc_final: 0.0389 (mmp) REVERT: S 294 TYR cc_start: 0.8910 (m-80) cc_final: 0.8679 (m-10) outliers start: 1 outliers final: 0 residues processed: 846 average time/residue: 0.5936 time to fit residues: 882.4625 Evaluate side-chains 651 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 651 time to evaluate : 6.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 529 optimal weight: 9.9990 chunk 341 optimal weight: 0.7980 chunk 511 optimal weight: 30.0000 chunk 257 optimal weight: 20.0000 chunk 168 optimal weight: 0.9980 chunk 165 optimal weight: 20.0000 chunk 544 optimal weight: 30.0000 chunk 583 optimal weight: 7.9990 chunk 423 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 672 optimal weight: 30.0000 overall best weight: 4.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 HIS E 184 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 514 ASN G 380 GLN ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 GLN ** L 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 350 GLN ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN M 184 GLN ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 475 GLN ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 69352 Z= 0.220 Angle : 0.621 11.462 93580 Z= 0.326 Chirality : 0.044 0.275 11151 Planarity : 0.004 0.066 12026 Dihedral : 4.988 32.886 9514 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: -0.51 (0.09), residues: 8910 helix: 0.89 (0.08), residues: 4509 sheet: -0.97 (0.16), residues: 947 loop : -1.80 (0.10), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 114 HIS 0.011 0.001 HIS M 182 PHE 0.022 0.002 PHE D 137 TYR 0.023 0.002 TYR E 137 ARG 0.011 0.000 ARG Q 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 812 time to evaluate : 6.083 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: A 239 PHE cc_start: 0.7971 (t80) cc_final: 0.7684 (t80) REVERT: A 306 MET cc_start: 0.8000 (mpp) cc_final: 0.7268 (mmt) REVERT: A 430 MET cc_start: 0.6083 (pmm) cc_final: 0.5621 (pmm) REVERT: A 526 ARG cc_start: 0.7733 (tpm170) cc_final: 0.6719 (tpm170) REVERT: B 89 ARG cc_start: 0.8536 (mmp80) cc_final: 0.8240 (mmp-170) REVERT: B 110 LEU cc_start: 0.8582 (mm) cc_final: 0.8242 (mm) REVERT: B 445 MET cc_start: 0.9459 (tpt) cc_final: 0.9059 (tpp) REVERT: C 59 MET cc_start: 0.9115 (pmm) cc_final: 0.8837 (pmm) REVERT: C 151 MET cc_start: 0.5048 (ttp) cc_final: 0.4819 (ttt) REVERT: C 152 MET cc_start: 0.8840 (mtm) cc_final: 0.7624 (mmt) REVERT: C 490 MET cc_start: 0.8591 (mmt) cc_final: 0.7582 (mmp) REVERT: E 12 TYR cc_start: 0.7833 (t80) cc_final: 0.6768 (t80) REVERT: E 37 HIS cc_start: 0.9092 (m90) cc_final: 0.8845 (m90) REVERT: E 39 MET cc_start: 0.7920 (mtp) cc_final: 0.7687 (mtp) REVERT: E 48 MET cc_start: 0.8957 (mtp) cc_final: 0.8451 (ttm) REVERT: E 429 CYS cc_start: 0.8940 (m) cc_final: 0.8712 (m) REVERT: F 177 LEU cc_start: 0.8762 (mt) cc_final: 0.8442 (mt) REVERT: F 196 MET cc_start: 0.7142 (ttp) cc_final: 0.6903 (ttp) REVERT: H 14 MET cc_start: 0.7996 (ptp) cc_final: 0.7296 (tmm) REVERT: H 52 MET cc_start: 0.8397 (ptm) cc_final: 0.8165 (ptp) REVERT: I 171 MET cc_start: 0.6912 (ptm) cc_final: 0.6673 (ptm) REVERT: I 384 MET cc_start: 0.8056 (ppp) cc_final: 0.7597 (ppp) REVERT: I 388 MET cc_start: 0.8324 (mpp) cc_final: 0.7724 (mpp) REVERT: I 396 LEU cc_start: 0.8826 (tt) cc_final: 0.8293 (pp) REVERT: J 275 MET cc_start: 0.7930 (mmp) cc_final: 0.7171 (mmm) REVERT: J 436 MET cc_start: 0.6743 (ppp) cc_final: 0.6495 (ppp) REVERT: K 101 LEU cc_start: 0.9024 (mt) cc_final: 0.8665 (mt) REVERT: L 28 ASP cc_start: 0.9013 (t0) cc_final: 0.8511 (p0) REVERT: L 57 MET cc_start: 0.4568 (mpp) cc_final: 0.4339 (mpp) REVERT: L 99 ASP cc_start: 0.8203 (m-30) cc_final: 0.7786 (m-30) REVERT: L 137 PHE cc_start: 0.7845 (m-80) cc_final: 0.7542 (m-80) REVERT: L 209 LYS cc_start: 0.7840 (tptp) cc_final: 0.7588 (mtmm) REVERT: L 307 ASP cc_start: 0.9066 (p0) cc_final: 0.8424 (m-30) REVERT: L 446 MET cc_start: 0.5275 (tmm) cc_final: 0.5036 (tmm) REVERT: M 16 PHE cc_start: 0.5819 (p90) cc_final: 0.5589 (p90) REVERT: N 46 MET cc_start: 0.7822 (tmm) cc_final: 0.7587 (tmm) REVERT: N 67 MET cc_start: 0.7114 (mmp) cc_final: 0.6593 (mmp) REVERT: N 190 MET cc_start: 0.8755 (mpp) cc_final: 0.8449 (mpp) REVERT: O 14 ASP cc_start: 0.9470 (t70) cc_final: 0.9082 (p0) REVERT: O 46 ASP cc_start: 0.8624 (m-30) cc_final: 0.7966 (m-30) REVERT: O 125 PHE cc_start: 0.8650 (m-10) cc_final: 0.8389 (m-80) REVERT: O 194 MET cc_start: 0.6583 (tpp) cc_final: 0.6016 (tpp) REVERT: O 199 LYS cc_start: 0.7165 (mttt) cc_final: 0.6777 (mmtt) REVERT: O 227 MET cc_start: 0.8341 (mmm) cc_final: 0.7779 (mmm) REVERT: O 358 TYR cc_start: 0.7837 (m-10) cc_final: 0.7466 (m-10) REVERT: O 389 LEU cc_start: 0.9135 (tp) cc_final: 0.8778 (pp) REVERT: P 324 LEU cc_start: 0.8911 (mt) cc_final: 0.8592 (mt) REVERT: P 492 MET cc_start: 0.7588 (mmt) cc_final: 0.7322 (mmt) REVERT: S 294 TYR cc_start: 0.8927 (m-80) cc_final: 0.8713 (m-10) outliers start: 0 outliers final: 0 residues processed: 812 average time/residue: 0.6068 time to fit residues: 866.4176 Evaluate side-chains 636 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 636 time to evaluate : 5.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 778 optimal weight: 7.9990 chunk 819 optimal weight: 8.9990 chunk 748 optimal weight: 30.0000 chunk 797 optimal weight: 6.9990 chunk 480 optimal weight: 4.9990 chunk 347 optimal weight: 9.9990 chunk 626 optimal weight: 30.0000 chunk 244 optimal weight: 0.9990 chunk 720 optimal weight: 1.9990 chunk 754 optimal weight: 6.9990 chunk 794 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 HIS ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 396 GLN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 GLN ** L 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 GLN ** O 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN P 32 ASN ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 69352 Z= 0.186 Angle : 0.607 12.208 93580 Z= 0.317 Chirality : 0.044 0.398 11151 Planarity : 0.004 0.065 12026 Dihedral : 4.916 33.022 9514 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: -0.42 (0.09), residues: 8910 helix: 0.97 (0.08), residues: 4505 sheet: -0.90 (0.17), residues: 950 loop : -1.78 (0.10), residues: 3455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP S 356 HIS 0.010 0.001 HIS M 182 PHE 0.024 0.001 PHE B 29 TYR 0.033 0.001 TYR P 132 ARG 0.013 0.000 ARG Q 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 824 time to evaluate : 6.072 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: A 225 MET cc_start: 0.7153 (tpt) cc_final: 0.6916 (tpt) REVERT: A 239 PHE cc_start: 0.7922 (t80) cc_final: 0.7689 (t80) REVERT: A 306 MET cc_start: 0.8047 (mpp) cc_final: 0.7502 (mmt) REVERT: A 430 MET cc_start: 0.6073 (pmm) cc_final: 0.5575 (pmm) REVERT: A 526 ARG cc_start: 0.7894 (tpm170) cc_final: 0.6802 (tpm170) REVERT: B 89 ARG cc_start: 0.8519 (mmp80) cc_final: 0.8236 (mmp-170) REVERT: B 110 LEU cc_start: 0.8602 (mm) cc_final: 0.8335 (mm) REVERT: B 387 GLU cc_start: 0.8415 (pp20) cc_final: 0.7823 (pp20) REVERT: B 445 MET cc_start: 0.9510 (tpt) cc_final: 0.9131 (tpp) REVERT: C 59 MET cc_start: 0.9115 (pmm) cc_final: 0.8783 (pmm) REVERT: C 134 ILE cc_start: 0.8901 (mm) cc_final: 0.8599 (pt) REVERT: C 152 MET cc_start: 0.8822 (mtm) cc_final: 0.7632 (mmt) REVERT: C 490 MET cc_start: 0.8562 (mmt) cc_final: 0.7564 (mmp) REVERT: D 205 LEU cc_start: 0.9341 (tt) cc_final: 0.9115 (mm) REVERT: E 12 TYR cc_start: 0.7825 (t80) cc_final: 0.6752 (t80) REVERT: E 37 HIS cc_start: 0.9101 (m90) cc_final: 0.8874 (m90) REVERT: E 48 MET cc_start: 0.8952 (mtp) cc_final: 0.8449 (ttm) REVERT: E 232 LYS cc_start: 0.8525 (mmtp) cc_final: 0.7921 (mmtp) REVERT: E 288 MET cc_start: 0.8131 (mmm) cc_final: 0.7881 (mmm) REVERT: E 429 CYS cc_start: 0.8899 (m) cc_final: 0.8676 (m) REVERT: E 448 MET cc_start: 0.8158 (mpp) cc_final: 0.7902 (mpp) REVERT: F 177 LEU cc_start: 0.8704 (mt) cc_final: 0.8368 (mt) REVERT: H 14 MET cc_start: 0.8064 (ptp) cc_final: 0.7354 (tmm) REVERT: I 384 MET cc_start: 0.8002 (ppp) cc_final: 0.7558 (ppp) REVERT: I 388 MET cc_start: 0.8357 (mpp) cc_final: 0.7682 (mpp) REVERT: I 396 LEU cc_start: 0.8785 (tt) cc_final: 0.8264 (pp) REVERT: J 275 MET cc_start: 0.7987 (mmp) cc_final: 0.7164 (mmm) REVERT: J 436 MET cc_start: 0.6716 (ppp) cc_final: 0.6447 (ppp) REVERT: K 101 LEU cc_start: 0.9011 (mt) cc_final: 0.8648 (mt) REVERT: L 28 ASP cc_start: 0.8931 (t0) cc_final: 0.8400 (p0) REVERT: L 57 MET cc_start: 0.4547 (mpp) cc_final: 0.4311 (mpp) REVERT: L 99 ASP cc_start: 0.8153 (m-30) cc_final: 0.7770 (m-30) REVERT: L 137 PHE cc_start: 0.7740 (m-80) cc_final: 0.7521 (m-80) REVERT: L 209 LYS cc_start: 0.7790 (tptp) cc_final: 0.7517 (mtmm) REVERT: L 446 MET cc_start: 0.5286 (tmm) cc_final: 0.5084 (tmm) REVERT: M 16 PHE cc_start: 0.5709 (p90) cc_final: 0.5154 (p90) REVERT: M 61 MET cc_start: 0.7286 (pmm) cc_final: 0.6709 (pmm) REVERT: M 77 ILE cc_start: 0.9096 (mp) cc_final: 0.8685 (mm) REVERT: M 80 MET cc_start: 0.8401 (ppp) cc_final: 0.7316 (ppp) REVERT: N 46 MET cc_start: 0.7771 (tmm) cc_final: 0.7479 (tmm) REVERT: N 67 MET cc_start: 0.7066 (mmp) cc_final: 0.6683 (mmm) REVERT: N 127 LYS cc_start: 0.8825 (tttt) cc_final: 0.8617 (tttt) REVERT: N 190 MET cc_start: 0.8769 (mpp) cc_final: 0.8452 (mpp) REVERT: O 14 ASP cc_start: 0.9456 (t70) cc_final: 0.9087 (p0) REVERT: O 46 ASP cc_start: 0.8652 (m-30) cc_final: 0.7980 (m-30) REVERT: O 125 PHE cc_start: 0.8608 (m-10) cc_final: 0.8338 (m-80) REVERT: O 194 MET cc_start: 0.6484 (tpp) cc_final: 0.6037 (tpp) REVERT: O 227 MET cc_start: 0.8313 (mmm) cc_final: 0.7746 (mmm) REVERT: O 358 TYR cc_start: 0.7779 (m-10) cc_final: 0.7366 (m-10) REVERT: O 389 LEU cc_start: 0.9101 (tp) cc_final: 0.8755 (pp) REVERT: P 223 PHE cc_start: 0.7640 (m-80) cc_final: 0.7429 (m-80) REVERT: P 324 LEU cc_start: 0.8817 (mt) cc_final: 0.8597 (mt) REVERT: P 492 MET cc_start: 0.7528 (mmt) cc_final: 0.7265 (mmt) REVERT: S 294 TYR cc_start: 0.8917 (m-80) cc_final: 0.8697 (m-10) outliers start: 0 outliers final: 0 residues processed: 824 average time/residue: 0.5899 time to fit residues: 853.3048 Evaluate side-chains 643 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 643 time to evaluate : 7.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 523 optimal weight: 20.0000 chunk 843 optimal weight: 7.9990 chunk 514 optimal weight: 1.9990 chunk 400 optimal weight: 8.9990 chunk 586 optimal weight: 0.1980 chunk 884 optimal weight: 6.9990 chunk 814 optimal weight: 30.0000 chunk 704 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 544 optimal weight: 20.0000 chunk 431 optimal weight: 0.6980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 ASN ** P 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 69352 Z= 0.192 Angle : 0.613 14.031 93580 Z= 0.319 Chirality : 0.044 0.371 11151 Planarity : 0.004 0.065 12026 Dihedral : 4.892 32.701 9514 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: -0.44 (0.09), residues: 8910 helix: 0.94 (0.08), residues: 4516 sheet: -0.88 (0.17), residues: 928 loop : -1.79 (0.10), residues: 3466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP M 304 HIS 0.008 0.001 HIS M 182 PHE 0.034 0.001 PHE D 137 TYR 0.042 0.001 TYR E 137 ARG 0.011 0.000 ARG Q 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17820 Ramachandran restraints generated. 8910 Oldfield, 0 Emsley, 8910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 821 time to evaluate : 6.052 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: A 239 PHE cc_start: 0.7797 (t80) cc_final: 0.7585 (t80) REVERT: A 306 MET cc_start: 0.8016 (mpp) cc_final: 0.7420 (mmt) REVERT: A 430 MET cc_start: 0.6102 (pmm) cc_final: 0.5586 (pmm) REVERT: A 526 ARG cc_start: 0.7973 (tpm170) cc_final: 0.6889 (tpm170) REVERT: B 89 ARG cc_start: 0.8552 (mmp80) cc_final: 0.8330 (mmp-170) REVERT: B 110 LEU cc_start: 0.8680 (mm) cc_final: 0.8335 (mm) REVERT: B 445 MET cc_start: 0.9533 (tpt) cc_final: 0.9161 (tpp) REVERT: C 152 MET cc_start: 0.8815 (mtm) cc_final: 0.7617 (mmt) REVERT: C 490 MET cc_start: 0.8571 (mmt) cc_final: 0.7563 (mmp) REVERT: D 205 LEU cc_start: 0.9337 (tt) cc_final: 0.9107 (mm) REVERT: D 458 MET cc_start: 0.1884 (tmm) cc_final: 0.1532 (tmm) REVERT: E 12 TYR cc_start: 0.7801 (t80) cc_final: 0.6780 (t80) REVERT: E 39 MET cc_start: 0.7927 (mtp) cc_final: 0.7602 (mtp) REVERT: E 48 MET cc_start: 0.8932 (mtp) cc_final: 0.8345 (ttm) REVERT: E 60 MET cc_start: 0.7917 (tmm) cc_final: 0.7623 (tmm) REVERT: E 107 THR cc_start: 0.6820 (p) cc_final: 0.5972 (p) REVERT: E 239 MET cc_start: 0.9055 (ptp) cc_final: 0.8569 (ptp) REVERT: E 429 CYS cc_start: 0.8894 (m) cc_final: 0.8676 (m) REVERT: E 448 MET cc_start: 0.8134 (mpp) cc_final: 0.7873 (mpp) REVERT: F 63 LEU cc_start: 0.9453 (tp) cc_final: 0.9242 (tp) REVERT: F 177 LEU cc_start: 0.8716 (mt) cc_final: 0.8371 (mt) REVERT: F 461 GLU cc_start: 0.8847 (mp0) cc_final: 0.8607 (mp0) REVERT: H 14 MET cc_start: 0.7956 (ptp) cc_final: 0.7299 (tmm) REVERT: I 199 LYS cc_start: 0.6548 (pttm) cc_final: 0.5809 (pttm) REVERT: I 384 MET cc_start: 0.8045 (ppp) cc_final: 0.7607 (ppp) REVERT: I 388 MET cc_start: 0.8343 (mpp) cc_final: 0.7711 (mpp) REVERT: I 396 LEU cc_start: 0.8777 (tt) cc_final: 0.8257 (pp) REVERT: J 62 MET cc_start: 0.3841 (pmm) cc_final: 0.3442 (pmm) REVERT: J 275 MET cc_start: 0.7958 (mmp) cc_final: 0.7122 (mmm) REVERT: J 436 MET cc_start: 0.6683 (ppp) cc_final: 0.6443 (ppp) REVERT: K 101 LEU cc_start: 0.8996 (mt) cc_final: 0.8640 (mt) REVERT: L 28 ASP cc_start: 0.8946 (t0) cc_final: 0.8427 (p0) REVERT: L 57 MET cc_start: 0.4438 (mpp) cc_final: 0.4216 (mpp) REVERT: L 99 ASP cc_start: 0.8152 (m-30) cc_final: 0.7759 (m-30) REVERT: L 137 PHE cc_start: 0.7729 (m-80) cc_final: 0.7522 (m-80) REVERT: L 446 MET cc_start: 0.5374 (tmm) cc_final: 0.5148 (tmm) REVERT: M 16 PHE cc_start: 0.5699 (p90) cc_final: 0.5114 (p90) REVERT: M 39 MET cc_start: 0.8449 (ppp) cc_final: 0.8167 (ppp) REVERT: M 61 MET cc_start: 0.7360 (pmm) cc_final: 0.6723 (pmm) REVERT: M 77 ILE cc_start: 0.9159 (mp) cc_final: 0.8883 (mm) REVERT: M 80 MET cc_start: 0.8590 (ppp) cc_final: 0.7363 (ppp) REVERT: M 185 MET cc_start: 0.8319 (mpp) cc_final: 0.8053 (mpp) REVERT: M 393 MET cc_start: 0.8108 (mtm) cc_final: 0.7821 (mpp) REVERT: M 526 MET cc_start: 0.7552 (ttt) cc_final: 0.7307 (tmm) REVERT: N 67 MET cc_start: 0.7087 (mmp) cc_final: 0.6751 (mmm) REVERT: N 190 MET cc_start: 0.8755 (mpp) cc_final: 0.8431 (mpp) REVERT: O 14 ASP cc_start: 0.9452 (t70) cc_final: 0.9085 (p0) REVERT: O 46 ASP cc_start: 0.8629 (m-30) cc_final: 0.7988 (m-30) REVERT: O 125 PHE cc_start: 0.8643 (m-10) cc_final: 0.8386 (m-80) REVERT: O 227 MET cc_start: 0.8308 (mmm) cc_final: 0.7748 (mmm) REVERT: O 358 TYR cc_start: 0.7777 (m-10) cc_final: 0.7376 (m-10) REVERT: O 389 LEU cc_start: 0.9094 (tp) cc_final: 0.8750 (pp) REVERT: P 492 MET cc_start: 0.7506 (mmt) cc_final: 0.7265 (mmt) REVERT: S 294 TYR cc_start: 0.8919 (m-80) cc_final: 0.8691 (m-10) outliers start: 0 outliers final: 0 residues processed: 821 average time/residue: 0.5914 time to fit residues: 855.9539 Evaluate side-chains 643 residues out of total 7485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 643 time to evaluate : 6.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 559 optimal weight: 6.9990 chunk 750 optimal weight: 5.9990 chunk 215 optimal weight: 0.2980 chunk 649 optimal weight: 0.0970 chunk 104 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 705 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 chunk 724 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 129 optimal weight: 0.6980 overall best weight: 2.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 514 ASN ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 HIS ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN M 184 GLN ** M 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 522 ASN P 32 ASN ** P 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.077509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.065961 restraints weight = 533460.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.066911 restraints weight = 424008.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.067663 restraints weight = 346197.441| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 69352 Z= 0.174 Angle : 0.607 14.669 93580 Z= 0.315 Chirality : 0.044 0.303 11151 Planarity : 0.004 0.065 12026 Dihedral : 4.835 32.730 9514 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % 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: 8910 helix: 1.04 (0.08), residues: 4498 sheet: -0.85 (0.16), residues: 958 loop : -1.72 (0.10), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP M 304 HIS 0.010 0.001 HIS E 37 PHE 0.046 0.001 PHE B 29 TYR 0.034 0.001 TYR P 132 ARG 0.009 0.000 ARG Q 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13873.82 seconds wall clock time: 247 minutes 38.14 seconds (14858.14 seconds total)