Starting phenix.real_space_refine on Mon Aug 25 12:21:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vom_21269/08_2025/6vom_21269.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vom_21269/08_2025/6vom_21269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vom_21269/08_2025/6vom_21269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vom_21269/08_2025/6vom_21269.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vom_21269/08_2025/6vom_21269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vom_21269/08_2025/6vom_21269.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 103 5.16 5 C 17261 2.51 5 N 4744 2.21 5 O 5368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27492 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3818 Classifications: {'peptide': 497} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 478} Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Chain: "D" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3627 Classifications: {'peptide': 479} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 453} Chain: "F" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Chain: "d" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1383 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2497 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'ATP': 1, 'TTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.68, per 1000 atoms: 0.21 Number of scatterers: 27492 At special positions: 0 Unit cell: (170.586, 137.943, 132.678, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 P 16 15.00 O 5368 8.00 N 4744 7.00 C 17261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 838.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6554 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 57 sheets defined 48.3% alpha, 55.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.968A pdb=" N TYR A 104 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 105 " --> pdb=" O GLU A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 221 removed outlier: 3.538A pdb=" N TYR A 221 " --> pdb=" O ALA A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix removed outlier: 3.724A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.691A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.645A pdb=" N ALA A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 395 removed outlier: 3.556A pdb=" N LYS A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 4.173A pdb=" N SER A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 430 through 440 Processing helix chain 'A' and resid 450 through 468 removed outlier: 4.658A pdb=" N ARG A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 removed outlier: 3.949A pdb=" N GLU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 501 Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 187 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 253 Proline residue: B 240 - end of helix removed outlier: 3.567A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 288 through 289 No H-bonds generated for 'chain 'B' and resid 288 through 289' Processing helix chain 'B' and resid 290 through 301 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.891A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 393 removed outlier: 4.360A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 397 removed outlier: 3.684A pdb=" N ALA B 397 " --> pdb=" O GLU B 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 394 through 397' Processing helix chain 'B' and resid 404 through 422 removed outlier: 3.764A pdb=" N LYS B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 444 removed outlier: 3.633A pdb=" N GLY B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 470 through 480 removed outlier: 3.988A pdb=" N GLU B 474 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 504 Processing helix chain 'C' and resid 6 through 20 removed outlier: 3.732A pdb=" N GLY C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.667A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 187 through 190 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix removed outlier: 3.944A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.942A pdb=" N ALA C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 289 No H-bonds generated for 'chain 'C' and resid 288 through 289' Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.690A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.814A pdb=" N ALA C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 381 Processing helix chain 'C' and resid 382 through 397 Processing helix chain 'C' and resid 404 through 421 Processing helix chain 'C' and resid 430 through 443 Processing helix chain 'C' and resid 444 through 448 removed outlier: 3.700A pdb=" N ASP C 447 " --> pdb=" O GLY C 444 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER C 448 " --> pdb=" O TYR C 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 444 through 448' Processing helix chain 'C' and resid 452 through 469 removed outlier: 4.397A pdb=" N LYS C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 483 through 504 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.516A pdb=" N LEU D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 177 through 192 Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 242 through 263 removed outlier: 3.628A pdb=" N MET D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 290 removed outlier: 3.532A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 311 removed outlier: 3.619A pdb=" N LEU D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 333 removed outlier: 3.955A pdb=" N ASP D 332 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 346 Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.571A pdb=" N ALA D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 381 through 409 removed outlier: 4.845A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA D 406 " --> pdb=" O GLN D 402 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 450 through 463 Processing helix chain 'D' and resid 470 through 475 Processing helix chain 'D' and resid 479 through 496 removed outlier: 3.552A pdb=" N LEU D 496 " --> pdb=" O MET D 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.558A pdb=" N LEU E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.543A pdb=" N LEU E 142 " --> pdb=" O PHE E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 177 through 190 Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 242 through 263 removed outlier: 5.212A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 290 removed outlier: 4.045A pdb=" N VAL E 279 " --> pdb=" O ILE E 275 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 330 through 333 Processing helix chain 'E' and resid 336 through 346 removed outlier: 4.227A pdb=" N ALA E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.550A pdb=" N GLY E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 381 through 409 removed outlier: 4.590A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 431 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 450 through 464 Processing helix chain 'E' and resid 470 through 475 Processing helix chain 'E' and resid 480 through 496 Processing helix chain 'F' and resid 103 through 107 removed outlier: 3.511A pdb=" N THR F 106 " --> pdb=" O GLY F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 160 removed outlier: 3.758A pdb=" N ALA F 160 " --> pdb=" O VAL F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 190 Processing helix chain 'F' and resid 205 through 219 Processing helix chain 'F' and resid 242 through 247 Processing helix chain 'F' and resid 248 through 265 Processing helix chain 'F' and resid 274 through 290 removed outlier: 3.952A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 311 removed outlier: 3.634A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 333 Processing helix chain 'F' and resid 336 through 346 removed outlier: 4.447A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 408 removed outlier: 4.566A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 removed outlier: 3.662A pdb=" N GLU F 412 " --> pdb=" O GLY F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 431 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 450 through 464 removed outlier: 3.907A pdb=" N ARG F 456 " --> pdb=" O ALA F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 469 removed outlier: 4.459A pdb=" N SER F 468 " --> pdb=" O GLU F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 493 Processing helix chain 'd' and resid 73 through 90 Processing helix chain 'd' and resid 91 through 107 removed outlier: 3.547A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 117 Processing helix chain 'd' and resid 121 through 137 Processing helix chain 'd' and resid 139 through 153 Processing helix chain 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing helix chain 'd' and resid 157 through 174 removed outlier: 4.442A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 Processing helix chain 'd' and resid 237 through 246 Processing helix chain 'g' and resid 44 through 100 removed outlier: 3.529A pdb=" N LEU g 66 " --> pdb=" O GLU g 62 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN g 81 " --> pdb=" O GLU g 77 " (cutoff:3.500A) Proline residue: g 84 - end of helix removed outlier: 3.594A pdb=" N ASN g 97 " --> pdb=" O LEU g 93 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.758A pdb=" N LEU g 137 " --> pdb=" O PHE g 133 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU g 142 " --> pdb=" O LEU g 138 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 171 removed outlier: 3.742A pdb=" N ILE g 169 " --> pdb=" O ASN g 165 " (cutoff:3.500A) Processing helix chain 'g' and resid 188 through 204 removed outlier: 3.860A pdb=" N SER g 204 " --> pdb=" O SER g 200 " (cutoff:3.500A) Processing helix chain 'g' and resid 241 through 245 removed outlier: 3.602A pdb=" N LYS g 245 " --> pdb=" O ILE g 242 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 363 Proline residue: g 297 - end of helix removed outlier: 3.643A pdb=" N ILE g 304 " --> pdb=" O LEU g 300 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP g 328 " --> pdb=" O SER g 324 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY g 359 " --> pdb=" O GLU g 355 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 105 Processing helix chain 'e' and resid 108 through 130 removed outlier: 3.628A pdb=" N ASN e 130 " --> pdb=" O VAL e 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36 removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 36 removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 36 removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 32 through 36 removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 32 through 36 removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 32 through 36 removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 54 through 55 removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 62 through 67 removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 62 through 67 removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 62 through 67 removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 62 through 67 removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 62 through 67 removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 62 through 67 removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 206 through 213 removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 206 through 213 removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 206 through 213 removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 206 through 213 removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 206 through 213 removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN F 45 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 46 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 206 through 213 removed outlier: 3.963A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AD7, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.286A pdb=" N ILE A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.319A pdb=" N ILE A 168 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A 342 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 89 through 91 removed outlier: 5.746A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 66 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LEU B 33 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY E 70 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 89 through 91 removed outlier: 5.746A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 66 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LEU B 33 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY E 70 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU E 68 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ARG E 73 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP E 32 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.071A pdb=" N GLU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.835A pdb=" N LYS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG B 107 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA B 226 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR B 228 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE B 260 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASP B 262 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL B 197 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 319 through 321 removed outlier: 8.267A pdb=" N VAL B 320 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 168 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU B 167 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 97 through 99 Processing sheet with id=AE6, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AE7, first strand: chain 'C' and resid 319 through 321 removed outlier: 6.433A pdb=" N ILE C 168 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU C 345 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 169 " --> pdb=" O LEU C 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 19 through 27 removed outlier: 6.498A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU D 90 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN D 19 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AF1, first strand: chain 'D' and resid 148 through 149 removed outlier: 4.256A pdb=" N TYR D 162 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 232 through 238 removed outlier: 7.767A pdb=" N SER D 197 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N VAL D 235 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE D 199 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLY D 237 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLY D 201 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 272 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS D 167 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR D 350 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY D 169 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU D 352 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE D 171 " --> pdb=" O LEU D 352 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AF4, first strand: chain 'E' and resid 110 through 111 removed outlier: 3.856A pdb=" N TYR E 236 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 233 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE E 168 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 327 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU E 170 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS E 167 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR E 350 " --> pdb=" O LYS E 167 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY E 169 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU E 352 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE E 171 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 10.536A pdb=" N THR E 349 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N LEU E 368 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL E 351 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AF6, first strand: chain 'F' and resid 110 through 111 removed outlier: 7.226A pdb=" N SER F 197 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N VAL F 235 " --> pdb=" O SER F 197 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE F 199 " --> pdb=" O VAL F 235 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLY F 237 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLY F 201 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 269 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL F 268 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE F 324 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU F 270 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA F 326 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE F 272 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR F 328 " --> pdb=" O ILE F 272 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE F 168 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL F 327 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU F 170 " --> pdb=" O VAL F 327 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 148 through 149 removed outlier: 3.886A pdb=" N TYR F 162 " --> pdb=" O PHE F 149 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 154 through 160 removed outlier: 6.403A pdb=" N VAL g 118 " --> pdb=" O THR g 156 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE g 158 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE g 160 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL g 122 " --> pdb=" O ILE g 160 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LYS g 117 " --> pdb=" O LYS g 209 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N GLU g 211 " --> pdb=" O LYS g 117 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL g 210 " --> pdb=" O LEU g 230 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 254 through 259 removed outlier: 3.557A pdb=" N LEU g 254 " --> pdb=" O ASP g 269 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 5 through 7 removed outlier: 3.597A pdb=" N TRP e 15 " --> pdb=" O VAL e 7 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 21 through 24 Processing sheet with id=AG3, first strand: chain 'e' and resid 65 through 68 2104 hydrogen bonds defined for protein. 5940 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: 7.78 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9102 1.34 - 1.46: 3722 1.46 - 1.58: 14832 1.58 - 1.70: 26 1.70 - 1.82: 195 Bond restraints: 27877 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.27e+01 bond pdb=" C4 ATP F 502 " pdb=" C5 ATP F 502 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.15e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.02e+01 bond pdb=" C5 ATP C 601 " pdb=" C6 ATP C 601 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.01e+01 ... (remaining 27872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 37561 3.92 - 7.85: 201 7.85 - 11.77: 16 11.77 - 15.69: 3 15.69 - 19.62: 6 Bond angle restraints: 37787 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.25 19.62 1.00e+00 1.00e+00 3.85e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.54 19.33 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 121.96 17.91 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 118.96 17.87 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 119.12 17.71 1.00e+00 1.00e+00 3.14e+02 ... (remaining 37782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.16: 16602 33.16 - 66.31: 508 66.31 - 99.47: 51 99.47 - 132.63: 3 132.63 - 165.79: 2 Dihedral angle restraints: 17166 sinusoidal: 6954 harmonic: 10212 Sorted by residual: dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual -180.00 -132.03 -47.97 0 5.00e+00 4.00e-02 9.20e+01 dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -134.11 -45.89 0 5.00e+00 4.00e-02 8.42e+01 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -143.76 -36.24 0 5.00e+00 4.00e-02 5.25e+01 ... (remaining 17163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3374 0.052 - 0.105: 855 0.105 - 0.157: 197 0.157 - 0.209: 14 0.209 - 0.262: 3 Chirality restraints: 4443 Sorted by residual: chirality pdb=" CB ILE F 27 " pdb=" CA ILE F 27 " pdb=" CG1 ILE F 27 " pdb=" CG2 ILE F 27 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE g 112 " pdb=" CA ILE g 112 " pdb=" CG1 ILE g 112 " pdb=" CG2 ILE g 112 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL A 367 " pdb=" CA VAL A 367 " pdb=" CG1 VAL A 367 " pdb=" CG2 VAL A 367 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4440 not shown) Planarity restraints: 4907 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 TTX F 501 " 0.684 2.00e-02 2.50e+03 6.32e-01 5.99e+03 pdb=" C12 TTX F 501 " -0.071 2.00e-02 2.50e+03 pdb=" C13 TTX F 501 " 0.880 2.00e-02 2.50e+03 pdb=" C9 TTX F 501 " -0.627 2.00e-02 2.50e+03 pdb=" N3 TTX F 501 " 0.005 2.00e-02 2.50e+03 pdb=" O3 TTX F 501 " -0.870 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 TTX F 501 " 0.332 2.00e-02 2.50e+03 3.97e-01 2.36e+03 pdb=" C5 TTX F 501 " -0.514 2.00e-02 2.50e+03 pdb=" C6 TTX F 501 " 0.079 2.00e-02 2.50e+03 pdb=" C7 TTX F 501 " -0.576 2.00e-02 2.50e+03 pdb=" N1 TTX F 501 " 0.325 2.00e-02 2.50e+03 pdb=" O1 TTX F 501 " 0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 TTX F 501 " -0.544 2.00e-02 2.50e+03 2.72e-01 1.48e+03 pdb=" C14 TTX F 501 " 0.138 2.00e-02 2.50e+03 pdb=" C15 TTX F 501 " 0.094 2.00e-02 2.50e+03 pdb=" C16 TTX F 501 " -0.083 2.00e-02 2.50e+03 pdb=" C17 TTX F 501 " -0.175 2.00e-02 2.50e+03 pdb=" N1 TTX F 501 " 0.236 2.00e-02 2.50e+03 pdb=" N4 TTX F 501 " 0.412 2.00e-02 2.50e+03 pdb=" O4 TTX F 501 " -0.079 2.00e-02 2.50e+03 ... (remaining 4904 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1072 2.71 - 3.25: 28727 3.25 - 3.80: 45888 3.80 - 4.35: 59024 4.35 - 4.90: 97878 Nonbonded interactions: 232589 Sorted by model distance: nonbonded pdb=" O ALA D 295 " pdb=" N GLY D 297 " model vdw 2.157 3.120 nonbonded pdb=" O GLY F 450 " pdb=" OG1 THR F 454 " model vdw 2.157 3.040 nonbonded pdb=" O ALA E 295 " pdb=" N GLY E 297 " model vdw 2.165 3.120 nonbonded pdb=" OE1 GLU C 58 " pdb=" OG1 THR C 60 " model vdw 2.175 3.040 nonbonded pdb=" OD1 ASP C 404 " pdb=" OG1 THR C 407 " model vdw 2.192 3.040 ... (remaining 232584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 7 through 503 or resid 601)) selection = (chain 'C' and (resid 7 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and resid 18 through 494) selection = (chain 'E' and resid 18 through 494) selection = (chain 'F' and resid 18 through 494) } 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: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.940 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.006 0.079 27877 Z= 0.304 Angle : 0.917 19.617 37787 Z= 0.585 Chirality : 0.049 0.262 4443 Planarity : 0.013 0.632 4907 Dihedral : 15.877 165.787 10612 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 0.10 % Allowed : 7.66 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.12), residues: 3548 helix: -1.52 (0.11), residues: 1495 sheet: -2.52 (0.18), residues: 569 loop : -2.44 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 261 TYR 0.029 0.002 TYR C 20 PHE 0.016 0.002 PHE A 396 TRP 0.018 0.004 TRP e 57 HIS 0.010 0.001 HIS d 141 Details of bonding type rmsd covalent geometry : bond 0.00570 (27877) covalent geometry : angle 0.91670 (37787) hydrogen bonds : bond 0.14407 ( 1345) hydrogen bonds : angle 8.38388 ( 5940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 832 time to evaluate : 0.906 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: A 363 SER cc_start: 0.8469 (m) cc_final: 0.8170 (p) REVERT: A 405 LYS cc_start: 0.6244 (pttt) cc_final: 0.6022 (ptmt) REVERT: B 215 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7160 (pt0) REVERT: B 384 LYS cc_start: 0.8049 (mttt) cc_final: 0.7708 (mtmt) REVERT: C 197 VAL cc_start: 0.9067 (t) cc_final: 0.8837 (m) REVERT: C 327 VAL cc_start: 0.7274 (t) cc_final: 0.6976 (t) REVERT: D 379 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8386 (mp) REVERT: D 416 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6883 (mp0) REVERT: E 106 THR cc_start: 0.8377 (p) cc_final: 0.7444 (p) REVERT: E 217 LYS cc_start: 0.8507 (mttt) cc_final: 0.8269 (ttmm) REVERT: E 336 ASP cc_start: 0.7236 (t0) cc_final: 0.6984 (t0) REVERT: F 213 TYR cc_start: 0.7545 (t80) cc_final: 0.7313 (t80) REVERT: d 196 LYS cc_start: 0.7606 (mmmm) cc_final: 0.7252 (pttt) REVERT: g 92 VAL cc_start: 0.7730 (t) cc_final: 0.7493 (t) REVERT: g 126 ASP cc_start: 0.4999 (m-30) cc_final: 0.4703 (m-30) REVERT: g 286 GLN cc_start: 0.7189 (tt0) cc_final: 0.6957 (tt0) REVERT: e 9 THR cc_start: 0.8175 (t) cc_final: 0.7708 (m) REVERT: e 21 GLU cc_start: 0.4611 (tt0) cc_final: 0.4205 (tp30) REVERT: e 58 LEU cc_start: 0.5214 (tp) cc_final: 0.4979 (mt) REVERT: e 72 ASN cc_start: 0.6737 (m-40) cc_final: 0.6496 (m110) REVERT: e 110 ARG cc_start: 0.4772 (mtt180) cc_final: 0.4125 (ptp90) outliers start: 3 outliers final: 0 residues processed: 835 average time/residue: 0.1828 time to fit residues: 230.6049 Evaluate side-chains 492 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 490 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain D residue 379 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 256 HIS A 295 HIS A 351 ASN A 389 GLN A 443 ASN B 34 GLN B 187 GLN B 236 GLN B 256 HIS B 415 GLN B 453 GLN C 187 GLN C 201 GLN C 208 GLN C 214 GLN C 389 GLN C 409 ASN D 19 ASN D 112 ASN D 133 HIS D 223 ASN D 345 HIS D 376 GLN D 384 HIS E 25 GLN E 72 ASN E 120 ASN E 188 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 ASN F 45 ASN F 66 GLN F 112 ASN F 133 HIS F 141 GLN F 223 ASN F 238 GLN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS d 170 ASN d 193 GLN g 81 ASN g 243 ASN e 16 ASN e 93 GLN e 111 GLN e 116 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.109904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.093470 restraints weight = 65355.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096266 restraints weight = 31427.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.098040 restraints weight = 18228.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.099216 restraints weight = 12137.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099880 restraints weight = 9023.579| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27877 Z= 0.147 Angle : 0.683 12.092 37787 Z= 0.346 Chirality : 0.046 0.229 4443 Planarity : 0.005 0.055 4907 Dihedral : 8.764 172.993 4050 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.23 % Favored : 95.66 % Rotamer: Outliers : 2.52 % Allowed : 15.66 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.13), residues: 3548 helix: 0.02 (0.12), residues: 1509 sheet: -2.02 (0.19), residues: 585 loop : -1.79 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 355 TYR 0.019 0.002 TYR D 259 PHE 0.020 0.002 PHE A 390 TRP 0.014 0.002 TRP e 57 HIS 0.007 0.001 HIS d 141 Details of bonding type rmsd covalent geometry : bond 0.00324 (27877) covalent geometry : angle 0.68278 (37787) hydrogen bonds : bond 0.04409 ( 1345) hydrogen bonds : angle 4.31540 ( 5940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 569 time to evaluate : 0.861 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: A 121 GLU cc_start: 0.7567 (tp30) cc_final: 0.7293 (tp30) REVERT: A 224 VAL cc_start: 0.8935 (m) cc_final: 0.8712 (p) REVERT: A 405 LYS cc_start: 0.6576 (pttt) cc_final: 0.6305 (ptmt) REVERT: A 422 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7971 (mtmt) REVERT: A 433 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8000 (mp0) REVERT: B 9 ILE cc_start: 0.8072 (mm) cc_final: 0.7226 (mm) REVERT: B 172 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6805 (mtt180) REVERT: B 384 LYS cc_start: 0.8667 (mttt) cc_final: 0.8042 (mtmt) REVERT: C 201 GLN cc_start: 0.6957 (mt0) cc_final: 0.6742 (mt0) REVERT: D 79 MET cc_start: 0.8348 (mmt) cc_final: 0.7903 (mmp) REVERT: D 106 THR cc_start: 0.9067 (p) cc_final: 0.8867 (t) REVERT: D 184 GLU cc_start: 0.6895 (tp30) cc_final: 0.6568 (tp30) REVERT: D 223 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7328 (t0) REVERT: D 362 TYR cc_start: 0.8620 (m-80) cc_final: 0.8120 (m-10) REVERT: D 385 TYR cc_start: 0.8539 (t80) cc_final: 0.8156 (t80) REVERT: D 416 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6934 (mp0) REVERT: E 79 MET cc_start: 0.7937 (mmt) cc_final: 0.7518 (mmt) REVERT: E 146 LEU cc_start: 0.8727 (tp) cc_final: 0.8371 (tt) REVERT: E 247 MET cc_start: 0.7471 (mtm) cc_final: 0.7099 (mtm) REVERT: F 79 MET cc_start: 0.8473 (mmm) cc_final: 0.8190 (mmp) REVERT: F 216 MET cc_start: 0.8205 (mtp) cc_final: 0.7995 (mtp) REVERT: F 248 ARG cc_start: 0.7591 (mmt-90) cc_final: 0.7272 (mmt-90) REVERT: F 354 ARG cc_start: 0.7088 (ttm-80) cc_final: 0.6867 (mtt-85) REVERT: F 361 ILE cc_start: 0.8913 (mp) cc_final: 0.8404 (mp) REVERT: F 374 MET cc_start: 0.8663 (mmp) cc_final: 0.8397 (mmp) REVERT: F 475 TYR cc_start: 0.8240 (t80) cc_final: 0.8002 (t80) REVERT: F 482 GLU cc_start: 0.7859 (mp0) cc_final: 0.7453 (mp0) REVERT: d 196 LYS cc_start: 0.7913 (mmmm) cc_final: 0.7567 (ttpt) REVERT: d 208 ARG cc_start: 0.7931 (ttm170) cc_final: 0.7273 (mtm110) REVERT: g 107 VAL cc_start: 0.7903 (t) cc_final: 0.7697 (t) REVERT: g 163 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7448 (mmmt) REVERT: g 341 TYR cc_start: 0.8603 (t80) cc_final: 0.8320 (t80) REVERT: e 21 GLU cc_start: 0.4659 (tt0) cc_final: 0.3846 (tp30) REVERT: e 58 LEU cc_start: 0.5685 (tp) cc_final: 0.5250 (mt) REVERT: e 63 MET cc_start: 0.4561 (mmt) cc_final: 0.4022 (mmt) REVERT: e 110 ARG cc_start: 0.6022 (mtt180) cc_final: 0.5116 (ptp90) REVERT: e 111 GLN cc_start: 0.7238 (mp10) cc_final: 0.7015 (mp-120) REVERT: e 125 ARG cc_start: 0.7505 (ttm110) cc_final: 0.7186 (ttp80) REVERT: e 127 GLU cc_start: 0.8079 (tt0) cc_final: 0.7744 (pt0) outliers start: 74 outliers final: 39 residues processed: 614 average time/residue: 0.1839 time to fit residues: 173.7279 Evaluate side-chains 494 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 454 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain g residue 93 LEU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 247 VAL Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 363 CYS Chi-restraints excluded: chain e residue 16 ASN Chi-restraints excluded: chain e residue 130 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 156 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 341 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 338 optimal weight: 0.6980 chunk 267 optimal weight: 2.9990 chunk 216 optimal weight: 0.3980 chunk 277 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 398 GLN C 256 HIS ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN F 45 ASN F 57 GLN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN g 134 ASN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 16 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.091787 restraints weight = 65769.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.094517 restraints weight = 31553.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.096264 restraints weight = 18309.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097410 restraints weight = 12163.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098077 restraints weight = 9037.813| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27877 Z= 0.150 Angle : 0.648 10.729 37787 Z= 0.326 Chirality : 0.045 0.288 4443 Planarity : 0.004 0.060 4907 Dihedral : 8.168 162.685 4045 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.49 % Rotamer: Outliers : 3.30 % Allowed : 17.98 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 3548 helix: 0.70 (0.13), residues: 1519 sheet: -1.62 (0.20), residues: 601 loop : -1.51 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 378 TYR 0.018 0.001 TYR D 259 PHE 0.038 0.001 PHE A 390 TRP 0.015 0.003 TRP e 15 HIS 0.003 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.00335 (27877) covalent geometry : angle 0.64757 (37787) hydrogen bonds : bond 0.04000 ( 1345) hydrogen bonds : angle 3.96445 ( 5940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 501 time to evaluate : 1.155 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: A 121 GLU cc_start: 0.7576 (tp30) cc_final: 0.7319 (tp30) REVERT: A 171 ASP cc_start: 0.7718 (t0) cc_final: 0.7420 (t0) REVERT: A 224 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8670 (p) REVERT: A 355 ARG cc_start: 0.7721 (mtt90) cc_final: 0.7398 (mtt90) REVERT: A 405 LYS cc_start: 0.6479 (pttt) cc_final: 0.6173 (ptmt) REVERT: A 433 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8075 (mp0) REVERT: B 70 ASN cc_start: 0.7960 (OUTLIER) cc_final: 0.7733 (t0) REVERT: B 384 LYS cc_start: 0.8674 (mttt) cc_final: 0.8189 (mtmt) REVERT: B 387 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8361 (mm) REVERT: C 398 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: D 79 MET cc_start: 0.8521 (mmt) cc_final: 0.8124 (mmp) REVERT: D 204 GLU cc_start: 0.6454 (tp30) cc_final: 0.6186 (tp30) REVERT: D 259 TYR cc_start: 0.8699 (t80) cc_final: 0.8405 (t80) REVERT: D 362 TYR cc_start: 0.8651 (m-80) cc_final: 0.8255 (m-10) REVERT: E 79 MET cc_start: 0.7994 (mmt) cc_final: 0.7552 (mmt) REVERT: E 214 MET cc_start: 0.8053 (mmm) cc_final: 0.7717 (mmm) REVERT: E 247 MET cc_start: 0.7329 (mtm) cc_final: 0.6968 (mtm) REVERT: E 258 GLU cc_start: 0.8089 (tt0) cc_final: 0.7775 (tp30) REVERT: E 369 ASP cc_start: 0.6242 (t0) cc_final: 0.5988 (t0) REVERT: E 374 MET cc_start: 0.8455 (mmm) cc_final: 0.8077 (mmm) REVERT: E 403 ASP cc_start: 0.7015 (t70) cc_final: 0.6773 (p0) REVERT: F 79 MET cc_start: 0.8226 (mmm) cc_final: 0.7973 (mpp) REVERT: F 354 ARG cc_start: 0.7092 (ttm-80) cc_final: 0.6702 (mtt-85) REVERT: F 379 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8814 (mt) REVERT: d 196 LYS cc_start: 0.7814 (mmmm) cc_final: 0.7556 (ttpt) REVERT: d 208 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7294 (mtm110) REVERT: g 47 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8352 (mt) REVERT: g 53 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8184 (t) REVERT: g 103 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.6062 (pm20) REVERT: g 107 VAL cc_start: 0.7916 (t) cc_final: 0.7684 (t) REVERT: g 127 ARG cc_start: 0.7014 (mmm160) cc_final: 0.6677 (mmt180) REVERT: g 192 GLN cc_start: 0.8663 (tp40) cc_final: 0.8303 (tp-100) REVERT: g 224 ASP cc_start: 0.8475 (t0) cc_final: 0.8248 (m-30) REVERT: g 341 TYR cc_start: 0.8581 (t80) cc_final: 0.8365 (t80) REVERT: e 7 VAL cc_start: 0.6401 (OUTLIER) cc_final: 0.6075 (m) REVERT: e 58 LEU cc_start: 0.5829 (tp) cc_final: 0.5365 (mt) REVERT: e 68 ARG cc_start: 0.5454 (ttt90) cc_final: 0.4289 (tpt170) REVERT: e 110 ARG cc_start: 0.5784 (mtt180) cc_final: 0.4839 (ptp90) REVERT: e 111 GLN cc_start: 0.7266 (mp10) cc_final: 0.7022 (mp-120) REVERT: e 125 ARG cc_start: 0.7440 (ttm110) cc_final: 0.7239 (ttp80) outliers start: 97 outliers final: 46 residues processed: 565 average time/residue: 0.1639 time to fit residues: 144.6201 Evaluate side-chains 489 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 434 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 398 GLN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 441 PHE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 53 SER Chi-restraints excluded: chain g residue 103 GLU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 247 VAL Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 363 CYS Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 130 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 209 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 230 optimal weight: 0.9990 chunk 316 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 257 optimal weight: 0.4980 chunk 203 optimal weight: 3.9990 chunk 320 optimal weight: 4.9990 chunk 325 optimal weight: 0.6980 chunk 290 optimal weight: 0.4980 chunk 104 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS B 84 GLN B 97 GLN B 473 GLN C 208 GLN D 223 ASN E 325 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.092046 restraints weight = 64886.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.094754 restraints weight = 31027.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096526 restraints weight = 18055.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097678 restraints weight = 11995.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098391 restraints weight = 8912.646| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27877 Z= 0.128 Angle : 0.629 9.709 37787 Z= 0.314 Chirality : 0.044 0.331 4443 Planarity : 0.004 0.058 4907 Dihedral : 7.748 151.949 4045 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 3.54 % Allowed : 19.24 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.14), residues: 3548 helix: 1.04 (0.13), residues: 1518 sheet: -1.45 (0.20), residues: 593 loop : -1.30 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG e 52 TYR 0.036 0.001 TYR F 259 PHE 0.031 0.001 PHE A 390 TRP 0.014 0.002 TRP e 57 HIS 0.003 0.001 HIS F 345 Details of bonding type rmsd covalent geometry : bond 0.00285 (27877) covalent geometry : angle 0.62935 (37787) hydrogen bonds : bond 0.03715 ( 1345) hydrogen bonds : angle 3.78589 ( 5940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 497 time to evaluate : 0.662 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: A 68 GLU cc_start: 0.7864 (tp30) cc_final: 0.7534 (mm-30) REVERT: A 121 GLU cc_start: 0.7590 (tp30) cc_final: 0.7370 (tp30) REVERT: A 171 ASP cc_start: 0.7788 (t0) cc_final: 0.7525 (t0) REVERT: A 201 GLN cc_start: 0.7576 (mm110) cc_final: 0.7344 (mm110) REVERT: A 224 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8678 (p) REVERT: A 405 LYS cc_start: 0.6488 (pttt) cc_final: 0.6163 (ptmt) REVERT: B 384 LYS cc_start: 0.8725 (mttt) cc_final: 0.8216 (mtmt) REVERT: B 394 GLU cc_start: 0.6530 (pm20) cc_final: 0.6213 (pm20) REVERT: C 398 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: D 40 MET cc_start: 0.7360 (tpp) cc_final: 0.7160 (tpp) REVERT: D 223 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7365 (t0) REVERT: D 259 TYR cc_start: 0.8674 (t80) cc_final: 0.8413 (t80) REVERT: D 362 TYR cc_start: 0.8700 (m-80) cc_final: 0.8342 (m-10) REVERT: E 79 MET cc_start: 0.8089 (mmt) cc_final: 0.7636 (mmt) REVERT: E 208 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7137 (mt-10) REVERT: E 214 MET cc_start: 0.8049 (mmm) cc_final: 0.7771 (mmm) REVERT: E 258 GLU cc_start: 0.8059 (tt0) cc_final: 0.7758 (tp30) REVERT: E 408 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7914 (tp) REVERT: F 79 MET cc_start: 0.8137 (mmm) cc_final: 0.7830 (mpp) REVERT: F 374 MET cc_start: 0.8257 (mmp) cc_final: 0.7716 (mmp) REVERT: F 488 MET cc_start: 0.7538 (mmm) cc_final: 0.6719 (tmm) REVERT: d 113 TYR cc_start: 0.7928 (t80) cc_final: 0.7666 (t80) REVERT: d 150 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8055 (pt) REVERT: d 196 LYS cc_start: 0.7766 (mmmm) cc_final: 0.7547 (ttpt) REVERT: d 208 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7310 (mtm110) REVERT: d 243 GLU cc_start: 0.7480 (pt0) cc_final: 0.7124 (pt0) REVERT: g 103 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6105 (pm20) REVERT: g 107 VAL cc_start: 0.7963 (t) cc_final: 0.7700 (t) REVERT: g 192 GLN cc_start: 0.8609 (tp40) cc_final: 0.8269 (tp-100) REVERT: g 224 ASP cc_start: 0.8425 (t0) cc_final: 0.8202 (m-30) REVERT: g 286 GLN cc_start: 0.6798 (tt0) cc_final: 0.6509 (tt0) REVERT: g 341 TYR cc_start: 0.8620 (t80) cc_final: 0.8405 (t80) REVERT: e 58 LEU cc_start: 0.6227 (tp) cc_final: 0.5642 (mt) REVERT: e 63 MET cc_start: 0.4548 (mmt) cc_final: 0.4285 (mmt) REVERT: e 110 ARG cc_start: 0.5779 (mtt180) cc_final: 0.4773 (ptp90) outliers start: 104 outliers final: 45 residues processed: 565 average time/residue: 0.1721 time to fit residues: 150.2522 Evaluate side-chains 469 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 418 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 398 GLN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 103 GLU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 226 VAL Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 363 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 157 optimal weight: 0.2980 chunk 152 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS D 223 ASN E 112 ASN E 325 GLN e 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.106976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.090531 restraints weight = 65539.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.093220 restraints weight = 31622.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094961 restraints weight = 18504.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.096062 restraints weight = 12382.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.096834 restraints weight = 9294.387| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27877 Z= 0.149 Angle : 0.642 9.789 37787 Z= 0.319 Chirality : 0.044 0.293 4443 Planarity : 0.004 0.058 4907 Dihedral : 7.565 138.055 4045 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 3.81 % Allowed : 19.95 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.14), residues: 3548 helix: 1.19 (0.13), residues: 1516 sheet: -1.33 (0.20), residues: 605 loop : -1.17 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 355 TYR 0.034 0.001 TYR F 259 PHE 0.029 0.001 PHE A 390 TRP 0.018 0.003 TRP e 15 HIS 0.003 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.00336 (27877) covalent geometry : angle 0.64232 (37787) hydrogen bonds : bond 0.03743 ( 1345) hydrogen bonds : angle 3.75763 ( 5940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 464 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8689 (p) REVERT: A 405 LYS cc_start: 0.6695 (pttt) cc_final: 0.6306 (ptmt) REVERT: B 384 LYS cc_start: 0.8773 (mttt) cc_final: 0.8247 (mtmt) REVERT: B 387 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8417 (mm) REVERT: C 65 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8304 (mm) REVERT: D 259 TYR cc_start: 0.8679 (t80) cc_final: 0.8423 (t80) REVERT: D 292 MET cc_start: 0.8226 (ttm) cc_final: 0.8015 (ttm) REVERT: D 362 TYR cc_start: 0.8750 (m-80) cc_final: 0.8446 (m-80) REVERT: E 79 MET cc_start: 0.8098 (mmt) cc_final: 0.7716 (mmt) REVERT: E 208 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7107 (mt-10) REVERT: E 214 MET cc_start: 0.8130 (mmm) cc_final: 0.7891 (mmm) REVERT: E 247 MET cc_start: 0.7381 (mtp) cc_final: 0.7080 (mtm) REVERT: E 261 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8536 (ptt90) REVERT: F 79 MET cc_start: 0.8171 (mmm) cc_final: 0.7935 (mpp) REVERT: F 145 LYS cc_start: 0.6345 (pttp) cc_final: 0.6107 (pttp) REVERT: F 333 ASP cc_start: 0.7503 (m-30) cc_final: 0.7199 (m-30) REVERT: F 379 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8805 (mt) REVERT: F 488 MET cc_start: 0.7565 (mmm) cc_final: 0.6813 (tmm) REVERT: d 113 TYR cc_start: 0.7963 (t80) cc_final: 0.7620 (t80) REVERT: d 150 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8204 (pt) REVERT: d 196 LYS cc_start: 0.7708 (mmmm) cc_final: 0.7487 (ttpt) REVERT: d 208 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7267 (mtm110) REVERT: d 239 LYS cc_start: 0.5762 (ptpp) cc_final: 0.5111 (ptpp) REVERT: d 243 GLU cc_start: 0.7543 (pt0) cc_final: 0.7175 (pt0) REVERT: g 103 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6244 (pm20) REVERT: g 107 VAL cc_start: 0.8000 (t) cc_final: 0.7744 (t) REVERT: g 192 GLN cc_start: 0.8654 (tp40) cc_final: 0.8167 (tp-100) REVERT: g 224 ASP cc_start: 0.8417 (t0) cc_final: 0.8184 (m-30) REVERT: g 286 GLN cc_start: 0.6761 (tt0) cc_final: 0.6474 (tt0) REVERT: e 58 LEU cc_start: 0.6225 (tp) cc_final: 0.5350 (mt) REVERT: e 68 ARG cc_start: 0.5456 (ttt90) cc_final: 0.4459 (tpt170) REVERT: e 110 ARG cc_start: 0.5649 (mtt180) cc_final: 0.4625 (ptp90) outliers start: 112 outliers final: 60 residues processed: 537 average time/residue: 0.1716 time to fit residues: 142.4414 Evaluate side-chains 493 residues out of total 2937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 426 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 325 GLN Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 151 ASP Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 222 THR Chi-restraints excluded: chain g residue 103 GLU Chi-restraints excluded: chain g residue 112 ILE Chi-restraints excluded: chain g residue 122 VAL Chi-restraints excluded: chain g residue 226 VAL Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 363 CYS Chi-restraints excluded: chain e residue 20 LYS Chi-restraints excluded: chain e residue 130 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5887 > 50: distance: 27 - 50: 4.679 distance: 32 - 59: 6.968 distance: 36 - 41: 3.229 distance: 37 - 67: 3.557 distance: 42 - 45: 5.556 distance: 43 - 44: 9.441 distance: 43 - 50: 3.636 distance: 46 - 47: 6.827 distance: 47 - 48: 9.246 distance: 47 - 49: 4.679 distance: 51 - 52: 4.432 distance: 51 - 54: 4.292 distance: 52 - 53: 3.446 distance: 52 - 59: 4.707 distance: 53 - 86: 9.675 distance: 57 - 58: 10.187 distance: 60 - 61: 3.734 distance: 60 - 63: 3.560 distance: 61 - 62: 4.268 distance: 62 - 94: 7.677 distance: 63 - 64: 5.217 distance: 64 - 65: 5.919 distance: 64 - 66: 5.503 distance: 67 - 68: 4.670 distance: 68 - 69: 9.621 distance: 68 - 71: 6.407 distance: 69 - 70: 10.232 distance: 70 - 105: 20.917 distance: 71 - 73: 3.688 distance: 72 - 74: 7.657 distance: 75 - 76: 3.191 distance: 76 - 77: 4.644 distance: 77 - 78: 10.995 distance: 77 - 86: 8.376 distance: 79 - 80: 4.892 distance: 80 - 81: 4.298 distance: 81 - 82: 6.090 distance: 83 - 84: 13.420 distance: 83 - 85: 4.119 distance: 86 - 87: 7.653 distance: 87 - 88: 3.930 distance: 87 - 90: 5.415 distance: 88 - 89: 8.311 distance: 88 - 94: 5.056 distance: 90 - 91: 16.031 distance: 90 - 92: 6.726 distance: 91 - 93: 19.962 distance: 95 - 96: 8.880 distance: 95 - 98: 6.872 distance: 96 - 97: 17.501 distance: 96 - 105: 24.523 distance: 98 - 99: 4.306 distance: 99 - 100: 8.019 distance: 99 - 101: 9.029 distance: 100 - 102: 10.170 distance: 101 - 103: 8.832 distance: 102 - 104: 6.547 distance: 103 - 104: 4.501 distance: 105 - 106: 31.934 distance: 106 - 107: 8.980 distance: 106 - 109: 17.627 distance: 107 - 108: 14.176 distance: 107 - 111: 5.648 distance: 109 - 110: 31.828 distance: 111 - 112: 4.665 distance: 112 - 115: 5.145 distance: 113 - 120: 6.708 distance: 114 - 143: 3.288 distance: 116 - 117: 3.149 distance: 117 - 118: 3.308 distance: 117 - 119: 3.911 distance: 120 - 121: 6.470 distance: 121 - 124: 3.593 distance: 122 - 123: 4.079 distance: 123 - 151: 7.350 distance: 125 - 126: 6.123 distance: 126 - 127: 5.591 distance: 126 - 128: 4.733