Starting phenix.real_space_refine on Fri May 23 21:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zi3_60120/05_2025/8zi3_60120.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zi3_60120/05_2025/8zi3_60120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zi3_60120/05_2025/8zi3_60120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zi3_60120/05_2025/8zi3_60120.map" model { file = "/net/cci-nas-00/data/ceres_data/8zi3_60120/05_2025/8zi3_60120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zi3_60120/05_2025/8zi3_60120.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 5 5.21 5 S 99 5.16 5 C 15504 2.51 5 N 4231 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24671 Number of models: 1 Model: "" Number of chains: 13 Chain: "e" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 587 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "B" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 471} Chain: "C" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 471} Chain: "D" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "g" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2243 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain: "E" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "A" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 471} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Time building chain proxies: 15.61, per 1000 atoms: 0.63 Number of scatterers: 24671 At special positions: 0 Unit cell: (138.138, 138.138, 145.002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 99 16.00 P 14 15.00 Mg 5 11.99 O 4818 8.00 N 4231 7.00 C 15504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.27 Conformation dependent library (CDL) restraints added in 3.1 seconds 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5858 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 25 sheets defined 47.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.251A pdb=" N SER B 82 " --> pdb=" O ASN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.860A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.692A pdb=" N ARG B 140 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.531A pdb=" N MET B 179 " --> pdb=" O GLY B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 217 through 220 removed outlier: 3.887A pdb=" N ALA B 220 " --> pdb=" O GLY B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 217 through 220' Processing helix chain 'B' and resid 232 through 253 Proline residue: B 240 - end of helix removed outlier: 3.823A pdb=" N TYR B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.897A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.905A pdb=" N HIS B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.537A pdb=" N SER B 348 " --> pdb=" O THR B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 364 Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.825A pdb=" N SER B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 382 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 383 " --> pdb=" O GLY B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 383' Processing helix chain 'B' and resid 384 through 404 removed outlier: 4.551A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLY B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.938A pdb=" N GLN B 409 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 455 through 458 Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 494 through 511 removed outlier: 3.534A pdb=" N GLU B 498 " --> pdb=" O ASN B 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.689A pdb=" N LEU C 104 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.850A pdb=" N THR C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.679A pdb=" N MET C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.650A pdb=" N THR C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 220 removed outlier: 3.867A pdb=" N ALA C 220 " --> pdb=" O GLY C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 220' Processing helix chain 'C' and resid 232 through 252 removed outlier: 3.502A pdb=" N LEU C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Proline residue: C 240 - end of helix removed outlier: 3.737A pdb=" N TYR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.976A pdb=" N GLN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 291 through 300 removed outlier: 4.097A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 299 " --> pdb=" O HIS C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.516A pdb=" N THR C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 348 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 364 Processing helix chain 'C' and resid 378 through 383 removed outlier: 3.981A pdb=" N SER C 381 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 391 Processing helix chain 'C' and resid 393 through 409 removed outlier: 3.815A pdb=" N ALA C 397 " --> pdb=" O GLY C 393 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 432 Processing helix chain 'C' and resid 441 through 455 Processing helix chain 'C' and resid 464 through 479 Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 494 through 509 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.822A pdb=" N THR D 82 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 83 " --> pdb=" O THR D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 83' Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.706A pdb=" N GLU D 117 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN D 118 " --> pdb=" O TYR D 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 114 through 118' Processing helix chain 'D' and resid 129 through 136 removed outlier: 3.525A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 167 removed outlier: 3.750A pdb=" N LYS D 167 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.613A pdb=" N TYR D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS D 190 " --> pdb=" O ASN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 211 through 217 removed outlier: 3.516A pdb=" N ARG D 215 " --> pdb=" O PRO D 211 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 231 removed outlier: 3.620A pdb=" N GLY D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE D 229 " --> pdb=" O MET D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 264 removed outlier: 4.274A pdb=" N ALA D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.603A pdb=" N LEU D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 310 through 316 removed outlier: 3.930A pdb=" N THR D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 320 removed outlier: 3.773A pdb=" N LEU D 320 " --> pdb=" O PHE D 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 317 through 320' Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.504A pdb=" N ALA D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 356 through 374 removed outlier: 3.526A pdb=" N GLU D 374 " --> pdb=" O GLN D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 382 removed outlier: 3.511A pdb=" N ILE D 379 " --> pdb=" O LEU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 405 Processing helix chain 'D' and resid 412 through 417 removed outlier: 3.768A pdb=" N THR D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 438 removed outlier: 3.824A pdb=" N GLY D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 448 Processing helix chain 'D' and resid 454 through 461 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.881A pdb=" N THR F 82 " --> pdb=" O GLY F 79 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU F 83 " --> pdb=" O THR F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing helix chain 'F' and resid 114 through 118 removed outlier: 3.635A pdb=" N GLN F 118 " --> pdb=" O TYR F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 153 through 169 Processing helix chain 'F' and resid 181 through 195 Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 211 through 217 removed outlier: 3.572A pdb=" N ARG F 215 " --> pdb=" O PRO F 211 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG F 217 " --> pdb=" O GLY F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 232 removed outlier: 3.983A pdb=" N THR F 221 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY F 222 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 removed outlier: 3.985A pdb=" N TYR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR F 253 " --> pdb=" O ILE F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 276 through 285 removed outlier: 3.846A pdb=" N LEU F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.665A pdb=" N ASP F 306 " --> pdb=" O VAL F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 317 Processing helix chain 'F' and resid 327 through 333 removed outlier: 3.618A pdb=" N ALA F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'F' and resid 355 through 383 removed outlier: 3.932A pdb=" N TYR F 359 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 405 removed outlier: 3.784A pdb=" N LYS F 392 " --> pdb=" O ALA F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 411 No H-bonds generated for 'chain 'F' and resid 409 through 411' Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 424 through 438 Processing helix chain 'F' and resid 444 through 449 Processing helix chain 'F' and resid 454 through 464 Processing helix chain 'g' and resid 3 through 60 removed outlier: 3.640A pdb=" N ILE g 7 " --> pdb=" O ASN g 3 " (cutoff:3.500A) Proline residue: g 44 - end of helix Processing helix chain 'g' and resid 91 through 109 Processing helix chain 'g' and resid 119 through 125 Processing helix chain 'g' and resid 126 through 129 removed outlier: 3.839A pdb=" N TYR g 129 " --> pdb=" O PHE g 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 126 through 129' Processing helix chain 'g' and resid 150 through 162 removed outlier: 3.522A pdb=" N GLN g 154 " --> pdb=" O THR g 150 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET g 156 " --> pdb=" O SER g 152 " (cutoff:3.500A) Processing helix chain 'g' and resid 217 through 289 removed outlier: 3.799A pdb=" N LEU g 221 " --> pdb=" O LEU g 217 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL g 289 " --> pdb=" O GLY g 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.917A pdb=" N THR E 82 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.627A pdb=" N GLU E 117 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN E 118 " --> pdb=" O TYR E 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 114 through 118' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 181 through 195 removed outlier: 3.675A pdb=" N GLY E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR E 189 " --> pdb=" O GLY E 185 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 211 through 232 removed outlier: 3.586A pdb=" N ARG E 215 " --> pdb=" O PRO E 211 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG E 217 " --> pdb=" O GLY E 213 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ALA E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR E 221 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 264 removed outlier: 3.664A pdb=" N THR E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 Processing helix chain 'E' and resid 275 through 285 Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 310 through 317 removed outlier: 3.598A pdb=" N THR E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE E 317 " --> pdb=" O PRO E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 355 through 374 removed outlier: 3.933A pdb=" N TYR E 359 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 382 Processing helix chain 'E' and resid 388 through 405 Processing helix chain 'E' and resid 412 through 417 removed outlier: 3.580A pdb=" N THR E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 438 removed outlier: 3.651A pdb=" N GLY E 438 " --> pdb=" O GLY E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 449 removed outlier: 4.107A pdb=" N TYR E 449 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 462 removed outlier: 4.095A pdb=" N GLU E 462 " --> pdb=" O ILE E 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.055A pdb=" N SER A 82 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.857A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.541A pdb=" N ARG A 140 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.868A pdb=" N MET A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.532A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Proline residue: A 240 - end of helix removed outlier: 3.798A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 4.037A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 300 removed outlier: 4.162A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 299 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.588A pdb=" N ILE A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.230A pdb=" N SER A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 382 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 383 " --> pdb=" O GLY A 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 383' Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 393 through 408 removed outlier: 4.038A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.840A pdb=" N ARG A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 Processing helix chain 'A' and resid 464 through 479 Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.858A pdb=" N ALA A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'e' and resid 7 through 9 removed outlier: 6.718A pdb=" N ASP e 7 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA e 80 " --> pdb=" O ASP e 7 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL e 9 " --> pdb=" O ALA e 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'e' and resid 22 through 24 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 36 removed outlier: 3.581A pdb=" N HIS B 43 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG B 41 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU B 77 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY B 62 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 64 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N MET B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.263A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.990A pdb=" N CYS B 194 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA B 198 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR B 261 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 167 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.521A pdb=" N VAL B 160 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 36 removed outlier: 3.651A pdb=" N THR C 31 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE C 61 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 64 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET C 53 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 89 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.511A pdb=" N ASP C 128 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.823A pdb=" N CYS C 194 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 198 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 330 through 332 removed outlier: 6.449A pdb=" N ILE C 168 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 375 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 10 removed outlier: 5.895A pdb=" N ILE D 6 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL D 49 " --> pdb=" O GLN D 44 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN D 44 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL D 67 " --> pdb=" O GLY D 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB4, first strand: chain 'D' and resid 86 through 87 removed outlier: 6.107A pdb=" N MET D 87 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 202 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL D 144 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL D 301 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU D 146 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 124 through 125 removed outlier: 3.748A pdb=" N LEU D 125 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE D 138 " --> pdb=" O LEU D 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 4 through 10 removed outlier: 3.505A pdb=" N ARG F 5 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL F 13 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE F 53 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL F 41 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL F 67 " --> pdb=" O GLY F 4 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 75 through 77 Processing sheet with id=AB8, first strand: chain 'F' and resid 86 through 87 removed outlier: 6.602A pdb=" N MET F 87 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLN F 207 " --> pdb=" O MET F 87 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 174 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL F 242 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'g' and resid 77 through 80 removed outlier: 3.821A pdb=" N TYR g 78 " --> pdb=" O GLN g 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'g' and resid 169 through 175 Processing sheet with id=AC2, first strand: chain 'E' and resid 5 through 10 removed outlier: 5.729A pdb=" N ILE E 6 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU E 17 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL E 49 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLN E 44 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG E 51 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 77 Processing sheet with id=AC4, first strand: chain 'E' and resid 86 through 87 removed outlier: 6.616A pdb=" N MET E 87 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL E 242 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ILE E 298 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU E 244 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ALA E 300 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL E 246 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N TYR E 302 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL E 144 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL E 301 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU E 146 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR E 345 " --> pdb=" O THR E 323 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 29 through 36 removed outlier: 6.917A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU A 67 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE A 61 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.000A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 107 through 110 removed outlier: 3.957A pdb=" N ARG A 107 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS A 194 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA A 198 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 261 " --> pdb=" O LEU A 328 " (cutoff:3.500A) 1097 hydrogen bonds defined for protein. 3120 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: 9.66 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4276 1.32 - 1.44: 6005 1.44 - 1.56: 14566 1.56 - 1.69: 21 1.69 - 1.81: 184 Bond restraints: 25052 Sorted by residual: bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.40e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.42e+01 bond pdb=" C5 ATP C 602 " pdb=" C6 ATP C 602 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C8 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.310 1.360 -0.050 1.00e-02 1.00e+04 2.49e+01 ... (remaining 25047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 33850 4.07 - 8.14: 102 8.14 - 12.21: 6 12.21 - 16.28: 2 16.28 - 20.34: 2 Bond angle restraints: 33962 Sorted by residual: angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 119.53 20.34 1.00e+00 1.00e+00 4.14e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.74 20.13 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 121.48 15.35 1.00e+00 1.00e+00 2.36e+02 angle pdb=" PA ATP C 602 " pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 136.83 121.63 15.20 1.00e+00 1.00e+00 2.31e+02 angle pdb=" C5 ATP C 602 " pdb=" C4 ATP C 602 " pdb=" N3 ATP C 602 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.48e+01 ... (remaining 33957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 14083 22.75 - 45.49: 1028 45.49 - 68.24: 120 68.24 - 90.98: 24 90.98 - 113.73: 1 Dihedral angle restraints: 15256 sinusoidal: 6055 harmonic: 9201 Sorted by residual: dihedral pdb=" C5' ADP E 502 " pdb=" O5' ADP E 502 " pdb=" PA ADP E 502 " pdb=" O2A ADP E 502 " ideal model delta sinusoidal sigma weight residual -60.00 53.73 -113.73 1 2.00e+01 2.50e-03 3.37e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 -150.75 90.75 1 2.00e+01 2.50e-03 2.43e+01 dihedral pdb=" O1B ADP E 502 " pdb=" O3A ADP E 502 " pdb=" PB ADP E 502 " pdb=" PA ADP E 502 " ideal model delta sinusoidal sigma weight residual -60.00 -149.30 89.30 1 2.00e+01 2.50e-03 2.37e+01 ... (remaining 15253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2694 0.036 - 0.072: 837 0.072 - 0.108: 275 0.108 - 0.144: 106 0.144 - 0.181: 4 Chirality restraints: 3916 Sorted by residual: chirality pdb=" CA THR E 122 " pdb=" N THR E 122 " pdb=" C THR E 122 " pdb=" CB THR E 122 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA ILE C 54 " pdb=" N ILE C 54 " pdb=" C ILE C 54 " pdb=" CB ILE C 54 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA PHE A 341 " pdb=" N PHE A 341 " pdb=" C PHE A 341 " pdb=" CB PHE A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 3913 not shown) Planarity restraints: 4418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 468 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.26e+00 pdb=" C PHE B 468 " -0.050 2.00e-02 2.50e+03 pdb=" O PHE B 468 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP B 469 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 342 " 0.038 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A 343 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 343 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 343 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 47 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" CG ASP E 47 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP E 47 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP E 47 " 0.013 2.00e-02 2.50e+03 ... (remaining 4415 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 110 2.45 - 3.06: 15663 3.06 - 3.67: 35202 3.67 - 4.29: 51001 4.29 - 4.90: 89238 Nonbonded interactions: 191214 Sorted by model distance: nonbonded pdb="MG MG C 601 " pdb=" O2B ATP C 602 " model vdw 1.833 2.170 nonbonded pdb=" O ASP A 262 " pdb=" OD1 ASP A 263 " model vdw 1.855 3.040 nonbonded pdb=" O ASP B 262 " pdb=" OD1 ASP B 263 " model vdw 1.910 3.040 nonbonded pdb="MG MG A 601 " pdb=" O2B ATP A 602 " model vdw 2.028 2.170 nonbonded pdb="MG MG A 601 " pdb=" O2G ATP A 602 " model vdw 2.064 2.170 ... (remaining 191209 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 514) selection = (chain 'B' and resid 26 through 514) selection = (chain 'C' and resid 26 through 514) } ncs_group { reference = (chain 'D' and resid 2 through 464) selection = (chain 'E' and resid 2 through 464) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.900 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: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 56.950 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 25052 Z= 0.206 Angle : 0.615 20.345 33962 Z= 0.379 Chirality : 0.042 0.181 3916 Planarity : 0.003 0.056 4418 Dihedral : 15.151 113.727 9398 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3210 helix: 1.56 (0.15), residues: 1235 sheet: 0.52 (0.24), residues: 482 loop : -1.02 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 139 HIS 0.007 0.001 HIS g 55 PHE 0.020 0.001 PHE C 508 TYR 0.017 0.001 TYR E 252 ARG 0.004 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.19284 ( 1097) hydrogen bonds : angle 6.50641 ( 3120) covalent geometry : bond 0.00326 (25052) covalent geometry : angle 0.61499 (33962) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 2.903 Fit side-chains REVERT: D 189 TYR cc_start: 0.7655 (t80) cc_final: 0.7451 (t80) REVERT: D 238 LYS cc_start: 0.8633 (ptpt) cc_final: 0.8215 (ptpp) REVERT: F 225 MET cc_start: 0.8346 (mtt) cc_final: 0.8033 (mtm) REVERT: g 49 MET cc_start: 0.7704 (ttt) cc_final: 0.7158 (mpp) REVERT: g 278 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8134 (mp0) REVERT: E 47 ASP cc_start: 0.8035 (t0) cc_final: 0.7811 (t0) outliers start: 0 outliers final: 1 residues processed: 204 average time/residue: 1.4091 time to fit residues: 330.6060 Evaluate side-chains 166 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.6980 chunk 241 optimal weight: 0.0070 chunk 133 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN g 3 ASN g 25 GLN A 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.114020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.081697 restraints weight = 44979.191| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.87 r_work: 0.2971 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25052 Z= 0.112 Angle : 0.528 8.346 33962 Z= 0.272 Chirality : 0.043 0.157 3916 Planarity : 0.004 0.046 4418 Dihedral : 6.873 87.420 3644 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.01 % Allowed : 15.70 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3210 helix: 1.71 (0.15), residues: 1257 sheet: 0.57 (0.24), residues: 496 loop : -0.96 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 139 HIS 0.006 0.001 HIS g 55 PHE 0.025 0.001 PHE C 508 TYR 0.015 0.001 TYR E 252 ARG 0.003 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 1097) hydrogen bonds : angle 5.02873 ( 3120) covalent geometry : bond 0.00235 (25052) covalent geometry : angle 0.52757 (33962) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 2.867 Fit side-chains REVERT: B 28 ASN cc_start: 0.7656 (p0) cc_final: 0.7331 (p0) REVERT: B 94 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7406 (mtm110) REVERT: B 157 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7740 (mmp) REVERT: B 461 GLU cc_start: 0.7763 (tp30) cc_final: 0.7489 (tm-30) REVERT: C 53 MET cc_start: 0.8186 (mmt) cc_final: 0.7706 (mmt) REVERT: C 110 ASP cc_start: 0.8598 (t0) cc_final: 0.8175 (t0) REVERT: D 189 TYR cc_start: 0.7756 (t80) cc_final: 0.7478 (t80) REVERT: D 232 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7262 (pp20) REVERT: D 238 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8261 (pttt) REVERT: F 446 GLN cc_start: 0.8584 (tp40) cc_final: 0.7997 (tm-30) REVERT: g 49 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7076 (mpp) REVERT: g 133 VAL cc_start: 0.7200 (t) cc_final: 0.6985 (t) REVERT: g 139 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: g 278 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8133 (mp0) REVERT: E 47 ASP cc_start: 0.8214 (t0) cc_final: 0.7866 (t0) REVERT: E 167 LYS cc_start: 0.7598 (mmpt) cc_final: 0.7347 (mmmt) REVERT: A 419 ARG cc_start: 0.7405 (mpp80) cc_final: 0.7194 (mpt-90) outliers start: 52 outliers final: 19 residues processed: 220 average time/residue: 1.3769 time to fit residues: 350.1280 Evaluate side-chains 188 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 263 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 120 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 160 optimal weight: 0.0270 chunk 196 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN A 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.079786 restraints weight = 45198.203| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.78 r_work: 0.2932 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25052 Z= 0.165 Angle : 0.554 11.004 33962 Z= 0.284 Chirality : 0.044 0.150 3916 Planarity : 0.004 0.044 4418 Dihedral : 6.829 80.919 3642 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.47 % Allowed : 16.24 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 3210 helix: 1.73 (0.15), residues: 1242 sheet: 0.55 (0.24), residues: 480 loop : -1.02 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 139 HIS 0.005 0.001 HIS g 55 PHE 0.026 0.001 PHE C 508 TYR 0.019 0.001 TYR E 252 ARG 0.004 0.000 ARG F 347 Details of bonding type rmsd hydrogen bonds : bond 0.05284 ( 1097) hydrogen bonds : angle 4.84751 ( 3120) covalent geometry : bond 0.00395 (25052) covalent geometry : angle 0.55365 (33962) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 172 time to evaluate : 2.594 Fit side-chains REVERT: e 60 GLU cc_start: 0.2451 (OUTLIER) cc_final: 0.2030 (tm-30) REVERT: B 28 ASN cc_start: 0.7775 (p0) cc_final: 0.6903 (p0) REVERT: B 42 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 94 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7491 (mtm110) REVERT: B 157 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7900 (mmp) REVERT: B 365 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8173 (mm) REVERT: C 53 MET cc_start: 0.8288 (mmm) cc_final: 0.7866 (mmt) REVERT: C 110 ASP cc_start: 0.8593 (t0) cc_final: 0.8194 (t0) REVERT: C 489 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: D 232 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7134 (pp20) REVERT: D 238 LYS cc_start: 0.8611 (ptpt) cc_final: 0.8365 (ptpt) REVERT: D 280 MET cc_start: 0.8698 (tpp) cc_final: 0.8448 (tpp) REVERT: F 446 GLN cc_start: 0.8556 (tp40) cc_final: 0.7994 (tm-30) REVERT: g 49 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.6986 (mpp) REVERT: g 139 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: g 278 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8191 (mp0) REVERT: E 47 ASP cc_start: 0.8449 (t0) cc_final: 0.8135 (t0) REVERT: E 167 LYS cc_start: 0.7639 (mmpt) cc_final: 0.7408 (mmmt) REVERT: A 419 ARG cc_start: 0.7462 (mpp80) cc_final: 0.7238 (mpt-90) outliers start: 64 outliers final: 24 residues processed: 218 average time/residue: 1.4240 time to fit residues: 356.9068 Evaluate side-chains 189 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 60 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 493 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 181 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 291 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 304 optimal weight: 0.8980 chunk 232 optimal weight: 0.0050 chunk 209 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN A 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.112944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.080587 restraints weight = 45512.547| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.89 r_work: 0.2950 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25052 Z= 0.119 Angle : 0.519 9.115 33962 Z= 0.265 Chirality : 0.043 0.151 3916 Planarity : 0.003 0.044 4418 Dihedral : 6.656 86.795 3642 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.71 % Allowed : 17.05 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3210 helix: 1.80 (0.15), residues: 1242 sheet: 0.57 (0.23), residues: 486 loop : -0.98 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 139 HIS 0.005 0.001 HIS g 55 PHE 0.028 0.001 PHE C 508 TYR 0.017 0.001 TYR E 252 ARG 0.003 0.000 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 1097) hydrogen bonds : angle 4.62864 ( 3120) covalent geometry : bond 0.00273 (25052) covalent geometry : angle 0.51854 (33962) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 175 time to evaluate : 3.114 Fit side-chains REVERT: e 22 MET cc_start: 0.5832 (tmm) cc_final: 0.4483 (pmm) REVERT: e 41 LEU cc_start: 0.3752 (OUTLIER) cc_final: 0.3538 (tm) REVERT: e 60 GLU cc_start: 0.2333 (OUTLIER) cc_final: 0.1993 (tm-30) REVERT: B 28 ASN cc_start: 0.7772 (p0) cc_final: 0.6924 (p0) REVERT: B 42 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8542 (mp) REVERT: B 94 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7484 (mtm110) REVERT: B 365 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8121 (mm) REVERT: C 53 MET cc_start: 0.8219 (mmm) cc_final: 0.7870 (mmt) REVERT: C 110 ASP cc_start: 0.8554 (t0) cc_final: 0.8220 (t0) REVERT: C 403 GLU cc_start: 0.8517 (pp20) cc_final: 0.8235 (mm-30) REVERT: C 457 MET cc_start: 0.6714 (pmm) cc_final: 0.6189 (ptp) REVERT: C 489 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: D 182 THR cc_start: 0.7956 (p) cc_final: 0.7720 (p) REVERT: D 189 TYR cc_start: 0.7799 (t80) cc_final: 0.7521 (t80) REVERT: D 232 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7377 (tm-30) REVERT: D 238 LYS cc_start: 0.8615 (ptpt) cc_final: 0.8378 (ptpt) REVERT: D 280 MET cc_start: 0.8647 (tpp) cc_final: 0.8422 (tpp) REVERT: F 446 GLN cc_start: 0.8516 (tp40) cc_final: 0.7881 (tm-30) REVERT: g 49 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7064 (mpp) REVERT: g 139 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: g 278 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8141 (mp0) REVERT: E 47 ASP cc_start: 0.8446 (t0) cc_final: 0.8090 (t0) REVERT: E 167 LYS cc_start: 0.7691 (mmpt) cc_final: 0.7435 (mmmt) REVERT: E 238 LYS cc_start: 0.8478 (mmmm) cc_final: 0.8207 (mmmm) REVERT: A 63 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7832 (ptm) REVERT: A 298 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8947 (tp) REVERT: A 419 ARG cc_start: 0.7444 (mpp80) cc_final: 0.7186 (mpt-90) outliers start: 70 outliers final: 25 residues processed: 227 average time/residue: 1.2707 time to fit residues: 338.7577 Evaluate side-chains 201 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 60 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 493 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 259 optimal weight: 0.3980 chunk 205 optimal weight: 0.7980 chunk 287 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 25 GLN A 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.112266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.079971 restraints weight = 45463.832| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.87 r_work: 0.2935 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25052 Z= 0.138 Angle : 0.528 10.839 33962 Z= 0.270 Chirality : 0.043 0.153 3916 Planarity : 0.003 0.044 4418 Dihedral : 6.602 74.504 3642 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.82 % Allowed : 17.48 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3210 helix: 1.83 (0.15), residues: 1240 sheet: 0.51 (0.23), residues: 488 loop : -0.98 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 139 HIS 0.005 0.001 HIS g 55 PHE 0.026 0.001 PHE C 508 TYR 0.018 0.001 TYR E 252 ARG 0.003 0.000 ARG F 363 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 1097) hydrogen bonds : angle 4.60824 ( 3120) covalent geometry : bond 0.00329 (25052) covalent geometry : angle 0.52753 (33962) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 175 time to evaluate : 3.009 Fit side-chains REVERT: e 22 MET cc_start: 0.5684 (tmm) cc_final: 0.4868 (ppp) REVERT: e 60 GLU cc_start: 0.1972 (OUTLIER) cc_final: 0.1703 (tm-30) REVERT: B 28 ASN cc_start: 0.7834 (p0) cc_final: 0.6955 (p0) REVERT: B 42 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8549 (mp) REVERT: B 94 ARG cc_start: 0.7931 (mtm110) cc_final: 0.7491 (mtm110) REVERT: B 365 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8151 (mm) REVERT: C 53 MET cc_start: 0.8240 (mmm) cc_final: 0.7892 (mmt) REVERT: C 68 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8501 (mm-30) REVERT: C 110 ASP cc_start: 0.8560 (t0) cc_final: 0.8282 (t0) REVERT: C 403 GLU cc_start: 0.8530 (pp20) cc_final: 0.8259 (mm-30) REVERT: C 457 MET cc_start: 0.6768 (pmm) cc_final: 0.6402 (ptp) REVERT: C 489 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: D 15 ASP cc_start: 0.8269 (p0) cc_final: 0.8017 (p0) REVERT: D 182 THR cc_start: 0.7989 (p) cc_final: 0.7744 (p) REVERT: D 189 TYR cc_start: 0.7925 (t80) cc_final: 0.7643 (t80) REVERT: D 232 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7375 (tm-30) REVERT: D 238 LYS cc_start: 0.8584 (ptpt) cc_final: 0.8349 (ptpt) REVERT: D 280 MET cc_start: 0.8660 (tpp) cc_final: 0.8450 (tpp) REVERT: F 384 MET cc_start: 0.8263 (tpp) cc_final: 0.7987 (tpt) REVERT: F 446 GLN cc_start: 0.8495 (tp40) cc_final: 0.7858 (tm-30) REVERT: g 49 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6834 (mtp) REVERT: g 139 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: g 278 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8168 (mp0) REVERT: E 47 ASP cc_start: 0.8520 (t0) cc_final: 0.8192 (t0) REVERT: E 167 LYS cc_start: 0.7677 (mmpt) cc_final: 0.7436 (mmmt) REVERT: E 238 LYS cc_start: 0.8482 (mmmm) cc_final: 0.8202 (mmmm) REVERT: A 63 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7856 (ptm) REVERT: A 133 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7900 (p) REVERT: A 298 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8965 (tp) REVERT: A 419 ARG cc_start: 0.7418 (mpp80) cc_final: 0.7129 (mpt-90) outliers start: 73 outliers final: 37 residues processed: 233 average time/residue: 1.2435 time to fit residues: 339.0719 Evaluate side-chains 213 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 8 VAL Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 60 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 55 HIS Chi-restraints excluded: chain g residue 81 VAL Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 493 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 211 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.077151 restraints weight = 45840.842| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.84 r_work: 0.2885 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 25052 Z= 0.278 Angle : 0.641 10.453 33962 Z= 0.332 Chirality : 0.048 0.182 3916 Planarity : 0.004 0.048 4418 Dihedral : 7.130 83.505 3642 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.71 % Allowed : 16.90 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3210 helix: 1.49 (0.15), residues: 1252 sheet: 0.14 (0.23), residues: 495 loop : -1.15 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 139 HIS 0.004 0.001 HIS g 55 PHE 0.019 0.002 PHE C 508 TYR 0.021 0.002 TYR D 252 ARG 0.006 0.000 ARG F 347 Details of bonding type rmsd hydrogen bonds : bond 0.06197 ( 1097) hydrogen bonds : angle 4.88780 ( 3120) covalent geometry : bond 0.00686 (25052) covalent geometry : angle 0.64051 (33962) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 169 time to evaluate : 2.595 Fit side-chains REVERT: e 22 MET cc_start: 0.5646 (tmm) cc_final: 0.4784 (ppp) REVERT: e 60 GLU cc_start: 0.1962 (OUTLIER) cc_final: 0.1655 (tm-30) REVERT: B 28 ASN cc_start: 0.7875 (p0) cc_final: 0.7069 (p0) REVERT: B 42 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 63 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7356 (ttm) REVERT: B 332 GLU cc_start: 0.8718 (tt0) cc_final: 0.8499 (tt0) REVERT: B 365 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8226 (mm) REVERT: C 53 MET cc_start: 0.8309 (mmm) cc_final: 0.7976 (mmt) REVERT: C 68 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8483 (mm-30) REVERT: C 110 ASP cc_start: 0.8682 (t0) cc_final: 0.8238 (t0) REVERT: C 479 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7233 (mm-30) REVERT: C 489 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: D 182 THR cc_start: 0.8019 (p) cc_final: 0.7771 (p) REVERT: D 189 TYR cc_start: 0.8017 (t80) cc_final: 0.7765 (t80) REVERT: D 232 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7468 (tm-30) REVERT: D 238 LYS cc_start: 0.8577 (ptpt) cc_final: 0.8349 (ptpp) REVERT: D 240 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7430 (mtt90) REVERT: F 19 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7596 (tm-30) REVERT: F 225 MET cc_start: 0.8093 (mtt) cc_final: 0.7822 (mtm) REVERT: F 384 MET cc_start: 0.8251 (tpp) cc_final: 0.7990 (tpt) REVERT: F 446 GLN cc_start: 0.8530 (tp40) cc_final: 0.7899 (tm-30) REVERT: g 49 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6818 (mtp) REVERT: g 112 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6686 (tm-30) REVERT: g 128 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7131 (m110) REVERT: g 139 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: g 278 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8128 (mp0) REVERT: E 47 ASP cc_start: 0.8630 (t0) cc_final: 0.8343 (t0) REVERT: E 167 LYS cc_start: 0.7724 (mmpt) cc_final: 0.7468 (mmmt) REVERT: E 238 LYS cc_start: 0.8472 (mmmm) cc_final: 0.8200 (mmmm) REVERT: E 278 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: E 376 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8314 (mptm) REVERT: A 133 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7861 (p) REVERT: A 298 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9032 (tp) outliers start: 96 outliers final: 49 residues processed: 248 average time/residue: 1.2591 time to fit residues: 363.7227 Evaluate side-chains 223 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 160 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 8 VAL Chi-restraints excluded: chain e residue 24 ILE Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 60 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 240 ARG Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 55 HIS Chi-restraints excluded: chain g residue 81 VAL Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 128 ASN Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain g residue 180 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 493 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 192 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 295 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 307 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.112019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.079810 restraints weight = 45245.983| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.94 r_work: 0.2934 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25052 Z= 0.116 Angle : 0.544 11.416 33962 Z= 0.278 Chirality : 0.043 0.162 3916 Planarity : 0.003 0.045 4418 Dihedral : 6.734 77.997 3642 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.75 % Allowed : 18.52 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3210 helix: 1.74 (0.15), residues: 1242 sheet: 0.35 (0.23), residues: 483 loop : -1.05 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 139 HIS 0.005 0.001 HIS g 55 PHE 0.029 0.001 PHE C 508 TYR 0.017 0.001 TYR E 252 ARG 0.004 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 1097) hydrogen bonds : angle 4.59365 ( 3120) covalent geometry : bond 0.00258 (25052) covalent geometry : angle 0.54414 (33962) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 2.621 Fit side-chains REVERT: e 22 MET cc_start: 0.5666 (tmm) cc_final: 0.5020 (ppp) REVERT: e 60 GLU cc_start: 0.2021 (OUTLIER) cc_final: 0.1718 (tm-30) REVERT: B 28 ASN cc_start: 0.7898 (p0) cc_final: 0.7077 (p0) REVERT: B 94 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7443 (mtm110) REVERT: B 103 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: B 332 GLU cc_start: 0.8659 (tt0) cc_final: 0.8433 (tt0) REVERT: B 365 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8143 (mm) REVERT: C 34 MET cc_start: 0.7737 (ttp) cc_final: 0.7210 (ttm) REVERT: C 53 MET cc_start: 0.8237 (mmm) cc_final: 0.7933 (mmt) REVERT: C 68 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8449 (mm-30) REVERT: C 110 ASP cc_start: 0.8580 (t0) cc_final: 0.8199 (t0) REVERT: C 403 GLU cc_start: 0.8582 (pp20) cc_final: 0.8258 (mm-30) REVERT: C 457 MET cc_start: 0.6777 (pmm) cc_final: 0.5935 (ptp) REVERT: C 479 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: C 489 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: D 182 THR cc_start: 0.7982 (p) cc_final: 0.7740 (p) REVERT: D 189 TYR cc_start: 0.8000 (t80) cc_final: 0.7725 (t80) REVERT: D 232 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7388 (tm-30) REVERT: D 238 LYS cc_start: 0.8571 (ptpt) cc_final: 0.8340 (ptpp) REVERT: D 240 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7390 (mtt90) REVERT: F 19 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7556 (tm-30) REVERT: F 87 MET cc_start: 0.8579 (mtt) cc_final: 0.8315 (mtt) REVERT: F 384 MET cc_start: 0.8238 (tpp) cc_final: 0.7952 (tpt) REVERT: F 446 GLN cc_start: 0.8497 (tp40) cc_final: 0.7879 (tm-30) REVERT: g 49 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6893 (mtp) REVERT: g 68 MET cc_start: 0.6480 (tpt) cc_final: 0.6257 (mmm) REVERT: g 139 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7743 (mt0) REVERT: g 278 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8113 (mp0) REVERT: E 47 ASP cc_start: 0.8561 (t0) cc_final: 0.8230 (t0) REVERT: E 238 LYS cc_start: 0.8448 (mmmm) cc_final: 0.8092 (mmmm) REVERT: E 376 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8296 (mptm) REVERT: A 63 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7848 (ptm) REVERT: A 133 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7814 (p) outliers start: 71 outliers final: 33 residues processed: 235 average time/residue: 1.2982 time to fit residues: 356.2314 Evaluate side-chains 211 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 8 VAL Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 60 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 240 ARG Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 55 HIS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 102 HIS Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 493 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 174 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 316 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 171 optimal weight: 0.0000 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.079976 restraints weight = 45333.849| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.82 r_work: 0.2933 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25052 Z= 0.136 Angle : 0.551 11.176 33962 Z= 0.281 Chirality : 0.043 0.197 3916 Planarity : 0.004 0.044 4418 Dihedral : 6.679 77.418 3642 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.55 % Allowed : 18.95 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3210 helix: 1.77 (0.15), residues: 1243 sheet: 0.37 (0.24), residues: 483 loop : -1.03 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 139 HIS 0.005 0.001 HIS g 55 PHE 0.027 0.001 PHE C 508 TYR 0.017 0.001 TYR E 252 ARG 0.003 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 1097) hydrogen bonds : angle 4.55120 ( 3120) covalent geometry : bond 0.00321 (25052) covalent geometry : angle 0.55071 (33962) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 2.563 Fit side-chains REVERT: e 22 MET cc_start: 0.5816 (tmm) cc_final: 0.5146 (ppp) REVERT: e 60 GLU cc_start: 0.1872 (OUTLIER) cc_final: 0.1505 (tm-30) REVERT: B 28 ASN cc_start: 0.7948 (p0) cc_final: 0.7119 (p0) REVERT: B 42 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8547 (mp) REVERT: B 94 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7456 (mtm110) REVERT: B 103 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: B 324 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8437 (m) REVERT: B 332 GLU cc_start: 0.8669 (tt0) cc_final: 0.8438 (tt0) REVERT: B 365 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8189 (mm) REVERT: C 53 MET cc_start: 0.8231 (mmm) cc_final: 0.7923 (mmt) REVERT: C 68 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8517 (mm-30) REVERT: C 110 ASP cc_start: 0.8578 (t0) cc_final: 0.8278 (t0) REVERT: C 308 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8839 (mt-10) REVERT: C 403 GLU cc_start: 0.8559 (pp20) cc_final: 0.8268 (mm-30) REVERT: C 457 MET cc_start: 0.6745 (pmm) cc_final: 0.5926 (ptp) REVERT: C 479 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7146 (mm-30) REVERT: C 489 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: D 182 THR cc_start: 0.7990 (p) cc_final: 0.7776 (p) REVERT: D 189 TYR cc_start: 0.8066 (t80) cc_final: 0.7790 (t80) REVERT: D 232 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7382 (tm-30) REVERT: D 238 LYS cc_start: 0.8581 (ptpt) cc_final: 0.8350 (ptpp) REVERT: D 240 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7384 (mtt90) REVERT: F 19 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7569 (tm-30) REVERT: F 384 MET cc_start: 0.8271 (tpp) cc_final: 0.7948 (tpt) REVERT: F 446 GLN cc_start: 0.8497 (tp40) cc_final: 0.7867 (tm-30) REVERT: g 32 MET cc_start: 0.7852 (tmm) cc_final: 0.7423 (tmm) REVERT: g 49 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6872 (mtp) REVERT: g 139 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: g 278 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8167 (mp0) REVERT: E 47 ASP cc_start: 0.8571 (t0) cc_final: 0.8234 (t0) REVERT: E 238 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8157 (mmmm) REVERT: E 376 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8319 (mptm) REVERT: A 63 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7860 (ptm) REVERT: A 133 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7842 (p) outliers start: 66 outliers final: 42 residues processed: 228 average time/residue: 1.3076 time to fit residues: 344.7811 Evaluate side-chains 224 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 8 VAL Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 60 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 240 ARG Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 55 HIS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 102 HIS Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 493 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 152 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 25 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 209 optimal weight: 20.0000 chunk 100 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.110431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.078493 restraints weight = 45802.873| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.84 r_work: 0.2910 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25052 Z= 0.191 Angle : 0.595 12.432 33962 Z= 0.305 Chirality : 0.045 0.227 3916 Planarity : 0.004 0.046 4418 Dihedral : 6.837 80.020 3642 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.94 % Allowed : 18.64 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3210 helix: 1.64 (0.15), residues: 1253 sheet: 0.23 (0.23), residues: 495 loop : -1.09 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 139 HIS 0.005 0.001 HIS g 55 PHE 0.023 0.001 PHE C 508 TYR 0.018 0.001 TYR D 252 ARG 0.004 0.000 ARG F 347 Details of bonding type rmsd hydrogen bonds : bond 0.05296 ( 1097) hydrogen bonds : angle 4.66564 ( 3120) covalent geometry : bond 0.00466 (25052) covalent geometry : angle 0.59543 (33962) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 168 time to evaluate : 2.623 Fit side-chains REVERT: e 22 MET cc_start: 0.5811 (tmm) cc_final: 0.5155 (ppp) REVERT: e 60 GLU cc_start: 0.1995 (OUTLIER) cc_final: 0.1670 (tm-30) REVERT: B 28 ASN cc_start: 0.7938 (p0) cc_final: 0.7153 (p0) REVERT: B 42 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8591 (mp) REVERT: B 94 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7450 (mtm110) REVERT: B 103 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: B 324 SER cc_start: 0.9011 (OUTLIER) cc_final: 0.8411 (m) REVERT: B 332 GLU cc_start: 0.8688 (tt0) cc_final: 0.8448 (tt0) REVERT: B 365 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8175 (mm) REVERT: C 53 MET cc_start: 0.8221 (mmm) cc_final: 0.7901 (mmt) REVERT: C 68 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8511 (mm-30) REVERT: C 110 ASP cc_start: 0.8611 (t0) cc_final: 0.8258 (t0) REVERT: C 308 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8830 (mt-10) REVERT: C 403 GLU cc_start: 0.8611 (pp20) cc_final: 0.8285 (mm-30) REVERT: C 457 MET cc_start: 0.6816 (pmm) cc_final: 0.6015 (ptp) REVERT: C 479 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7185 (mm-30) REVERT: C 489 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: D 182 THR cc_start: 0.8092 (p) cc_final: 0.7842 (p) REVERT: D 189 TYR cc_start: 0.8039 (t80) cc_final: 0.7767 (t80) REVERT: D 232 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7411 (tm-30) REVERT: D 238 LYS cc_start: 0.8544 (ptpt) cc_final: 0.8302 (ptpp) REVERT: D 240 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7448 (mtt90) REVERT: F 19 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7596 (tm-30) REVERT: F 87 MET cc_start: 0.8597 (mtt) cc_final: 0.8294 (mtt) REVERT: F 446 GLN cc_start: 0.8508 (tp40) cc_final: 0.7881 (tm-30) REVERT: F 450 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8413 (tpp) REVERT: g 32 MET cc_start: 0.7897 (tmm) cc_final: 0.7463 (tmm) REVERT: g 49 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6847 (mtp) REVERT: g 112 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6701 (tm-30) REVERT: g 139 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: g 278 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8079 (mp0) REVERT: E 47 ASP cc_start: 0.8608 (t0) cc_final: 0.8295 (t0) REVERT: E 238 LYS cc_start: 0.8461 (mmmm) cc_final: 0.8136 (mmmm) REVERT: E 376 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8296 (mptm) REVERT: A 63 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7839 (ptm) REVERT: A 133 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7816 (p) outliers start: 76 outliers final: 45 residues processed: 230 average time/residue: 1.3033 time to fit residues: 350.0021 Evaluate side-chains 229 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 8 VAL Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 60 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 240 ARG Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 55 HIS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 102 HIS Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 280 MET Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 493 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 193 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 282 optimal weight: 0.6980 chunk 307 optimal weight: 4.9990 chunk 9 optimal weight: 0.0970 chunk 244 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.113288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.081322 restraints weight = 45227.390| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.89 r_work: 0.2964 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25052 Z= 0.103 Angle : 0.534 11.540 33962 Z= 0.272 Chirality : 0.043 0.173 3916 Planarity : 0.003 0.045 4418 Dihedral : 6.363 74.608 3642 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.97 % Allowed : 19.72 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3210 helix: 1.83 (0.15), residues: 1250 sheet: 0.42 (0.24), residues: 494 loop : -0.98 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 139 HIS 0.005 0.001 HIS g 55 PHE 0.031 0.001 PHE C 508 TYR 0.016 0.001 TYR E 252 ARG 0.004 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 1097) hydrogen bonds : angle 4.42254 ( 3120) covalent geometry : bond 0.00224 (25052) covalent geometry : angle 0.53445 (33962) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6420 Ramachandran restraints generated. 3210 Oldfield, 0 Emsley, 3210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 2.513 Fit side-chains REVERT: e 22 MET cc_start: 0.5776 (tmm) cc_final: 0.5212 (ppp) REVERT: B 28 ASN cc_start: 0.7932 (p0) cc_final: 0.7109 (p0) REVERT: B 94 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7434 (mtm110) REVERT: B 103 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: B 324 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8397 (m) REVERT: B 332 GLU cc_start: 0.8632 (tt0) cc_final: 0.8418 (tt0) REVERT: B 365 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8136 (mm) REVERT: C 53 MET cc_start: 0.8204 (mmm) cc_final: 0.7903 (mmt) REVERT: C 68 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8484 (mm-30) REVERT: C 110 ASP cc_start: 0.8492 (t0) cc_final: 0.8228 (t0) REVERT: C 403 GLU cc_start: 0.8577 (pp20) cc_final: 0.8279 (mm-30) REVERT: C 457 MET cc_start: 0.6692 (pmm) cc_final: 0.5839 (ptp) REVERT: C 479 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7084 (mm-30) REVERT: C 489 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: D 182 THR cc_start: 0.8043 (p) cc_final: 0.7797 (p) REVERT: D 189 TYR cc_start: 0.8053 (t80) cc_final: 0.7745 (t80) REVERT: D 238 LYS cc_start: 0.8547 (ptpt) cc_final: 0.8309 (ptpp) REVERT: F 19 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7558 (tm-30) REVERT: F 384 MET cc_start: 0.8240 (tpp) cc_final: 0.7933 (tpt) REVERT: F 446 GLN cc_start: 0.8470 (tp40) cc_final: 0.7882 (tm-30) REVERT: g 32 MET cc_start: 0.7830 (tmm) cc_final: 0.7389 (tmm) REVERT: g 49 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6836 (mtp) REVERT: g 139 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7681 (mt0) REVERT: g 278 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8097 (mp0) REVERT: E 47 ASP cc_start: 0.8549 (t0) cc_final: 0.8192 (t0) REVERT: E 167 LYS cc_start: 0.7580 (mmmt) cc_final: 0.7328 (mmpt) REVERT: E 238 LYS cc_start: 0.8515 (mmmm) cc_final: 0.8213 (mmmm) REVERT: E 376 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8283 (mptm) REVERT: A 133 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7805 (p) outliers start: 51 outliers final: 35 residues processed: 220 average time/residue: 1.2869 time to fit residues: 328.0278 Evaluate side-chains 214 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 7 ASP Chi-restraints excluded: chain e residue 8 VAL Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 55 HIS Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 102 HIS Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 493 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 183 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 288 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 211 optimal weight: 9.9990 chunk 185 optimal weight: 0.0870 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 25 GLN A 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.080380 restraints weight = 45396.960| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.86 r_work: 0.2949 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25052 Z= 0.126 Angle : 0.554 13.861 33962 Z= 0.281 Chirality : 0.043 0.185 3916 Planarity : 0.003 0.044 4418 Dihedral : 6.332 75.222 3642 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.20 % Allowed : 19.64 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3210 helix: 1.81 (0.15), residues: 1256 sheet: 0.48 (0.24), residues: 487 loop : -0.97 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 139 HIS 0.005 0.001 HIS g 55 PHE 0.027 0.001 PHE C 508 TYR 0.016 0.001 TYR E 252 ARG 0.005 0.000 ARG C 419 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 1097) hydrogen bonds : angle 4.45283 ( 3120) covalent geometry : bond 0.00293 (25052) covalent geometry : angle 0.55415 (33962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13598.03 seconds wall clock time: 235 minutes 28.87 seconds (14128.87 seconds total)