Starting phenix.real_space_refine on Sun Dec 10 00:55:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylu_33917/12_2023/7ylu_33917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylu_33917/12_2023/7ylu_33917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylu_33917/12_2023/7ylu_33917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylu_33917/12_2023/7ylu_33917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylu_33917/12_2023/7ylu_33917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylu_33917/12_2023/7ylu_33917.pdb" } resolution = 4.55 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= 0.008 sd= 0.059 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 325 5.16 5 C 41139 2.51 5 N 11365 2.21 5 O 12778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 247": "OE1" <-> "OE2" Residue "Z TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 65607 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4103 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 11, 'TRANS': 531} Chain: "B" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3930 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 10, 'TRANS': 506} Chain: "D" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3985 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "E" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4068 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "G" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3982 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 19, 'TRANS': 498} Chain: "H" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3969 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 12, 'TRANS': 506} Chain: "Q" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4125 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 19, 'TRANS': 523} Chain: "Z" Number of atoms: 4110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4110 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain: "a" Number of atoms: 4103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4103 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 11, 'TRANS': 531} Chain: "b" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3930 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 10, 'TRANS': 506} Chain: "d" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3985 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "e" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4068 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "g" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3982 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 19, 'TRANS': 498} Chain: "h" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3969 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 12, 'TRANS': 506} Chain: "q" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4125 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 19, 'TRANS': 523} Chain: "z" Number of atoms: 4110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4110 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain: "P" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1063 Classifications: {'peptide': 132} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 126} Time building chain proxies: 25.67, per 1000 atoms: 0.39 Number of scatterers: 65607 At special positions: 0 Unit cell: (195.064, 210.88, 197.7, 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 325 16.00 O 12778 8.00 N 11365 7.00 C 41139 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: 22.11 Conformation dependent library (CDL) restraints added in 8.8 seconds 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15970 Finding SS restraints... Secondary structure from input PDB file: 344 helices and 95 sheets defined 55.8% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 22 through 42 removed outlier: 4.647A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 79 through 94 removed outlier: 4.013A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 Processing helix chain 'A' and resid 121 through 143 Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.860A pdb=" N ILE A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 172 through 187 removed outlier: 4.585A pdb=" N ASN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 266 through 290 removed outlier: 3.944A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 removed outlier: 4.111A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 391 through 415 removed outlier: 3.637A pdb=" N SER A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 438 removed outlier: 3.832A pdb=" N THR A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 455 removed outlier: 3.520A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 521 through 540 Processing helix chain 'B' and resid 14 through 35 removed outlier: 3.912A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.789A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 114 Processing helix chain 'B' and resid 117 through 139 Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.543A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.584A pdb=" N GLN B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 183 Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.697A pdb=" N LEU B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 278 removed outlier: 4.022A pdb=" N SER B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 373 through 392 Processing helix chain 'B' and resid 393 through 396 Processing helix chain 'B' and resid 405 through 419 Processing helix chain 'B' and resid 423 through 448 removed outlier: 4.001A pdb=" N LEU B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix Processing helix chain 'B' and resid 451 through 465 Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 491 through 510 Processing helix chain 'D' and resid 17 through 37 removed outlier: 3.559A pdb=" N ARG D 21 " --> pdb=" O PRO D 17 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 69 removed outlier: 3.921A pdb=" N ALA D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 89 removed outlier: 3.986A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 113 removed outlier: 3.550A pdb=" N VAL D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 139 Processing helix chain 'D' and resid 146 through 159 removed outlier: 3.665A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 183 Proline residue: D 172 - end of helix removed outlier: 4.009A pdb=" N ILE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 194 removed outlier: 3.716A pdb=" N ASP D 193 " --> pdb=" O ASP D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 281 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 317 through 328 removed outlier: 3.877A pdb=" N LYS D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 383 through 407 Processing helix chain 'D' and resid 415 through 430 removed outlier: 3.844A pdb=" N ARG D 430 " --> pdb=" O SER D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 434 through 448 removed outlier: 3.773A pdb=" N PHE D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.617A pdb=" N VAL D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 520 Processing helix chain 'E' and resid 45 through 63 removed outlier: 3.519A pdb=" N ILE E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 93 Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.244A pdb=" N ASP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 139 Processing helix chain 'E' and resid 142 through 165 Processing helix chain 'E' and resid 172 through 190 removed outlier: 3.979A pdb=" N SER E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 removed outlier: 3.668A pdb=" N LYS E 195 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 removed outlier: 4.462A pdb=" N PHE E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.824A pdb=" N SER E 237 " --> pdb=" O ILE E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 317 Processing helix chain 'E' and resid 328 through 338 Processing helix chain 'E' and resid 347 through 359 Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 370 through 374 removed outlier: 3.504A pdb=" N LEU E 374 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 436 Processing helix chain 'E' and resid 444 through 459 removed outlier: 3.868A pdb=" N ASP E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 462 No H-bonds generated for 'chain 'E' and resid 460 through 462' Processing helix chain 'E' and resid 463 through 487 removed outlier: 3.964A pdb=" N TYR E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE E 479 " --> pdb=" O ALA E 475 " (cutoff:3.500A) Proline residue: E 480 - end of helix Processing helix chain 'E' and resid 490 through 505 removed outlier: 3.770A pdb=" N GLU E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 526 removed outlier: 3.863A pdb=" N LEU E 525 " --> pdb=" O ASP E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 550 Processing helix chain 'G' and resid 17 through 36 removed outlier: 4.471A pdb=" N GLN G 21 " --> pdb=" O GLY G 17 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 68 Processing helix chain 'G' and resid 72 through 89 removed outlier: 3.690A pdb=" N GLU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 113 removed outlier: 4.380A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) Proline residue: G 109 - end of helix Processing helix chain 'G' and resid 117 through 140 removed outlier: 3.528A pdb=" N ILE G 121 " --> pdb=" O HIS G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'G' and resid 162 through 166 removed outlier: 4.371A pdb=" N HIS G 166 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 removed outlier: 3.807A pdb=" N GLU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.520A pdb=" N GLU G 197 " --> pdb=" O PRO G 194 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 194 through 198' Processing helix chain 'G' and resid 199 through 204 removed outlier: 3.984A pdb=" N TYR G 203 " --> pdb=" O ASP G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 217 Processing helix chain 'G' and resid 265 through 268 Processing helix chain 'G' and resid 269 through 289 removed outlier: 4.062A pdb=" N LEU G 273 " --> pdb=" O TRP G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 312 Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.600A pdb=" N ASN G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG G 327 " --> pdb=" O SER G 323 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 344 through 348 removed outlier: 3.536A pdb=" N VAL G 348 " --> pdb=" O GLU G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 408 Processing helix chain 'G' and resid 417 through 432 Processing helix chain 'G' and resid 438 through 449 Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 465 through 478 Processing helix chain 'G' and resid 494 through 498 Processing helix chain 'G' and resid 503 through 523 removed outlier: 3.521A pdb=" N VAL G 523 " --> pdb=" O LEU G 519 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 41 Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 77 through 94 Processing helix chain 'H' and resid 97 through 118 Proline residue: H 114 - end of helix Processing helix chain 'H' and resid 121 through 144 Processing helix chain 'H' and resid 155 through 166 Processing helix chain 'H' and resid 174 through 188 removed outlier: 3.603A pdb=" N PHE H 178 " --> pdb=" O ASN H 174 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS H 180 " --> pdb=" O ASP H 176 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET H 181 " --> pdb=" O PHE H 177 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL H 186 " --> pdb=" O CYS H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 208 through 212 Processing helix chain 'H' and resid 263 through 288 Processing helix chain 'H' and resid 300 through 310 Processing helix chain 'H' and resid 319 through 331 Processing helix chain 'H' and resid 342 through 346 Processing helix chain 'H' and resid 382 through 406 removed outlier: 3.877A pdb=" N ASN H 406 " --> pdb=" O ARG H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 429 removed outlier: 3.720A pdb=" N LYS H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 447 removed outlier: 4.062A pdb=" N ILE H 438 " --> pdb=" O LYS H 434 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU H 447 " --> pdb=" O ALA H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 457 Processing helix chain 'H' and resid 460 through 473 removed outlier: 3.569A pdb=" N SER H 473 " --> pdb=" O ARG H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 500 through 519 Processing helix chain 'Q' and resid 26 through 44 removed outlier: 3.561A pdb=" N ILE Q 32 " --> pdb=" O ILE Q 28 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 75 Processing helix chain 'Q' and resid 79 through 96 removed outlier: 3.586A pdb=" N LYS Q 83 " --> pdb=" O HIS Q 79 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL Q 84 " --> pdb=" O PRO Q 80 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 120 removed outlier: 3.752A pdb=" N MET Q 104 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS Q 116 " --> pdb=" O ASN Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 143 removed outlier: 3.996A pdb=" N ASP Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 146 No H-bonds generated for 'chain 'Q' and resid 144 through 146' Processing helix chain 'Q' and resid 155 through 168 removed outlier: 3.758A pdb=" N LYS Q 161 " --> pdb=" O ASN Q 157 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) Proline residue: Q 165 - end of helix Processing helix chain 'Q' and resid 174 through 190 removed outlier: 4.252A pdb=" N GLU Q 180 " --> pdb=" O ASP Q 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 216 through 220 Processing helix chain 'Q' and resid 269 through 294 Processing helix chain 'Q' and resid 306 through 316 Processing helix chain 'Q' and resid 325 through 337 Processing helix chain 'Q' and resid 348 through 352 Processing helix chain 'Q' and resid 390 through 408 removed outlier: 3.662A pdb=" N VAL Q 408 " --> pdb=" O GLY Q 404 " (cutoff:3.500A) Processing helix chain 'Q' and resid 409 through 412 removed outlier: 3.987A pdb=" N MET Q 412 " --> pdb=" O LYS Q 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 409 through 412' Processing helix chain 'Q' and resid 424 through 441 Processing helix chain 'Q' and resid 444 through 456 removed outlier: 3.850A pdb=" N ALA Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE Q 456 " --> pdb=" O PHE Q 452 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 467 Processing helix chain 'Q' and resid 470 through 483 Proline residue: Q 476 - end of helix Processing helix chain 'Q' and resid 521 through 540 Processing helix chain 'Z' and resid 16 through 35 removed outlier: 4.265A pdb=" N THR Z 35 " --> pdb=" O SER Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 66 Processing helix chain 'Z' and resid 70 through 81 Processing helix chain 'Z' and resid 81 through 87 removed outlier: 4.021A pdb=" N GLU Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.595A pdb=" N GLU Z 111 " --> pdb=" O ARG Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 137 Processing helix chain 'Z' and resid 146 through 160 removed outlier: 3.898A pdb=" N THR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 182 Proline residue: Z 172 - end of helix removed outlier: 3.527A pdb=" N VAL Z 181 " --> pdb=" O ALA Z 177 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 192 No H-bonds generated for 'chain 'Z' and resid 190 through 192' Processing helix chain 'Z' and resid 203 through 207 removed outlier: 3.709A pdb=" N THR Z 207 " --> pdb=" O PRO Z 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 267 removed outlier: 3.922A pdb=" N ARG Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) Processing helix chain 'Z' and resid 267 through 284 removed outlier: 3.592A pdb=" N LYS Z 273 " --> pdb=" O PHE Z 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 302 through 312 Processing helix chain 'Z' and resid 321 through 332 removed outlier: 3.817A pdb=" N LEU Z 330 " --> pdb=" O GLU Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 339 through 343 Processing helix chain 'Z' and resid 344 through 348 Processing helix chain 'Z' and resid 384 through 408 Processing helix chain 'Z' and resid 416 through 434 removed outlier: 3.828A pdb=" N MET Z 431 " --> pdb=" O ARG Z 427 " (cutoff:3.500A) Processing helix chain 'Z' and resid 437 through 439 No H-bonds generated for 'chain 'Z' and resid 437 through 439' Processing helix chain 'Z' and resid 440 through 451 Processing helix chain 'Z' and resid 452 through 463 Processing helix chain 'Z' and resid 465 through 483 Processing helix chain 'Z' and resid 500 through 505 Processing helix chain 'Z' and resid 510 through 529 Processing helix chain 'a' and resid 22 through 42 removed outlier: 4.608A pdb=" N SER a 42 " --> pdb=" O ASN a 38 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 73 Processing helix chain 'a' and resid 77 through 94 Processing helix chain 'a' and resid 97 through 118 Processing helix chain 'a' and resid 121 through 144 Processing helix chain 'a' and resid 155 through 164 Processing helix chain 'a' and resid 167 through 171 removed outlier: 3.869A pdb=" N ALA a 171 " --> pdb=" O ILE a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 172 through 186 removed outlier: 4.388A pdb=" N ASN a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.650A pdb=" N SER a 216 " --> pdb=" O ALA a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 291 removed outlier: 3.723A pdb=" N LEU a 270 " --> pdb=" O ASP a 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 313 Processing helix chain 'a' and resid 322 through 334 Processing helix chain 'a' and resid 391 through 415 removed outlier: 3.763A pdb=" N GLU a 397 " --> pdb=" O TYR a 393 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG a 400 " --> pdb=" O ASP a 396 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER a 415 " --> pdb=" O ARG a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 438 Processing helix chain 'a' and resid 444 through 455 Processing helix chain 'a' and resid 456 through 466 Processing helix chain 'a' and resid 469 through 487 Processing helix chain 'a' and resid 488 through 491 Processing helix chain 'a' and resid 512 through 516 Processing helix chain 'a' and resid 521 through 540 Processing helix chain 'b' and resid 14 through 35 removed outlier: 4.396A pdb=" N ALA b 26 " --> pdb=" O ALA b 22 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER b 35 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 67 Processing helix chain 'b' and resid 71 through 88 removed outlier: 3.596A pdb=" N VAL b 76 " --> pdb=" O PRO b 72 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU b 77 " --> pdb=" O ALA b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 112 Processing helix chain 'b' and resid 116 through 139 Processing helix chain 'b' and resid 145 through 161 removed outlier: 3.760A pdb=" N PHE b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU b 151 " --> pdb=" O THR b 147 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 168 removed outlier: 3.552A pdb=" N GLN b 168 " --> pdb=" O ILE b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 183 removed outlier: 3.757A pdb=" N PHE b 173 " --> pdb=" O ASP b 169 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 191 No H-bonds generated for 'chain 'b' and resid 189 through 191' Processing helix chain 'b' and resid 202 through 206 Processing helix chain 'b' and resid 254 through 278 removed outlier: 3.667A pdb=" N LEU b 258 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU b 265 " --> pdb=" O LEU b 261 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG b 266 " --> pdb=" O GLU b 262 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 301 Processing helix chain 'b' and resid 311 through 322 Processing helix chain 'b' and resid 373 through 397 removed outlier: 3.701A pdb=" N ALA b 380 " --> pdb=" O THR b 376 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN b 393 " --> pdb=" O SER b 389 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR b 394 " --> pdb=" O VAL b 390 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR b 395 " --> pdb=" O LEU b 391 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 421 removed outlier: 3.716A pdb=" N ASN b 421 " --> pdb=" O THR b 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 423 through 449 removed outlier: 3.892A pdb=" N ALA b 429 " --> pdb=" O LYS b 425 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU b 440 " --> pdb=" O ALA b 436 " (cutoff:3.500A) Proline residue: b 441 - end of helix Processing helix chain 'b' and resid 451 through 465 Processing helix chain 'b' and resid 482 through 486 Processing helix chain 'b' and resid 491 through 510 Processing helix chain 'd' and resid 16 through 37 removed outlier: 4.455A pdb=" N VAL d 20 " --> pdb=" O LYS d 16 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR d 37 " --> pdb=" O ASP d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 69 removed outlier: 3.787A pdb=" N ALA d 69 " --> pdb=" O LEU d 65 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 89 Processing helix chain 'd' and resid 92 through 113 Processing helix chain 'd' and resid 116 through 138 Processing helix chain 'd' and resid 146 through 159 Processing helix chain 'd' and resid 166 through 183 Proline residue: d 172 - end of helix removed outlier: 3.841A pdb=" N ILE d 181 " --> pdb=" O SER d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 192 No H-bonds generated for 'chain 'd' and resid 190 through 192' Processing helix chain 'd' and resid 257 through 281 removed outlier: 3.945A pdb=" N ASP d 261 " --> pdb=" O TYR d 257 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS d 262 " --> pdb=" O ARG d 258 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA d 281 " --> pdb=" O LYS d 277 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 308 Processing helix chain 'd' and resid 317 through 329 Processing helix chain 'd' and resid 335 through 339 Processing helix chain 'd' and resid 383 through 407 Processing helix chain 'd' and resid 415 through 430 removed outlier: 3.931A pdb=" N ARG d 430 " --> pdb=" O SER d 426 " (cutoff:3.500A) Processing helix chain 'd' and resid 431 through 433 No H-bonds generated for 'chain 'd' and resid 431 through 433' Processing helix chain 'd' and resid 434 through 448 removed outlier: 3.871A pdb=" N PHE d 438 " --> pdb=" O GLY d 434 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU d 448 " --> pdb=" O ALA d 444 " (cutoff:3.500A) Processing helix chain 'd' and resid 448 through 458 Processing helix chain 'd' and resid 461 through 473 Processing helix chain 'd' and resid 501 through 520 Processing helix chain 'e' and resid 42 through 62 removed outlier: 4.005A pdb=" N LYS e 48 " --> pdb=" O LEU e 44 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE e 61 " --> pdb=" O VAL e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 65 No H-bonds generated for 'chain 'e' and resid 63 through 65' Processing helix chain 'e' and resid 86 through 94 Processing helix chain 'e' and resid 98 through 113 removed outlier: 3.634A pdb=" N LEU e 104 " --> pdb=" O ILE e 100 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 139 Processing helix chain 'e' and resid 142 through 164 Processing helix chain 'e' and resid 172 through 189 Processing helix chain 'e' and resid 190 through 195 removed outlier: 6.839A pdb=" N VAL e 193 " --> pdb=" O SER e 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS e 195 " --> pdb=" O ILE e 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 196 through 211 Processing helix chain 'e' and resid 220 through 222 No H-bonds generated for 'chain 'e' and resid 220 through 222' Processing helix chain 'e' and resid 233 through 237 Processing helix chain 'e' and resid 291 through 316 Processing helix chain 'e' and resid 328 through 339 Processing helix chain 'e' and resid 347 through 359 Processing helix chain 'e' and resid 365 through 369 Processing helix chain 'e' and resid 412 through 436 Processing helix chain 'e' and resid 444 through 461 Processing helix chain 'e' and resid 464 through 477 removed outlier: 3.716A pdb=" N ALA e 468 " --> pdb=" O ILE e 464 " (cutoff:3.500A) Processing helix chain 'e' and resid 477 through 487 Processing helix chain 'e' and resid 490 through 504 Processing helix chain 'e' and resid 521 through 526 removed outlier: 3.682A pdb=" N LEU e 525 " --> pdb=" O ASP e 521 " (cutoff:3.500A) Processing helix chain 'e' and resid 531 through 550 Processing helix chain 'g' and resid 17 through 35 removed outlier: 4.227A pdb=" N ILE g 35 " --> pdb=" O VAL g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 68 Processing helix chain 'g' and resid 72 through 89 Processing helix chain 'g' and resid 92 through 113 Proline residue: g 109 - end of helix Processing helix chain 'g' and resid 117 through 139 Processing helix chain 'g' and resid 147 through 160 removed outlier: 3.583A pdb=" N ALA g 157 " --> pdb=" O LYS g 153 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER g 158 " --> pdb=" O LEU g 154 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 182 Processing helix chain 'g' and resid 199 through 204 Processing helix chain 'g' and resid 213 through 217 Processing helix chain 'g' and resid 265 through 289 Processing helix chain 'g' and resid 302 through 312 Processing helix chain 'g' and resid 321 through 333 removed outlier: 4.208A pdb=" N ARG g 327 " --> pdb=" O SER g 323 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG g 330 " --> pdb=" O ASN g 326 " (cutoff:3.500A) Processing helix chain 'g' and resid 339 through 343 Processing helix chain 'g' and resid 385 through 409 Processing helix chain 'g' and resid 417 through 432 removed outlier: 4.037A pdb=" N LYS g 432 " --> pdb=" O ALA g 428 " (cutoff:3.500A) Processing helix chain 'g' and resid 438 through 449 Processing helix chain 'g' and resid 450 through 461 Processing helix chain 'g' and resid 465 through 478 Processing helix chain 'g' and resid 494 through 498 Processing helix chain 'g' and resid 503 through 523 removed outlier: 3.614A pdb=" N VAL g 523 " --> pdb=" O LEU g 519 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 41 removed outlier: 4.122A pdb=" N ILE h 26 " --> pdb=" O GLY h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 44 No H-bonds generated for 'chain 'h' and resid 42 through 44' Processing helix chain 'h' and resid 65 through 74 removed outlier: 3.595A pdb=" N ASP h 74 " --> pdb=" O LEU h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 94 removed outlier: 3.844A pdb=" N LEU h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 118 removed outlier: 3.590A pdb=" N THR h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) Proline residue: h 114 - end of helix Processing helix chain 'h' and resid 121 through 144 Processing helix chain 'h' and resid 155 through 166 removed outlier: 4.110A pdb=" N CYS h 161 " --> pdb=" O LEU h 157 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR h 164 " --> pdb=" O ARG h 160 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA h 165 " --> pdb=" O CYS h 161 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET h 166 " --> pdb=" O ALA h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 174 through 188 removed outlier: 3.564A pdb=" N PHE h 178 " --> pdb=" O ASN h 174 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS h 180 " --> pdb=" O ASP h 176 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET h 181 " --> pdb=" O PHE h 177 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL h 186 " --> pdb=" O CYS h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 195 through 199 removed outlier: 3.547A pdb=" N ILE h 199 " --> pdb=" O ASP h 196 " (cutoff:3.500A) Processing helix chain 'h' and resid 208 through 212 Processing helix chain 'h' and resid 263 through 289 removed outlier: 3.651A pdb=" N VAL h 285 " --> pdb=" O LYS h 281 " (cutoff:3.500A) Processing helix chain 'h' and resid 300 through 310 Processing helix chain 'h' and resid 319 through 331 Processing helix chain 'h' and resid 337 through 341 removed outlier: 3.541A pdb=" N ASP h 340 " --> pdb=" O THR h 337 " (cutoff:3.500A) Processing helix chain 'h' and resid 342 through 346 Processing helix chain 'h' and resid 356 through 360 Processing helix chain 'h' and resid 382 through 406 removed outlier: 3.885A pdb=" N ASN h 406 " --> pdb=" O ARG h 402 " (cutoff:3.500A) Processing helix chain 'h' and resid 414 through 430 removed outlier: 3.653A pdb=" N THR h 430 " --> pdb=" O ASP h 426 " (cutoff:3.500A) Processing helix chain 'h' and resid 433 through 447 removed outlier: 3.994A pdb=" N MET h 437 " --> pdb=" O GLY h 433 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU h 447 " --> pdb=" O ALA h 443 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 457 Processing helix chain 'h' and resid 460 through 473 Processing helix chain 'h' and resid 491 through 495 Processing helix chain 'h' and resid 500 through 519 Processing helix chain 'q' and resid 26 through 44 removed outlier: 4.009A pdb=" N ILE q 32 " --> pdb=" O ILE q 28 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU q 37 " --> pdb=" O ALA q 33 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU q 38 " --> pdb=" O ALA q 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR q 44 " --> pdb=" O GLN q 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 75 Processing helix chain 'q' and resid 79 through 96 removed outlier: 3.516A pdb=" N LEU q 85 " --> pdb=" O ALA q 81 " (cutoff:3.500A) Processing helix chain 'q' and resid 99 through 121 Processing helix chain 'q' and resid 123 through 143 removed outlier: 3.883A pdb=" N ASP q 143 " --> pdb=" O LEU q 139 " (cutoff:3.500A) Processing helix chain 'q' and resid 155 through 168 removed outlier: 3.700A pdb=" N LYS q 161 " --> pdb=" O ASN q 157 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET q 162 " --> pdb=" O GLU q 158 " (cutoff:3.500A) Proline residue: q 165 - end of helix Processing helix chain 'q' and resid 174 through 190 removed outlier: 3.787A pdb=" N VAL q 189 " --> pdb=" O ALA q 185 " (cutoff:3.500A) Processing helix chain 'q' and resid 203 through 205 No H-bonds generated for 'chain 'q' and resid 203 through 205' Processing helix chain 'q' and resid 216 through 220 Processing helix chain 'q' and resid 269 through 294 Processing helix chain 'q' and resid 306 through 316 Processing helix chain 'q' and resid 325 through 337 Processing helix chain 'q' and resid 390 through 410 removed outlier: 3.697A pdb=" N GLY q 410 " --> pdb=" O ALA q 406 " (cutoff:3.500A) Processing helix chain 'q' and resid 424 through 441 Processing helix chain 'q' and resid 444 through 456 removed outlier: 3.923A pdb=" N ALA q 448 " --> pdb=" O LEU q 444 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE q 456 " --> pdb=" O PHE q 452 " (cutoff:3.500A) Processing helix chain 'q' and resid 457 through 467 Processing helix chain 'q' and resid 470 through 483 Proline residue: q 476 - end of helix Processing helix chain 'q' and resid 511 through 516 removed outlier: 4.082A pdb=" N GLU q 515 " --> pdb=" O ASP q 511 " (cutoff:3.500A) Processing helix chain 'q' and resid 521 through 540 Processing helix chain 'z' and resid 16 through 35 removed outlier: 4.561A pdb=" N THR z 35 " --> pdb=" O SER z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 65 Processing helix chain 'z' and resid 70 through 83 removed outlier: 3.819A pdb=" N GLN z 83 " --> pdb=" O ALA z 79 " (cutoff:3.500A) Processing helix chain 'z' and resid 90 through 110 Processing helix chain 'z' and resid 114 through 137 Processing helix chain 'z' and resid 146 through 160 removed outlier: 4.181A pdb=" N THR z 160 " --> pdb=" O SER z 156 " (cutoff:3.500A) Processing helix chain 'z' and resid 166 through 182 Proline residue: z 172 - end of helix removed outlier: 3.594A pdb=" N TYR z 182 " --> pdb=" O VAL z 178 " (cutoff:3.500A) Processing helix chain 'z' and resid 190 through 192 No H-bonds generated for 'chain 'z' and resid 190 through 192' Processing helix chain 'z' and resid 203 through 207 Processing helix chain 'z' and resid 255 through 284 removed outlier: 3.795A pdb=" N SER z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU z 266 " --> pdb=" O LEU z 262 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N PHE z 269 " --> pdb=" O SER z 265 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL z 270 " --> pdb=" O GLU z 266 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS z 276 " --> pdb=" O ALA z 272 " (cutoff:3.500A) Processing helix chain 'z' and resid 302 through 312 Processing helix chain 'z' and resid 321 through 333 Processing helix chain 'z' and resid 339 through 343 Processing helix chain 'z' and resid 344 through 348 Processing helix chain 'z' and resid 384 through 408 Processing helix chain 'z' and resid 416 through 434 Processing helix chain 'z' and resid 439 through 451 removed outlier: 4.285A pdb=" N GLY z 443 " --> pdb=" O LYS z 439 " (cutoff:3.500A) Processing helix chain 'z' and resid 452 through 462 Processing helix chain 'z' and resid 465 through 483 removed outlier: 3.504A pdb=" N VAL z 469 " --> pdb=" O ASP z 465 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA z 471 " --> pdb=" O LEU z 467 " (cutoff:3.500A) Processing helix chain 'z' and resid 500 through 505 Processing helix chain 'z' and resid 510 through 529 Processing helix chain 'P' and resid 103 through 105 No H-bonds generated for 'chain 'P' and resid 103 through 105' Processing helix chain 'P' and resid 106 through 111 Processing helix chain 'P' and resid 112 through 115 Processing helix chain 'P' and resid 147 through 162 Processing helix chain 'P' and resid 175 through 177 No H-bonds generated for 'chain 'P' and resid 175 through 177' Processing helix chain 'P' and resid 182 through 186 Processing helix chain 'P' and resid 203 through 207 Processing helix chain 'P' and resid 213 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.314A pdb=" N ILE A 541 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N MET D 47 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR A 543 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS D 49 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 545 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.663A pdb=" N LEU A 206 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 217 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 316 through 318 Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'A' and resid 500 through 503 Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 57 removed outlier: 6.469A pdb=" N ASP B 43 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP D 523 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 199 removed outlier: 6.580A pdb=" N GLN B 194 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU B 369 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 196 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY B 371 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 198 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 212 through 215 removed outlier: 6.725A pdb=" N VAL B 342 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU B 227 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLU B 344 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG B 225 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 212 through 215 removed outlier: 6.725A pdb=" N VAL B 342 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU B 227 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLU B 344 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG B 225 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N VAL B 326 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 233 " --> pdb=" O VAL B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 470 through 473 Processing sheet with id=AB5, first strand: chain 'B' and resid 511 through 514 removed outlier: 7.794A pdb=" N ILE E 73 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE B 514 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ILE E 75 " --> pdb=" O ILE B 514 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 195 through 200 removed outlier: 6.156A pdb=" N ARG D 195 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE D 379 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL D 197 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY D 381 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYS D 199 " --> pdb=" O GLY D 381 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 213 through 214 removed outlier: 3.564A pdb=" N THR D 364 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 349 " --> pdb=" O THR D 364 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP D 348 " --> pdb=" O LYS D 231 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 311 through 316 removed outlier: 3.726A pdb=" N ASP D 315 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY D 235 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 287 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ILE D 333 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU D 236 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AC1, first strand: chain 'D' and resid 480 through 483 removed outlier: 3.582A pdb=" N GLY D 488 " --> pdb=" O SER D 483 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 39 through 41 removed outlier: 3.589A pdb=" N VAL E 554 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP H 50 " --> pdb=" O ILE E 551 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN E 553 " --> pdb=" O ASP H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AC4, first strand: chain 'E' and resid 224 through 230 removed outlier: 6.373A pdb=" N LYS E 225 " --> pdb=" O CYS E 406 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL E 408 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN E 227 " --> pdb=" O VAL E 408 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N GLY E 410 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ARG E 229 " --> pdb=" O GLY E 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 342 through 343 removed outlier: 6.606A pdb=" N VAL E 321 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 379 through 383 removed outlier: 3.632A pdb=" N MET E 392 " --> pdb=" O GLN E 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 55 through 56 removed outlier: 7.653A pdb=" N LEU G 45 " --> pdb=" O GLU Z 532 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N LEU Z 534 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N MET G 47 " --> pdb=" O LEU Z 534 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AC9, first strand: chain 'G' and resid 206 through 210 removed outlier: 3.657A pdb=" N GLY G 383 " --> pdb=" O ILE G 209 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 315 through 318 removed outlier: 9.349A pdb=" N VAL G 337 " --> pdb=" O VAL G 243 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU G 245 " --> pdb=" O VAL G 337 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 482 through 484 Processing sheet with id=AD3, first strand: chain 'H' and resid 199 through 203 removed outlier: 3.649A pdb=" N THR H 375 " --> pdb=" O ILE H 215 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 219 through 220 Processing sheet with id=AD5, first strand: chain 'H' and resid 313 through 315 removed outlier: 6.413A pdb=" N LEU H 242 " --> pdb=" O LEU H 294 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLN H 335 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N SER H 243 " --> pdb=" O GLN H 335 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 409 through 411 Processing sheet with id=AD7, first strand: chain 'H' and resid 479 through 482 removed outlier: 3.904A pdb=" N ASN H 487 " --> pdb=" O VAL H 482 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 520 through 525 removed outlier: 4.130A pdb=" N VAL H 520 " --> pdb=" O ASN Q 52 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE Q 54 " --> pdb=" O VAL H 520 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU H 522 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL Q 56 " --> pdb=" O GLU H 522 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE H 524 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 19 through 22 removed outlier: 4.286A pdb=" N ILE Q 541 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N MET Z 45 " --> pdb=" O ILE Q 541 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN Q 543 " --> pdb=" O MET Z 45 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL Z 47 " --> pdb=" O GLN Q 543 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE Q 545 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 148 through 149 removed outlier: 3.779A pdb=" N GLY Q 148 " --> pdb=" O LEU Q 419 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 207 through 213 removed outlier: 3.501A pdb=" N GLY Q 388 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 226 through 228 removed outlier: 3.555A pdb=" N LYS Q 359 " --> pdb=" O VAL Q 370 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 319 through 322 removed outlier: 8.869A pdb=" N LEU Q 341 " --> pdb=" O VAL Q 247 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL Q 249 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 319 through 322 Processing sheet with id=AE6, first strand: chain 'Q' and resid 497 through 498 removed outlier: 3.855A pdb=" N LYS Q 510 " --> pdb=" O GLY Q 498 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AE8, first strand: chain 'Z' and resid 194 through 199 removed outlier: 6.348A pdb=" N GLU Z 195 " --> pdb=" O ILE Z 378 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE Z 380 " --> pdb=" O GLU Z 195 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N MET Z 197 " --> pdb=" O ILE Z 380 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR Z 208 " --> pdb=" O LEU Z 379 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 214 through 215 Processing sheet with id=AF1, first strand: chain 'Z' and resid 315 through 316 removed outlier: 5.373A pdb=" N TYR Z 232 " --> pdb=" O VAL Z 294 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N GLN Z 337 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE Z 235 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 490 through 491 Processing sheet with id=AF3, first strand: chain 'a' and resid 18 through 21 removed outlier: 4.282A pdb=" N ILE a 541 " --> pdb=" O ASP d 45 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N MET d 47 " --> pdb=" O ILE a 541 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR a 543 " --> pdb=" O MET d 47 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LYS d 49 " --> pdb=" O THR a 543 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE a 545 " --> pdb=" O LYS d 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 60 through 63 Processing sheet with id=AF5, first strand: chain 'a' and resid 145 through 146 removed outlier: 3.625A pdb=" N SER a 145 " --> pdb=" O VAL a 418 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 204 through 207 removed outlier: 6.139A pdb=" N ASN a 204 " --> pdb=" O ILE a 385 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU a 387 " --> pdb=" O ASN a 204 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU a 206 " --> pdb=" O LEU a 387 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 221 through 224 removed outlier: 3.761A pdb=" N CYS a 371 " --> pdb=" O ALA a 364 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA a 364 " --> pdb=" O CYS a 371 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL a 361 " --> pdb=" O ILE a 237 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE a 237 " --> pdb=" O VAL a 361 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 316 through 318 removed outlier: 6.634A pdb=" N VAL a 296 " --> pdb=" O VAL a 318 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 500 through 503 Processing sheet with id=AG1, first strand: chain 'b' and resid 55 through 57 removed outlier: 7.327A pdb=" N ASP b 43 " --> pdb=" O ASP d 523 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ALA d 525 " --> pdb=" O ASP b 43 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU b 45 " --> pdb=" O ALA d 525 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'b' and resid 140 through 141 Processing sheet with id=AG3, first strand: chain 'b' and resid 193 through 199 Processing sheet with id=AG4, first strand: chain 'b' and resid 304 through 306 removed outlier: 7.150A pdb=" N THR b 283 " --> pdb=" O ASN b 228 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LYS b 230 " --> pdb=" O THR b 283 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE b 285 " --> pdb=" O LYS b 230 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU b 232 " --> pdb=" O ILE b 285 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP b 341 " --> pdb=" O ASN b 228 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS b 230 " --> pdb=" O GLU b 339 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU b 339 " --> pdb=" O LYS b 230 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS b 340 " --> pdb=" O CYS b 359 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N CYS b 359 " --> pdb=" O CYS b 340 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 470 through 473 Processing sheet with id=AG6, first strand: chain 'd' and resid 194 through 200 removed outlier: 6.240A pdb=" N ARG d 195 " --> pdb=" O VAL d 377 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE d 379 " --> pdb=" O ARG d 195 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL d 197 " --> pdb=" O ILE d 379 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLY d 381 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS d 199 " --> pdb=" O GLY d 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'd' and resid 213 through 214 removed outlier: 3.812A pdb=" N ILE d 360 " --> pdb=" O ILE d 353 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU d 349 " --> pdb=" O THR d 364 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU d 349 " --> pdb=" O GLU d 230 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLU d 230 " --> pdb=" O LEU d 349 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU d 351 " --> pdb=" O ARG d 228 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG d 228 " --> pdb=" O GLU d 351 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 311 through 316 removed outlier: 6.007A pdb=" N LEU d 286 " --> pdb=" O VAL d 313 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASP d 315 " --> pdb=" O LEU d 286 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE d 288 " --> pdb=" O ASP d 315 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ILE d 333 " --> pdb=" O ILE d 234 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU d 236 " --> pdb=" O ILE d 333 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'd' and resid 410 through 412 Processing sheet with id=AH1, first strand: chain 'd' and resid 480 through 483 Processing sheet with id=AH2, first strand: chain 'e' and resid 72 through 75 Processing sheet with id=AH3, first strand: chain 'e' and resid 166 through 167 removed outlier: 3.521A pdb=" N ASP e 166 " --> pdb=" O VAL e 439 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'e' and resid 224 through 230 removed outlier: 3.627A pdb=" N GLY e 410 " --> pdb=" O ARG e 229 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'e' and resid 257 through 258 removed outlier: 3.679A pdb=" N ILE e 380 " --> pdb=" O VAL e 258 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG e 379 " --> pdb=" O GLU e 396 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'e' and resid 342 through 343 removed outlier: 6.532A pdb=" N VAL e 321 " --> pdb=" O VAL e 343 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'e' and resid 551 through 556 removed outlier: 6.745A pdb=" N ASP h 50 " --> pdb=" O ILE e 551 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN e 553 " --> pdb=" O ASP h 50 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER h 63 " --> pdb=" O ILE h 51 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'g' and resid 55 through 56 removed outlier: 7.916A pdb=" N LEU g 45 " --> pdb=" O GLU z 532 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N LEU z 534 " --> pdb=" O LEU g 45 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N MET g 47 " --> pdb=" O LEU z 534 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'g' and resid 141 through 142 Processing sheet with id=AI1, first strand: chain 'g' and resid 206 through 210 removed outlier: 3.791A pdb=" N GLY g 383 " --> pdb=" O ILE g 209 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'g' and resid 224 through 225 Processing sheet with id=AI3, first strand: chain 'g' and resid 315 through 318 removed outlier: 5.700A pdb=" N VAL g 295 " --> pdb=" O LEU g 317 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL g 244 " --> pdb=" O ILE g 296 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N VAL g 337 " --> pdb=" O VAL g 243 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU g 245 " --> pdb=" O VAL g 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'g' and resid 359 through 360 Processing sheet with id=AI5, first strand: chain 'g' and resid 482 through 484 Processing sheet with id=AI6, first strand: chain 'h' and resid 201 through 205 removed outlier: 3.894A pdb=" N GLY h 380 " --> pdb=" O ILE h 204 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'h' and resid 219 through 221 removed outlier: 3.527A pdb=" N LEU h 364 " --> pdb=" O GLU h 353 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU h 353 " --> pdb=" O LEU h 364 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'h' and resid 313 through 315 removed outlier: 6.287A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN h 335 " --> pdb=" O ILE h 241 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER h 243 " --> pdb=" O GLN h 335 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'h' and resid 313 through 315 removed outlier: 6.287A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'h' and resid 409 through 411 Processing sheet with id=AJ2, first strand: chain 'h' and resid 479 through 482 removed outlier: 4.031A pdb=" N ASN h 487 " --> pdb=" O VAL h 482 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'q' and resid 20 through 22 removed outlier: 6.849A pdb=" N LEU z 43 " --> pdb=" O ILE q 541 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN q 543 " --> pdb=" O LEU z 43 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET z 45 " --> pdb=" O GLN q 543 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL z 47 " --> pdb=" O ILE q 545 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS z 44 " --> pdb=" O THR z 56 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'q' and resid 53 through 56 removed outlier: 3.806A pdb=" N THR q 65 " --> pdb=" O LYS q 53 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'q' and resid 207 through 213 Processing sheet with id=AJ6, first strand: chain 'q' and resid 225 through 228 Processing sheet with id=AJ7, first strand: chain 'q' and resid 319 through 322 removed outlier: 7.546A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS q 298 " --> pdb=" O LYS q 246 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'q' and resid 419 through 421 Processing sheet with id=AJ9, first strand: chain 'z' and resid 138 through 139 Processing sheet with id=AK1, first strand: chain 'z' and resid 194 through 199 removed outlier: 6.406A pdb=" N GLU z 195 " --> pdb=" O ILE z 378 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE z 380 " --> pdb=" O GLU z 195 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N MET z 197 " --> pdb=" O ILE z 380 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU z 379 " --> pdb=" O THR z 208 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR z 208 " --> pdb=" O LEU z 379 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'z' and resid 214 through 215 Processing sheet with id=AK3, first strand: chain 'z' and resid 315 through 316 removed outlier: 3.518A pdb=" N LEU z 315 " --> pdb=" O PHE z 293 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TYR z 232 " --> pdb=" O VAL z 294 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N GLN z 337 " --> pdb=" O VAL z 233 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE z 235 " --> pdb=" O GLN z 337 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'z' and resid 490 through 491 Processing sheet with id=AK5, first strand: chain 'P' and resid 99 through 101 removed outlier: 6.373A pdb=" N PHE P 100 " --> pdb=" O GLU P 171 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU P 189 " --> pdb=" O ASN P 200 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN P 200 " --> pdb=" O LEU P 189 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL P 191 " --> pdb=" O ILE P 198 " (cutoff:3.500A) 3752 hydrogen bonds defined for protein. 10749 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: 30.98 Time building geometry restraints manager: 24.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11683 1.32 - 1.44: 14458 1.44 - 1.57: 39670 1.57 - 1.69: 10 1.69 - 1.81: 526 Bond restraints: 66347 Sorted by residual: bond pdb=" CA GLU P 98 " pdb=" C GLU P 98 " ideal model delta sigma weight residual 1.521 1.588 -0.067 1.21e-02 6.83e+03 3.08e+01 bond pdb=" CA GLU P 218 " pdb=" C GLU P 218 " ideal model delta sigma weight residual 1.523 1.586 -0.063 1.30e-02 5.92e+03 2.32e+01 bond pdb=" CA GLU P 206 " pdb=" C GLU P 206 " ideal model delta sigma weight residual 1.523 1.590 -0.068 1.41e-02 5.03e+03 2.31e+01 bond pdb=" CA LEU P 205 " pdb=" C LEU P 205 " ideal model delta sigma weight residual 1.522 1.587 -0.065 1.39e-02 5.18e+03 2.19e+01 bond pdb=" CA ILE P 198 " pdb=" C ILE P 198 " ideal model delta sigma weight residual 1.523 1.586 -0.063 1.37e-02 5.33e+03 2.11e+01 ... (remaining 66342 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.25: 1528 107.25 - 113.93: 39127 113.93 - 120.61: 26407 120.61 - 127.29: 22023 127.29 - 133.97: 408 Bond angle restraints: 89493 Sorted by residual: angle pdb=" N LYS P 95 " pdb=" CA LYS P 95 " pdb=" C LYS P 95 " ideal model delta sigma weight residual 111.28 124.22 -12.94 1.09e+00 8.42e-01 1.41e+02 angle pdb=" N PRO P 173 " pdb=" CA PRO P 173 " pdb=" C PRO P 173 " ideal model delta sigma weight residual 111.03 101.07 9.96 1.54e+00 4.22e-01 4.18e+01 angle pdb=" O ILE P 202 " pdb=" C ILE P 202 " pdb=" N THR P 203 " ideal model delta sigma weight residual 123.18 116.20 6.98 1.08e+00 8.57e-01 4.17e+01 angle pdb=" N THR P 125 " pdb=" CA THR P 125 " pdb=" C THR P 125 " ideal model delta sigma weight residual 108.34 116.17 -7.83 1.31e+00 5.83e-01 3.57e+01 angle pdb=" CA ASN P 108 " pdb=" C ASN P 108 " pdb=" N LYS P 109 " ideal model delta sigma weight residual 118.13 110.61 7.52 1.28e+00 6.10e-01 3.45e+01 ... (remaining 89488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 40635 17.35 - 34.69: 479 34.69 - 52.04: 56 52.04 - 69.38: 13 69.38 - 86.73: 8 Dihedral angle restraints: 41191 sinusoidal: 16536 harmonic: 24655 Sorted by residual: dihedral pdb=" CA GLN P 116 " pdb=" C GLN P 116 " pdb=" N GLY P 117 " pdb=" CA GLY P 117 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LEU P 113 " pdb=" C LEU P 113 " pdb=" N ALA P 114 " pdb=" CA ALA P 114 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA SER P 143 " pdb=" C SER P 143 " pdb=" N LEU P 144 " pdb=" CA LEU P 144 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 41188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 9391 0.061 - 0.122: 1229 0.122 - 0.183: 67 0.183 - 0.244: 7 0.244 - 0.305: 2 Chirality restraints: 10696 Sorted by residual: chirality pdb=" CA VAL P 99 " pdb=" N VAL P 99 " pdb=" C VAL P 99 " pdb=" CB VAL P 99 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LYS P 95 " pdb=" N LYS P 95 " pdb=" C LYS P 95 " pdb=" CB LYS P 95 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA VAL P 197 " pdb=" N VAL P 197 " pdb=" C VAL P 197 " pdb=" CB VAL P 197 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 10693 not shown) Planarity restraints: 11542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS P 109 " -0.067 2.00e-02 2.50e+03 1.40e-01 1.95e+02 pdb=" C LYS P 109 " 0.242 2.00e-02 2.50e+03 pdb=" O LYS P 109 " -0.092 2.00e-02 2.50e+03 pdb=" N GLU P 110 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN P 108 " 0.063 2.00e-02 2.50e+03 1.35e-01 1.82e+02 pdb=" C ASN P 108 " -0.233 2.00e-02 2.50e+03 pdb=" O ASN P 108 " 0.090 2.00e-02 2.50e+03 pdb=" N LYS P 109 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE P 202 " 0.035 2.00e-02 2.50e+03 6.69e-02 4.47e+01 pdb=" C ILE P 202 " -0.116 2.00e-02 2.50e+03 pdb=" O ILE P 202 " 0.042 2.00e-02 2.50e+03 pdb=" N THR P 203 " 0.039 2.00e-02 2.50e+03 ... (remaining 11539 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 3 2.02 - 2.74: 6641 2.74 - 3.46: 96538 3.46 - 4.18: 147461 4.18 - 4.90: 274811 Nonbonded interactions: 525454 Sorted by model distance: nonbonded pdb=" OD2 ASP G 69 " pdb=" ND2 ASN P 210 " model vdw 1.304 2.520 nonbonded pdb=" CG ASP G 69 " pdb=" ND2 ASN P 210 " model vdw 1.432 3.350 nonbonded pdb=" CG PRO G 51 " pdb=" OE2 GLU P 206 " model vdw 1.508 3.440 nonbonded pdb=" O PRO D 226 " pdb=" OG1 THR D 227 " model vdw 2.046 2.440 nonbonded pdb=" O PRO d 226 " pdb=" OG1 THR d 227 " model vdw 2.060 2.440 ... (remaining 525449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 6.110 Check model and map are aligned: 0.710 Set scattering table: 0.450 Process input model: 142.880 Find NCS groups from input model: 5.840 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 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 : 0.002 0.068 66347 Z= 0.160 Angle : 0.444 12.943 89493 Z= 0.279 Chirality : 0.040 0.305 10696 Planarity : 0.003 0.140 11542 Dihedral : 6.304 86.731 25221 Min Nonbonded Distance : 1.304 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.88 % Favored : 98.03 % Rotamer: Outliers : 0.11 % Allowed : 1.09 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.01 % 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: 2.63 (0.10), residues: 8544 helix: 3.23 (0.08), residues: 4307 sheet: 0.62 (0.18), residues: 927 loop : 0.07 (0.11), residues: 3310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP h 497 HIS 0.002 0.000 HIS H 394 PHE 0.007 0.001 PHE H 279 TYR 0.005 0.001 TYR D 270 ARG 0.003 0.000 ARG P 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2952 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2944 time to evaluate : 5.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 2951 average time/residue: 0.7031 time to fit residues: 3417.5980 Evaluate side-chains 2005 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2004 time to evaluate : 5.382 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5151 time to fit residues: 8.6881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 716 optimal weight: 6.9990 chunk 643 optimal weight: 4.9990 chunk 357 optimal weight: 10.0000 chunk 219 optimal weight: 0.0770 chunk 434 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 chunk 665 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 chunk 404 optimal weight: 9.9990 chunk 495 optimal weight: 0.9990 chunk 770 optimal weight: 3.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN A 141 ASN A 435 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 HIS B 484 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 149 GLN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN E 138 GLN E 210 ASN E 466 GLN E 509 ASN G 19 GLN G 188 GLN G 438 GLN G 470 GLN G 507 GLN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 16 GLN Q 19 ASN Q 52 ASN Q 91 GLN Q 157 ASN Q 188 HIS Q 219 ASN Q 451 GLN ** Z 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 ASN ** a 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 481 HIS ** a 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 220 ASN ** b 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 484 GLN d 238 GLN d 303 HIS d 395 HIS ** e 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 424 HIS e 474 GLN ** e 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 507 GLN ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 245 ASN h 345 HIS h 394 HIS ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 132 ASN q 154 ASN ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 393 ASN ** q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 22 ASN z 36 ASN z 67 GLN ** z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 237 ASN z 329 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 66347 Z= 0.282 Angle : 0.680 11.831 89493 Z= 0.358 Chirality : 0.045 0.210 10696 Planarity : 0.004 0.064 11542 Dihedral : 3.748 21.255 9070 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.20 % Rotamer: Outliers : 0.14 % Allowed : 3.02 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.01 % 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: 1.37 (0.09), residues: 8544 helix: 1.97 (0.08), residues: 4362 sheet: 0.48 (0.18), residues: 841 loop : -0.38 (0.11), residues: 3341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP h 497 HIS 0.016 0.002 HIS q 311 PHE 0.048 0.003 PHE P 157 TYR 0.031 0.002 TYR Z 419 ARG 0.036 0.001 ARG z 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2285 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 2275 time to evaluate : 5.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 2279 average time/residue: 0.6958 time to fit residues: 2652.0840 Evaluate side-chains 1929 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1928 time to evaluate : 5.425 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4716 time to fit residues: 8.7188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 428 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 641 optimal weight: 4.9990 chunk 524 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 772 optimal weight: 0.1980 chunk 834 optimal weight: 6.9990 chunk 687 optimal weight: 1.9990 chunk 765 optimal weight: 6.9990 chunk 263 optimal weight: 7.9990 chunk 619 optimal weight: 0.9980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN B 112 GLN B 168 GLN ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN D 461 ASN E 138 GLN ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN G 405 ASN G 439 GLN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 ASN Q 91 GLN ** Q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 392 ASN Q 477 ASN Q 516 ASN Z 69 GLN ** Z 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 192 HIS ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 404 ASN ** a 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 435 ASN ** a 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 84 GLN b 375 GLN b 439 GLN d 62 HIS d 116 HIS ** e 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 509 ASN ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 482 HIS q 516 ASN z 22 ASN z 36 ASN ** z 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 282 ASN z 297 ASN ** z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 390 GLN P 116 GLN P 211 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 66347 Z= 0.208 Angle : 0.606 9.797 89493 Z= 0.315 Chirality : 0.044 0.271 10696 Planarity : 0.004 0.059 11542 Dihedral : 3.817 20.102 9070 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.01 % 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: 1.12 (0.09), residues: 8544 helix: 1.80 (0.08), residues: 4347 sheet: 0.38 (0.18), residues: 813 loop : -0.54 (0.11), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP h 478 HIS 0.019 0.001 HIS P 141 PHE 0.033 0.002 PHE P 157 TYR 0.018 0.002 TYR z 355 ARG 0.019 0.001 ARG h 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2196 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2192 time to evaluate : 6.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 2194 average time/residue: 0.6627 time to fit residues: 2413.4790 Evaluate side-chains 1886 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1883 time to evaluate : 5.350 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4873 time to fit residues: 10.5654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 763 optimal weight: 8.9990 chunk 580 optimal weight: 6.9990 chunk 400 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 368 optimal weight: 1.9990 chunk 518 optimal weight: 10.0000 chunk 775 optimal weight: 7.9990 chunk 820 optimal weight: 8.9990 chunk 404 optimal weight: 0.8980 chunk 734 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN E 537 GLN G 188 GLN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 GLN H 37 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 ASN H 515 ASN Q 19 ASN Q 91 GLN ** Q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 392 ASN ** Z 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 329 GLN ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 HIS ** e 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 432 ASN ** e 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 394 HIS q 132 ASN ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 477 ASN z 22 ASN ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 221 HIS ** z 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 66347 Z= 0.216 Angle : 0.612 12.536 89493 Z= 0.321 Chirality : 0.044 0.380 10696 Planarity : 0.004 0.103 11542 Dihedral : 3.942 20.612 9070 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 0.01 % Allowed : 2.51 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.01 % 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: 0.89 (0.09), residues: 8544 helix: 1.61 (0.08), residues: 4363 sheet: 0.19 (0.18), residues: 820 loop : -0.64 (0.11), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 440 HIS 0.014 0.001 HIS P 141 PHE 0.046 0.002 PHE z 122 TYR 0.024 0.002 TYR Z 386 ARG 0.016 0.001 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2141 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2140 time to evaluate : 7.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 2140 average time/residue: 0.6576 time to fit residues: 2358.9192 Evaluate side-chains 1859 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1858 time to evaluate : 5.380 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5370 time to fit residues: 8.6793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 683 optimal weight: 10.0000 chunk 465 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 611 optimal weight: 10.0000 chunk 338 optimal weight: 10.0000 chunk 700 optimal weight: 8.9990 chunk 567 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 419 optimal weight: 7.9990 chunk 736 optimal weight: 0.2980 chunk 207 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN G 188 GLN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 ASN Q 91 GLN Q 101 ASN ** Q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 ASN a 191 ASN ** a 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 424 HIS e 432 ASN ** e 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN h 77 HIS h 394 HIS ** h 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 132 ASN ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 22 ASN ** z 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 312 HIS ** z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 66347 Z= 0.224 Angle : 0.625 11.651 89493 Z= 0.329 Chirality : 0.044 0.228 10696 Planarity : 0.004 0.071 11542 Dihedral : 4.054 20.207 9070 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.36 % Favored : 96.54 % Rotamer: Outliers : 0.01 % Allowed : 1.53 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.01 % 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: 0.68 (0.09), residues: 8544 helix: 1.45 (0.08), residues: 4354 sheet: -0.01 (0.18), residues: 828 loop : -0.72 (0.11), residues: 3362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 440 HIS 0.010 0.001 HIS e 50 PHE 0.037 0.002 PHE z 122 TYR 0.021 0.001 TYR G 442 ARG 0.019 0.001 ARG D 520 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2150 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2149 time to evaluate : 5.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 2150 average time/residue: 0.6699 time to fit residues: 2405.1528 Evaluate side-chains 1892 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1892 time to evaluate : 5.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 276 optimal weight: 7.9990 chunk 739 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 481 optimal weight: 7.9990 chunk 202 optimal weight: 9.9990 chunk 821 optimal weight: 1.9990 chunk 681 optimal weight: 6.9990 chunk 380 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 271 optimal weight: 1.9990 chunk 431 optimal weight: 2.9990 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 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 HIS ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS E 432 ASN E 486 ASN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 477 GLN G 507 GLN ** H 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 515 ASN Q 19 ASN Q 91 GLN Q 101 ASN ** Q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 482 HIS Z 22 ASN ** Z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 ASN b 476 ASN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 GLN ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 58 GLN ** h 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 39 HIS ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 221 HIS ** z 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 66347 Z= 0.264 Angle : 0.665 10.303 89493 Z= 0.355 Chirality : 0.046 0.382 10696 Planarity : 0.004 0.066 11542 Dihedral : 4.287 24.236 9070 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 0.07 % Allowed : 1.89 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.01 % 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: 0.30 (0.09), residues: 8544 helix: 1.13 (0.08), residues: 4365 sheet: -0.10 (0.18), residues: 811 loop : -0.91 (0.10), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 440 HIS 0.017 0.002 HIS z 221 PHE 0.043 0.002 PHE z 122 TYR 0.018 0.002 TYR z 386 ARG 0.019 0.001 ARG e 431 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2141 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2136 time to evaluate : 5.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 2139 average time/residue: 0.6744 time to fit residues: 2418.0096 Evaluate side-chains 1907 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1904 time to evaluate : 5.474 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5351 time to fit residues: 10.9337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 791 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 468 optimal weight: 9.9990 chunk 599 optimal weight: 0.0670 chunk 464 optimal weight: 4.9990 chunk 691 optimal weight: 3.9990 chunk 458 optimal weight: 0.7980 chunk 818 optimal weight: 8.9990 chunk 512 optimal weight: 2.9990 chunk 498 optimal weight: 7.9990 chunk 377 optimal weight: 7.9990 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN E 333 HIS E 432 ASN E 486 ASN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 GLN Q 19 ASN Q 91 GLN Q 101 ASN ** Q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 64 ASN a 191 ASN ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 296 GLN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 GLN ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 424 HIS ** e 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 553 ASN ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 405 ASN ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 58 GLN h 394 HIS ** h 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 22 ASN z 221 HIS ** z 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 66347 Z= 0.225 Angle : 0.650 10.268 89493 Z= 0.346 Chirality : 0.046 0.395 10696 Planarity : 0.004 0.077 11542 Dihedral : 4.332 24.586 9070 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.75 % Favored : 96.15 % Rotamer: Outliers : 0.07 % Allowed : 1.38 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.01 % 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: 0.24 (0.09), residues: 8544 helix: 1.10 (0.08), residues: 4369 sheet: -0.16 (0.18), residues: 808 loop : -0.97 (0.10), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 269 HIS 0.013 0.001 HIS z 221 PHE 0.032 0.002 PHE z 122 TYR 0.025 0.001 TYR a 198 ARG 0.020 0.001 ARG e 546 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2138 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2133 time to evaluate : 6.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 2136 average time/residue: 0.6764 time to fit residues: 2424.1619 Evaluate side-chains 1873 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1871 time to evaluate : 5.415 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5416 time to fit residues: 9.8321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 506 optimal weight: 0.7980 chunk 326 optimal weight: 1.9990 chunk 488 optimal weight: 10.0000 chunk 246 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 520 optimal weight: 3.9990 chunk 557 optimal weight: 20.0000 chunk 404 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 643 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS ** E 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 GLN ** H 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 515 ASN Q 19 ASN Q 91 GLN Q 101 ASN ** Q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 ASN ** Z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 282 ASN a 7 ASN ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 HIS ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 367 GLN e 424 HIS ** e 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 58 GLN ** h 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 91 GLN ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 221 HIS ** z 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 66347 Z= 0.216 Angle : 0.660 12.603 89493 Z= 0.349 Chirality : 0.046 0.368 10696 Planarity : 0.004 0.085 11542 Dihedral : 4.358 24.718 9070 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.99 % Rotamer: Outliers : 0.03 % Allowed : 0.90 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.01 % 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: 0.22 (0.09), residues: 8544 helix: 1.09 (0.08), residues: 4380 sheet: -0.13 (0.18), residues: 806 loop : -1.01 (0.10), residues: 3358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP Z 507 HIS 0.013 0.001 HIS Z 217 PHE 0.044 0.002 PHE z 122 TYR 0.025 0.001 TYR z 386 ARG 0.014 0.001 ARG e 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2133 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2131 time to evaluate : 5.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 2133 average time/residue: 0.6659 time to fit residues: 2375.0315 Evaluate side-chains 1876 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1876 time to evaluate : 5.428 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 744 optimal weight: 1.9990 chunk 783 optimal weight: 50.0000 chunk 715 optimal weight: 7.9990 chunk 762 optimal weight: 20.0000 chunk 458 optimal weight: 3.9990 chunk 332 optimal weight: 8.9990 chunk 598 optimal weight: 9.9990 chunk 234 optimal weight: 0.1980 chunk 689 optimal weight: 2.9990 chunk 721 optimal weight: 1.9990 chunk 759 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN H 291 ASN Q 19 ASN Q 91 GLN ** Q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 392 ASN ** Q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 356 GLN a 191 ASN a 499 ASN ** b 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 HIS ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 172 ASN e 424 HIS ** e 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 58 GLN h 394 HIS ** h 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 91 GLN ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 477 ASN z 221 HIS ** z 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 461 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 66347 Z= 0.213 Angle : 0.679 12.123 89493 Z= 0.359 Chirality : 0.047 0.303 10696 Planarity : 0.004 0.074 11542 Dihedral : 4.391 24.489 9070 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 0.06 % Allowed : 0.57 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.01 % 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: 0.15 (0.09), residues: 8544 helix: 1.02 (0.08), residues: 4349 sheet: -0.14 (0.18), residues: 812 loop : -1.01 (0.10), residues: 3383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP H 497 HIS 0.015 0.001 HIS Z 217 PHE 0.038 0.002 PHE z 122 TYR 0.026 0.001 TYR z 366 ARG 0.015 0.001 ARG a 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2108 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2104 time to evaluate : 5.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 2105 average time/residue: 0.6897 time to fit residues: 2440.8876 Evaluate side-chains 1871 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1869 time to evaluate : 5.490 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5269 time to fit residues: 9.9428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 500 optimal weight: 10.0000 chunk 806 optimal weight: 4.9990 chunk 492 optimal weight: 10.0000 chunk 382 optimal weight: 0.9980 chunk 560 optimal weight: 10.0000 chunk 845 optimal weight: 4.9990 chunk 778 optimal weight: 6.9990 chunk 673 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 520 optimal weight: 0.4980 chunk 412 optimal weight: 0.8980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 491 ASN Q 19 ASN Q 91 GLN Q 101 ASN Q 392 ASN ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 430 ASN ** Z 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 ASN ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 HIS ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 250 ASN ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 367 GLN e 424 HIS ** e 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 553 ASN ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 58 GLN ** h 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 91 GLN ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 221 HIS ** z 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 390 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.6947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 66347 Z= 0.242 Angle : 0.717 11.918 89493 Z= 0.380 Chirality : 0.047 0.283 10696 Planarity : 0.004 0.066 11542 Dihedral : 4.490 25.290 9070 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.15 % Favored : 95.74 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.09), residues: 8544 helix: 0.87 (0.08), residues: 4346 sheet: -0.13 (0.18), residues: 833 loop : -1.07 (0.10), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 497 HIS 0.016 0.001 HIS Z 217 PHE 0.035 0.002 PHE z 122 TYR 0.028 0.002 TYR Z 386 ARG 0.023 0.001 ARG B 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17088 Ramachandran restraints generated. 8544 Oldfield, 0 Emsley, 8544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2112 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2110 time to evaluate : 5.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 2112 average time/residue: 0.6849 time to fit residues: 2434.8455 Evaluate side-chains 1879 residues out of total 7249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1879 time to evaluate : 5.480 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 534 optimal weight: 2.9990 chunk 717 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 621 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 674 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 692 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 85 GLN D 112 ASN ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 ASN Q 40 GLN Q 101 ASN ** Q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS ** Q 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 HIS ** Z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 ASN b 79 ASN b 296 GLN ** b 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 HIS ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 367 GLN e 424 HIS ** e 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 58 GLN h 394 HIS ** h 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 132 ASN ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 477 ASN z 221 HIS ** z 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.141400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102424 restraints weight = 184131.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.106201 restraints weight = 122034.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.108914 restraints weight = 88554.919| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 66347 Z= 0.222 Angle : 0.711 11.704 89493 Z= 0.378 Chirality : 0.047 0.293 10696 Planarity : 0.004 0.086 11542 Dihedral : 4.511 24.149 9070 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 0.07 % Allowed : 0.26 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.01 % 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: -0.01 (0.09), residues: 8544 helix: 0.84 (0.08), residues: 4343 sheet: -0.15 (0.18), residues: 836 loop : -1.04 (0.10), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 497 HIS 0.014 0.001 HIS Z 217 PHE 0.037 0.002 PHE e 276 TYR 0.026 0.001 TYR Z 386 ARG 0.018 0.001 ARG Z 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30200.69 seconds wall clock time: 523 minutes 10.36 seconds (31390.36 seconds total)