Starting phenix.real_space_refine (version: dev) on Fri May 13 22:38:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/05_2022/6z1r_11039_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/05_2022/6z1r_11039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/05_2022/6z1r_11039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/05_2022/6z1r_11039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/05_2022/6z1r_11039_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/05_2022/6z1r_11039_trim_updated.pdb" } resolution = 3.29 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 ------------------------------------------------------------------------------- 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 65754 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 7521 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'CIS': 1, 'TRANS': 467, 'PCIS': 1} Chain: "B" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 7658 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 16, 'CIS': 1, 'TRANS': 476, 'PCIS': 1} Chain breaks: 1 Chain: "C" Number of atoms: 7742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 7742 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'CIS': 1, 'TRANS': 482, 'PCIS': 1} Chain breaks: 1 Chain: "D" Number of atoms: 7163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7163 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'CIS': 1, 'TRANS': 444, 'PCIS': 1} Chain: "E" Number of atoms: 7132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7132 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 22, 'CIS': 1, 'TRANS': 442, 'PCIS': 1} Chain: "F" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7131 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 22, 'CIS': 1, 'TRANS': 442, 'PCIS': 1} Chain: "G" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4300 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1957 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 764 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 731 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3004 Classifications: {'peptide': 188} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "b" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1247 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "h" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 711 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 21.79, per 1000 atoms: 0.33 Number of scatterers: 65754 At special positions: 0 Unit cell: (143.576, 129.952, 237.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 120 16.00 P 15 15.00 Mg 5 11.99 O 6223 8.00 N 5593 7.00 C 20661 6.00 H 33137 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.52 Conformation dependent library (CDL) restraints added in 4.7 seconds 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 154 helices and 23 sheets defined 49.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.562A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 240 through 260 Proline residue: A 247 - end of helix removed outlier: 4.012A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.704A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 375 through 378 removed outlier: 3.522A pdb=" N ALA A 378 " --> pdb=" O GLY A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 375 through 378' Processing helix chain 'A' and resid 381 through 399 removed outlier: 4.571A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 405 removed outlier: 3.712A pdb=" N GLN A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 402 through 405' Processing helix chain 'A' and resid 412 through 427 removed outlier: 3.778A pdb=" N VAL A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 458 through 475 removed outlier: 4.416A pdb=" N THR A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 469 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 475 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.683A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 240 through 260 removed outlier: 3.698A pdb=" N LEU B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Proline residue: B 247 - end of helix removed outlier: 4.172A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.710A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.501A pdb=" N TYR B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 358' Processing helix chain 'B' and resid 381 through 400 removed outlier: 4.213A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 475 removed outlier: 4.351A pdb=" N THR B 462 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE B 464 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE B 473 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 475 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'B' and resid 491 through 506 Processing helix chain 'C' and resid 9 through 16 removed outlier: 3.981A pdb=" N GLU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.652A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 240 through 260 Proline residue: C 247 - end of helix removed outlier: 3.873A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 284 removed outlier: 3.621A pdb=" N VAL C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 300 through 308 removed outlier: 3.847A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 397 removed outlier: 3.913A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 427 Processing helix chain 'C' and resid 438 through 450 Processing helix chain 'C' and resid 458 through 475 removed outlier: 4.287A pdb=" N THR C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN C 466 " --> pdb=" O THR C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 180 removed outlier: 3.704A pdb=" N LYS D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 180 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 230 through 233 No H-bonds generated for 'chain 'D' and resid 230 through 233' Processing helix chain 'D' and resid 236 through 249 Processing helix chain 'D' and resid 264 through 276 removed outlier: 3.843A pdb=" N GLY D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 297 removed outlier: 4.188A pdb=" N MET D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 319 No H-bonds generated for 'chain 'D' and resid 317 through 319' Processing helix chain 'D' and resid 324 through 332 removed outlier: 4.525A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N HIS D 332 " --> pdb=" O THR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 369 through 395 removed outlier: 3.993A pdb=" N ASP D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 418 Processing helix chain 'D' and resid 426 through 429 No H-bonds generated for 'chain 'D' and resid 426 through 429' Processing helix chain 'D' and resid 438 through 450 Processing helix chain 'D' and resid 458 through 461 Processing helix chain 'D' and resid 467 through 480 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 166 through 180 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 230 through 233 No H-bonds generated for 'chain 'E' and resid 230 through 233' Processing helix chain 'E' and resid 236 through 249 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 289 through 297 removed outlier: 3.769A pdb=" N MET E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 341 through 344 No H-bonds generated for 'chain 'E' and resid 341 through 344' Processing helix chain 'E' and resid 364 through 367 No H-bonds generated for 'chain 'E' and resid 364 through 367' Processing helix chain 'E' and resid 369 through 394 removed outlier: 3.955A pdb=" N ASP E 390 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE E 391 " --> pdb=" O SER E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 399 No H-bonds generated for 'chain 'E' and resid 397 through 399' Processing helix chain 'E' and resid 402 through 418 Processing helix chain 'E' and resid 426 through 429 No H-bonds generated for 'chain 'E' and resid 426 through 429' Processing helix chain 'E' and resid 438 through 450 Processing helix chain 'E' and resid 458 through 460 No H-bonds generated for 'chain 'E' and resid 458 through 460' Processing helix chain 'E' and resid 467 through 478 removed outlier: 3.688A pdb=" N ALA E 478 " --> pdb=" O ALA E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 180 removed outlier: 3.609A pdb=" N ALA F 180 " --> pdb=" O ASN F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 205 Processing helix chain 'F' and resid 230 through 233 No H-bonds generated for 'chain 'F' and resid 230 through 233' Processing helix chain 'F' and resid 236 through 249 removed outlier: 3.732A pdb=" N PHE F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 271 Processing helix chain 'F' and resid 289 through 297 removed outlier: 3.593A pdb=" N MET F 296 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 324 through 331 removed outlier: 4.771A pdb=" N ALA F 331 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 346 removed outlier: 3.640A pdb=" N LEU F 346 " --> pdb=" O ALA F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 395 removed outlier: 4.231A pdb=" N ASP F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE F 391 " --> pdb=" O SER F 387 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE F 394 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing helix chain 'F' and resid 402 through 418 Processing helix chain 'F' and resid 426 through 429 No H-bonds generated for 'chain 'F' and resid 426 through 429' Processing helix chain 'F' and resid 438 through 450 Processing helix chain 'F' and resid 458 through 461 Processing helix chain 'F' and resid 467 through 478 Processing helix chain 'G' and resid 3 through 54 removed outlier: 4.069A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.535A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 99 removed outlier: 4.114A pdb=" N ALA G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 116 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 181 through 186 removed outlier: 3.504A pdb=" N SER G 186 " --> pdb=" O ASP G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 192 removed outlier: 4.075A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 270 removed outlier: 3.947A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 105 through 120 removed outlier: 4.011A pdb=" N LEU H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 11 through 24 Processing helix chain 'I' and resid 28 through 34 removed outlier: 4.224A pdb=" N ALA I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 18 Processing helix chain 'J' and resid 21 through 51 Processing helix chain 'K' and resid 2 through 38 removed outlier: 4.373A pdb=" N PHE K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLY K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL K 18 " --> pdb=" O ALA K 14 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY K 20 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 73 removed outlier: 5.277A pdb=" N ILE K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 38 removed outlier: 4.352A pdb=" N GLY L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA L 19 " --> pdb=" O THR L 15 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY L 20 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 73 removed outlier: 3.963A pdb=" N CYS L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 38 removed outlier: 4.059A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 73 Processing helix chain 'N' and resid 2 through 38 removed outlier: 3.711A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA N 19 " --> pdb=" O THR N 15 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY N 20 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 73 removed outlier: 3.761A pdb=" N TYR N 49 " --> pdb=" O GLN N 45 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY N 61 " --> pdb=" O SER N 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 38 removed outlier: 4.191A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 72 removed outlier: 5.231A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY O 61 " --> pdb=" O SER O 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 14 Processing helix chain 'P' and resid 16 through 38 removed outlier: 4.108A pdb=" N ILE P 25 " --> pdb=" O GLY P 22 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 73 removed outlier: 3.721A pdb=" N SER P 48 " --> pdb=" O GLN P 45 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU P 56 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA P 59 " --> pdb=" O LEU P 56 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET P 60 " --> pdb=" O SER P 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 38 removed outlier: 3.620A pdb=" N THR Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 73 removed outlier: 3.963A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY Q 61 " --> pdb=" O SER Q 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 38 removed outlier: 4.211A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 73 removed outlier: 5.403A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY R 61 " --> pdb=" O SER R 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 27 Processing helix chain 'S' and resid 32 through 46 removed outlier: 3.775A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 56 removed outlier: 3.642A pdb=" N LEU S 56 " --> pdb=" O ALA S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 74 Processing helix chain 'S' and resid 80 through 92 Processing helix chain 'S' and resid 95 through 113 Proline residue: S 99 - end of helix removed outlier: 3.768A pdb=" N ILE S 102 " --> pdb=" O PRO S 99 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER S 103 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL S 111 " --> pdb=" O MET S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 141 removed outlier: 3.810A pdb=" N SER S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE S 141 " --> pdb=" O VAL S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 187 Processing helix chain 'b' and resid 139 through 184 removed outlier: 3.517A pdb=" N TYR b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN b 183 " --> pdb=" O LYS b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 208 Processing helix chain 'h' and resid 10 through 24 removed outlier: 3.814A pdb=" N THR h 24 " --> pdb=" O THR h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 49 Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.798A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 349 through 352 removed outlier: 7.251A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 229 through 234 removed outlier: 7.057A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.712A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.002A pdb=" N ALA B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 350 through 352 removed outlier: 8.069A pdb=" N GLU B 165 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA B 323 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE B 167 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N GLY B 169 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE B 327 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR B 268 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR B 200 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE B 267 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE B 202 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ASP B 269 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 204 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 230 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA B 205 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 232 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 29 through 35 removed outlier: 6.734A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.028A pdb=" N ALA C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 350 through 352 removed outlier: 8.283A pdb=" N GLU C 165 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA C 323 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE C 167 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY C 169 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE C 327 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 268 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 16 through 21 removed outlier: 6.554A pdb=" N ASP D 26 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL D 20 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.133A pdb=" N GLN D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 156 through 160 removed outlier: 3.933A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 14 through 16 removed outlier: 6.198A pdb=" N GLN E 28 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE E 17 " --> pdb=" O GLN E 28 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 87 through 89 Processing sheet with id= P, first strand: chain 'E' and resid 335 through 338 removed outlier: 8.299A pdb=" N ILE E 156 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER E 310 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU E 158 " --> pdb=" O SER E 310 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN E 312 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 14 through 16 removed outlier: 4.337A pdb=" N LYS F 78 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS F 56 " --> pdb=" O THR F 61 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN F 28 " --> pdb=" O ILE F 17 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE F 17 " --> pdb=" O GLN F 28 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 87 through 90 removed outlier: 4.565A pdb=" N GLN F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 335 through 338 removed outlier: 6.811A pdb=" N TYR F 184 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N PHE F 258 " --> pdb=" O TYR F 184 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL F 186 " --> pdb=" O PHE F 258 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 172 through 178 removed outlier: 5.344A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY G 107 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR G 127 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 17 through 22 removed outlier: 3.600A pdb=" N ALA H 94 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 45 through 47 removed outlier: 7.025A pdb=" N HIS H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL H 36 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL H 38 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'S' and resid 152 through 154 removed outlier: 8.035A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) 1590 hydrogen bonds defined for protein. 4398 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: 23.97 Time building geometry restraints manager: 42.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 33119 1.03 - 1.22: 76 1.22 - 1.42: 13112 1.42 - 1.61: 19685 1.61 - 1.81: 222 Bond restraints: 66214 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.57e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.23e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.79e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.68e+01 ... (remaining 66209 not shown) Histogram of bond angle deviations from ideal: 96.84 - 104.74: 491 104.74 - 112.65: 79472 112.65 - 120.56: 24245 120.56 - 128.47: 15692 128.47 - 136.38: 145 Bond angle restraints: 120045 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.35 23.52 1.00e+00 1.00e+00 5.53e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.49 23.38 1.00e+00 1.00e+00 5.47e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 121.57 18.30 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 119.64 17.19 1.00e+00 1.00e+00 2.96e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 119.65 17.18 1.00e+00 1.00e+00 2.95e+02 ... (remaining 120040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.52: 24023 20.52 - 41.03: 1717 41.03 - 61.55: 209 61.55 - 82.06: 56 82.06 - 102.58: 20 Dihedral angle restraints: 26025 sinusoidal: 12401 harmonic: 13624 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -162.58 102.58 1 2.00e+01 2.50e-03 2.92e+01 dihedral pdb=" C5' ADP F 600 " pdb=" O5' ADP F 600 " pdb=" PA ADP F 600 " pdb=" O2A ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 -153.71 93.71 1 2.00e+01 2.50e-03 2.56e+01 dihedral pdb=" O2A ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PA ADP D 600 " pdb=" PB ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 -148.31 88.31 1 2.00e+01 2.50e-03 2.33e+01 ... (remaining 26022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3880 0.048 - 0.095: 1075 0.095 - 0.143: 253 0.143 - 0.191: 10 0.191 - 0.239: 1 Chirality restraints: 5219 Sorted by residual: chirality pdb=" CG LEU R 56 " pdb=" CB LEU R 56 " pdb=" CD1 LEU R 56 " pdb=" CD2 LEU R 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.50 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 5216 not shown) Planarity restraints: 9831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 59 " 0.040 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO G 60 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU S 48 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO S 49 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO S 49 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 49 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 88 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO F 89 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 89 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 89 " 0.026 5.00e-02 4.00e+02 ... (remaining 9828 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1980 2.13 - 2.74: 126508 2.74 - 3.36: 192691 3.36 - 3.98: 251587 3.98 - 4.60: 401732 Nonbonded interactions: 974498 Sorted by model distance: nonbonded pdb=" H ARG B 210 " pdb=" OE2 GLU E 298 " model vdw 1.507 1.850 nonbonded pdb="HH22 ARG B 139 " pdb=" O GLU B 307 " model vdw 1.538 1.850 nonbonded pdb=" OD1 ASP G 194 " pdb="HH21 ARG L 38 " model vdw 1.539 1.850 nonbonded pdb=" OD1 ASP F 363 " pdb=" H ASN F 365 " model vdw 1.552 1.850 nonbonded pdb=" OD1 ASP C 109 " pdb=" H ALA C 110 " model vdw 1.553 1.850 ... (remaining 974493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 403 or (resid 411 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name H \ B2 or name HB3)) or resid 412 through 470 or (resid 471 and (name N or name CA o \ r name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) \ or resid 472 through 508 or resid 600 through 601)) selection = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 403 or (resid \ 411 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2 or name HA or name HB2 or name HB3)) or resid 412 through 470 or (r \ esid 471 and (name N or name CA or name C or name O or name CB or name CG or nam \ e ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or na \ me HB3 or name HD2 or name HE1)) or resid 472 through 508 or resid 600 through 6 \ 01)) selection = (chain 'C' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 470 or (resid \ 471 and (name N or name CA or name C or name O or name CB or name CG or name ND1 \ or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB \ 3 or name HD2 or name HE1)) or resid 472 through 508 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 13 through 479) selection = (chain 'E' and (resid 13 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 479)) selection = (chain 'F' and resid 13 through 479) } ncs_group { reference = chain 'K' selection = (chain 'L' and resid 1 through 74) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 120 5.16 5 C 20661 2.51 5 N 5593 2.21 5 O 6223 1.98 5 H 33137 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 7.290 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: 0.740 Extract box with map and model: 28.530 Check model and map are aligned: 0.710 Convert atoms to be neutral: 0.420 Process input model: 156.200 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 199.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 : 0.007 0.075 33077 Z= 0.465 Angle : 0.706 23.519 44726 Z= 0.438 Chirality : 0.044 0.239 5219 Planarity : 0.004 0.058 5731 Dihedral : 15.062 102.577 12225 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 4208 helix: 0.13 (0.11), residues: 2068 sheet: -1.72 (0.22), residues: 564 loop : -1.68 (0.15), residues: 1576 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 484 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 3.911 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 outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.8773 time to fit residues: 675.8837 Evaluate side-chains 420 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 3.868 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 352 optimal weight: 6.9990 chunk 316 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 108 optimal weight: 0.0040 chunk 213 optimal weight: 1.9990 chunk 169 optimal weight: 0.3980 chunk 327 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 379 optimal weight: 4.9990 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 432 GLN B 208 GLN C 349 GLN ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 33077 Z= 0.255 Angle : 0.551 9.495 44726 Z= 0.281 Chirality : 0.041 0.153 5219 Planarity : 0.003 0.044 5731 Dihedral : 5.813 84.198 4673 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4208 helix: 0.50 (0.12), residues: 2077 sheet: -1.53 (0.22), residues: 580 loop : -1.47 (0.16), residues: 1551 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 462 time to evaluate : 3.980 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 outliers start: 14 outliers final: 11 residues processed: 467 average time/residue: 0.8764 time to fit residues: 657.9563 Evaluate side-chains 442 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 431 time to evaluate : 3.862 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5938 time to fit residues: 17.1144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 210 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 315 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 380 optimal weight: 8.9990 chunk 410 optimal weight: 5.9990 chunk 338 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 305 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 GLN ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 33077 Z= 0.290 Angle : 0.550 10.397 44726 Z= 0.280 Chirality : 0.041 0.156 5219 Planarity : 0.003 0.058 5731 Dihedral : 5.653 74.509 4673 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4208 helix: 0.65 (0.12), residues: 2072 sheet: -1.42 (0.22), residues: 574 loop : -1.38 (0.16), residues: 1562 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 458 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 446 time to evaluate : 3.921 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 outliers start: 12 outliers final: 8 residues processed: 449 average time/residue: 0.8441 time to fit residues: 604.4709 Evaluate side-chains 438 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 430 time to evaluate : 3.890 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6440 time to fit residues: 13.9844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 375 optimal weight: 8.9990 chunk 285 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 381 optimal weight: 10.0000 chunk 404 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 361 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 33077 Z= 0.360 Angle : 0.563 9.853 44726 Z= 0.287 Chirality : 0.042 0.155 5219 Planarity : 0.004 0.042 5731 Dihedral : 5.626 72.547 4673 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 4208 helix: 0.69 (0.12), residues: 2072 sheet: -1.38 (0.22), residues: 577 loop : -1.37 (0.16), residues: 1559 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 442 time to evaluate : 3.948 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 outliers start: 13 outliers final: 8 residues processed: 447 average time/residue: 0.8666 time to fit residues: 627.0292 Evaluate side-chains 436 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 428 time to evaluate : 3.874 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6053 time to fit residues: 13.7339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 336 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 300 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 344 optimal weight: 5.9990 chunk 279 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 362 optimal weight: 10.0000 chunk 101 optimal weight: 0.0870 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 33077 Z= 0.259 Angle : 0.530 8.859 44726 Z= 0.268 Chirality : 0.041 0.155 5219 Planarity : 0.003 0.041 5731 Dihedral : 5.402 69.403 4673 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 4208 helix: 0.91 (0.12), residues: 2072 sheet: -1.28 (0.23), residues: 571 loop : -1.23 (0.16), residues: 1565 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 458 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 447 time to evaluate : 3.878 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 outliers start: 11 outliers final: 8 residues processed: 450 average time/residue: 0.8542 time to fit residues: 616.4108 Evaluate side-chains 436 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 428 time to evaluate : 3.896 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.6477 time to fit residues: 14.0045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 135 optimal weight: 2.9990 chunk 363 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 404 optimal weight: 0.0020 chunk 335 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 133 optimal weight: 0.0050 chunk 212 optimal weight: 1.9990 overall best weight: 1.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 33077 Z= 0.235 Angle : 0.522 8.663 44726 Z= 0.262 Chirality : 0.041 0.154 5219 Planarity : 0.003 0.042 5731 Dihedral : 5.252 66.280 4673 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 4208 helix: 1.04 (0.12), residues: 2068 sheet: -1.20 (0.23), residues: 559 loop : -1.15 (0.16), residues: 1581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 460 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 450 time to evaluate : 3.966 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 outliers start: 10 outliers final: 4 residues processed: 457 average time/residue: 0.8705 time to fit residues: 636.2142 Evaluate side-chains 441 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 437 time to evaluate : 3.917 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.5892 time to fit residues: 9.2111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 389 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 340 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 402 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 chunk 245 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 33077 Z= 0.251 Angle : 0.524 8.746 44726 Z= 0.263 Chirality : 0.041 0.153 5219 Planarity : 0.003 0.041 5731 Dihedral : 5.216 64.275 4673 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 4208 helix: 1.07 (0.12), residues: 2075 sheet: -1.17 (0.23), residues: 570 loop : -1.16 (0.16), residues: 1563 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 460 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 450 time to evaluate : 3.931 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 outliers start: 10 outliers final: 8 residues processed: 453 average time/residue: 0.8661 time to fit residues: 628.3604 Evaluate side-chains 442 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 434 time to evaluate : 3.871 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.6265 time to fit residues: 13.8549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 249 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 33077 Z= 0.229 Angle : 0.519 8.947 44726 Z= 0.260 Chirality : 0.041 0.152 5219 Planarity : 0.003 0.066 5731 Dihedral : 5.143 62.244 4673 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 4208 helix: 1.16 (0.12), residues: 2082 sheet: -1.12 (0.23), residues: 570 loop : -1.11 (0.16), residues: 1556 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 449 time to evaluate : 3.996 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 outliers start: 6 outliers final: 4 residues processed: 453 average time/residue: 0.8663 time to fit residues: 626.9668 Evaluate side-chains 441 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 437 time to evaluate : 3.875 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5659 time to fit residues: 8.9965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 366 optimal weight: 6.9990 chunk 385 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 375 optimal weight: 0.4980 chunk 225 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 294 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 339 optimal weight: 0.9980 chunk 355 optimal weight: 9.9990 chunk 374 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.134 33077 Z= 0.245 Angle : 0.526 10.965 44726 Z= 0.264 Chirality : 0.041 0.151 5219 Planarity : 0.003 0.085 5731 Dihedral : 5.127 61.586 4673 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 4208 helix: 1.19 (0.12), residues: 2082 sheet: -1.09 (0.23), residues: 571 loop : -1.07 (0.16), residues: 1555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 447 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 443 time to evaluate : 3.939 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 outliers start: 4 outliers final: 4 residues processed: 444 average time/residue: 0.8673 time to fit residues: 614.8270 Evaluate side-chains 439 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 435 time to evaluate : 4.863 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6035 time to fit residues: 10.4950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 246 optimal weight: 0.5980 chunk 397 optimal weight: 2.9990 chunk 242 optimal weight: 0.5980 chunk 188 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 416 optimal weight: 0.0980 chunk 383 optimal weight: 10.0000 chunk 331 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.117 33077 Z= 0.160 Angle : 0.503 10.441 44726 Z= 0.250 Chirality : 0.040 0.147 5219 Planarity : 0.003 0.061 5731 Dihedral : 4.885 55.576 4673 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 4208 helix: 1.38 (0.12), residues: 2085 sheet: -1.02 (0.23), residues: 567 loop : -0.88 (0.16), residues: 1556 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 453 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 450 time to evaluate : 3.933 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 outliers start: 3 outliers final: 1 residues processed: 452 average time/residue: 0.8659 time to fit residues: 625.5878 Evaluate side-chains 437 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 436 time to evaluate : 3.881 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5799 time to fit residues: 5.8755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 263 optimal weight: 1.9990 chunk 353 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 139 optimal weight: 0.1980 chunk 341 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.086349 restraints weight = 138052.009| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.76 r_work: 0.2861 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work: 0.2813 rms_B_bonded: 1.87 restraints_weight: 0.1250 r_work: 0.2778 rms_B_bonded: 2.32 restraints_weight: 0.0625 r_work: 0.2729 rms_B_bonded: 3.05 restraints_weight: 0.0312 r_work: 0.2661 rms_B_bonded: 4.22 restraints_weight: 0.0156 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 33077 Z= 0.304 Angle : 0.538 10.951 44726 Z= 0.270 Chirality : 0.041 0.149 5219 Planarity : 0.003 0.047 5731 Dihedral : 5.079 61.963 4673 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 4208 helix: 1.28 (0.12), residues: 2084 sheet: -0.98 (0.23), residues: 571 loop : -0.96 (0.16), residues: 1553 =============================================================================== Job complete usr+sys time: 11181.16 seconds wall clock time: 194 minutes 30.52 seconds (11670.52 seconds total)