Starting phenix.real_space_refine on Mon Aug 25 02:36:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zi3_60120/08_2025/8zi3_60120.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zi3_60120/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zi3_60120/08_2025/8zi3_60120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zi3_60120/08_2025/8zi3_60120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zi3_60120/08_2025/8zi3_60120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zi3_60120/08_2025/8zi3_60120.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.56, per 1000 atoms: 0.23 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: 2.03 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.92 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: 4.45 Time building geometry restraints manager: 2.72 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: 5.140 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.430 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (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 ARG 0.004 0.000 ARG B 94 TYR 0.017 0.001 TYR E 252 PHE 0.020 0.001 PHE C 508 TRP 0.005 0.001 TRP A 139 HIS 0.007 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00326 (25052) covalent geometry : angle 0.61499 (33962) hydrogen bonds : bond 0.19284 ( 1097) hydrogen bonds : angle 6.50641 ( 3120) *********************** 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 : 1.106 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: 0.6930 time to fit residues: 161.6354 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 : 0.991 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 GLN ** g 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.108612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.076293 restraints weight = 45976.126| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.84 r_work: 0.2867 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 25052 Z= 0.356 Angle : 0.714 9.196 33962 Z= 0.372 Chirality : 0.050 0.166 3916 Planarity : 0.005 0.052 4418 Dihedral : 7.537 87.285 3644 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.25 % Allowed : 15.78 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 3210 helix: 1.22 (0.15), residues: 1268 sheet: 0.13 (0.23), residues: 492 loop : -1.25 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 347 TYR 0.020 0.002 TYR E 252 PHE 0.031 0.002 PHE C 508 TRP 0.007 0.002 TRP A 139 HIS 0.006 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00875 (25052) covalent geometry : angle 0.71421 (33962) hydrogen bonds : bond 0.07228 ( 1097) hydrogen bonds : angle 5.41000 ( 3120) *********************** 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 249 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 165 time to evaluate : 0.876 Fit side-chains REVERT: B 28 ASN cc_start: 0.7849 (p0) cc_final: 0.7504 (p0) REVERT: B 42 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8642 (mp) REVERT: B 157 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8128 (mmp) REVERT: C 53 MET cc_start: 0.8378 (mmm) cc_final: 0.8058 (mmt) REVERT: C 484 MET cc_start: 0.7578 (mmt) cc_final: 0.7285 (mmt) REVERT: D 159 MET cc_start: 0.8444 (mmm) cc_final: 0.8237 (mmm) REVERT: D 189 TYR cc_start: 0.7758 (t80) cc_final: 0.7448 (t80) REVERT: D 232 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7362 (pp20) REVERT: D 238 LYS cc_start: 0.8532 (ptpt) cc_final: 0.8279 (pttt) REVERT: D 384 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7161 (ttt) REVERT: g 49 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7042 (mpp) REVERT: g 128 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7084 (m110) REVERT: g 139 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: g 278 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8190 (mp0) REVERT: E 47 ASP cc_start: 0.8446 (t0) cc_final: 0.8152 (t0) REVERT: E 123 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8313 (p0) REVERT: E 167 LYS cc_start: 0.7611 (mmpt) cc_final: 0.7363 (mmmt) REVERT: E 278 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7945 (tt0) outliers start: 84 outliers final: 41 residues processed: 229 average time/residue: 0.6987 time to fit residues: 184.2165 Evaluate side-chains 197 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 43 THR 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 495 LYS Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 358 THR 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 384 MET Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 81 VAL Chi-restraints excluded: chain g residue 99 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 157 LEU Chi-restraints excluded: chain g residue 180 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain A residue 65 LEU 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 171 ASP Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 493 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 234 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 291 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 225 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.112611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080218 restraints weight = 45379.858| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.89 r_work: 0.2947 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25052 Z= 0.112 Angle : 0.532 11.268 33962 Z= 0.273 Chirality : 0.043 0.159 3916 Planarity : 0.004 0.047 4418 Dihedral : 6.868 78.065 3642 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.47 % Allowed : 17.36 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.15), residues: 3210 helix: 1.63 (0.15), residues: 1241 sheet: 0.40 (0.24), residues: 482 loop : -1.09 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 94 TYR 0.017 0.001 TYR E 252 PHE 0.032 0.001 PHE C 508 TRP 0.003 0.000 TRP C 139 HIS 0.006 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00242 (25052) covalent geometry : angle 0.53176 (33962) hydrogen bonds : bond 0.04690 ( 1097) hydrogen bonds : angle 4.82644 ( 3120) *********************** 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 : 1.021 Fit side-chains REVERT: e 41 LEU cc_start: 0.3749 (OUTLIER) cc_final: 0.3544 (tm) REVERT: e 60 GLU cc_start: 0.2465 (OUTLIER) cc_final: 0.2066 (tm-30) REVERT: B 28 ASN cc_start: 0.7706 (p0) cc_final: 0.6790 (p0) REVERT: B 332 GLU cc_start: 0.8592 (tt0) cc_final: 0.8344 (tt0) REVERT: C 34 MET cc_start: 0.7784 (ttp) cc_final: 0.7193 (ttm) REVERT: C 53 MET cc_start: 0.8227 (mmm) cc_final: 0.7942 (mmt) REVERT: C 68 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8492 (mm-30) REVERT: C 110 ASP cc_start: 0.8585 (t0) cc_final: 0.8150 (t0) REVERT: C 457 MET cc_start: 0.6840 (pmm) cc_final: 0.6219 (ptp) REVERT: C 489 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: D 232 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7262 (pp20) REVERT: D 238 LYS cc_start: 0.8596 (ptpt) cc_final: 0.8331 (ptpt) REVERT: D 280 MET cc_start: 0.8645 (tpp) cc_final: 0.8434 (tpp) REVERT: F 446 GLN cc_start: 0.8546 (tp40) cc_final: 0.7951 (tm-30) REVERT: g 49 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7008 (mpp) REVERT: g 139 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: g 278 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8117 (mp0) REVERT: E 47 ASP cc_start: 0.8381 (t0) cc_final: 0.8060 (t0) REVERT: E 123 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8348 (p0) REVERT: E 167 LYS cc_start: 0.7675 (mmpt) cc_final: 0.7424 (mmmt) REVERT: A 298 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8991 (tp) outliers start: 64 outliers final: 21 residues processed: 219 average time/residue: 0.6888 time to fit residues: 172.5911 Evaluate side-chains 186 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 274 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 223 THR 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 240 ARG 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 375 LEU 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 E residue 122 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 298 LEU 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 33 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 269 optimal weight: 0.0370 chunk 235 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN g 3 ASN A 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.110912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.078810 restraints weight = 45431.575| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.80 r_work: 0.2920 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25052 Z= 0.179 Angle : 0.568 10.402 33962 Z= 0.291 Chirality : 0.044 0.154 3916 Planarity : 0.004 0.048 4418 Dihedral : 6.893 79.307 3642 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.52 % Allowed : 17.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.15), residues: 3210 helix: 1.64 (0.15), residues: 1240 sheet: 0.27 (0.23), residues: 487 loop : -1.12 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 347 TYR 0.019 0.001 TYR E 252 PHE 0.031 0.001 PHE C 508 TRP 0.004 0.001 TRP C 139 HIS 0.005 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00435 (25052) covalent geometry : angle 0.56753 (33962) hydrogen bonds : bond 0.05336 ( 1097) hydrogen bonds : angle 4.80527 ( 3120) *********************** 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 256 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 165 time to evaluate : 0.836 Fit side-chains REVERT: e 22 MET cc_start: 0.5817 (tmm) cc_final: 0.4441 (pmm) REVERT: e 60 GLU cc_start: 0.2331 (OUTLIER) cc_final: 0.1938 (tm-30) REVERT: B 28 ASN cc_start: 0.7855 (p0) cc_final: 0.6975 (p0) REVERT: B 42 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8614 (mp) REVERT: B 324 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8420 (m) REVERT: B 332 GLU cc_start: 0.8629 (tt0) cc_final: 0.8425 (tt0) REVERT: C 34 MET cc_start: 0.7792 (ttp) cc_final: 0.7217 (ttm) REVERT: C 68 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8498 (mm-30) REVERT: C 110 ASP cc_start: 0.8629 (t0) cc_final: 0.8240 (t0) REVERT: C 308 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8820 (mt-10) REVERT: C 489 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: D 189 TYR cc_start: 0.7909 (t80) cc_final: 0.7622 (t80) REVERT: D 232 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7288 (pp20) REVERT: D 238 LYS cc_start: 0.8584 (ptpt) cc_final: 0.8354 (ptpt) REVERT: D 384 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7176 (ttt) REVERT: F 19 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7598 (tm-30) REVERT: F 446 GLN cc_start: 0.8521 (tp40) cc_final: 0.7928 (tm-30) REVERT: g 49 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7038 (mpp) REVERT: g 128 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.7105 (m110) REVERT: g 139 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7786 (mt0) REVERT: g 146 LEU cc_start: 0.8539 (mm) cc_final: 0.8269 (tm) REVERT: g 278 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8126 (mp0) REVERT: E 47 ASP cc_start: 0.8533 (t0) cc_final: 0.8207 (t0) REVERT: E 123 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8314 (p0) REVERT: E 167 LYS cc_start: 0.7688 (mmpt) cc_final: 0.7446 (mmmt) REVERT: E 238 LYS cc_start: 0.8443 (mmmm) cc_final: 0.8184 (mmmm) REVERT: A 133 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7862 (p) REVERT: A 298 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9026 (tp) outliers start: 91 outliers final: 36 residues processed: 240 average time/residue: 0.5284 time to fit residues: 148.1412 Evaluate side-chains 208 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 274 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 331 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 263 ASP Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 322 THR 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 66 THR 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 384 MET 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 296 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain g residue 49 MET 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 157 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 152 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 316 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 314 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.108929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.076959 restraints weight = 45592.228| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.80 r_work: 0.2883 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1512 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= 0.280 Angle : 0.649 10.763 33962 Z= 0.336 Chirality : 0.048 0.172 3916 Planarity : 0.004 0.051 4418 Dihedral : 7.330 87.454 3642 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 4.33 % Allowed : 16.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.15), residues: 3210 helix: 1.36 (0.15), residues: 1251 sheet: 0.01 (0.23), residues: 503 loop : -1.25 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 347 TYR 0.020 0.002 TYR D 252 PHE 0.036 0.002 PHE C 508 TRP 0.006 0.002 TRP A 139 HIS 0.005 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00692 (25052) covalent geometry : angle 0.64925 (33962) hydrogen bonds : bond 0.06341 ( 1097) hydrogen bonds : angle 4.97800 ( 3120) *********************** 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 280 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 168 time to evaluate : 0.944 Fit side-chains REVERT: e 22 MET cc_start: 0.5774 (tmm) cc_final: 0.5047 (ppp) REVERT: e 60 GLU cc_start: 0.2047 (OUTLIER) cc_final: 0.1651 (tm-30) REVERT: B 28 ASN cc_start: 0.7888 (p0) cc_final: 0.7059 (p0) REVERT: B 42 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8625 (mp) REVERT: B 103 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: B 324 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8440 (m) REVERT: B 332 GLU cc_start: 0.8654 (tt0) cc_final: 0.8440 (tt0) REVERT: C 34 MET cc_start: 0.7865 (ttp) cc_final: 0.7257 (ttm) REVERT: C 68 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8521 (mm-30) REVERT: C 110 ASP cc_start: 0.8686 (t0) cc_final: 0.8253 (t0) REVERT: C 308 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8850 (mt-10) REVERT: C 479 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7238 (mm-30) REVERT: C 489 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: D 182 THR cc_start: 0.8057 (p) cc_final: 0.7821 (p) REVERT: D 189 TYR cc_start: 0.8037 (t80) cc_final: 0.7767 (t80) REVERT: D 238 LYS cc_start: 0.8568 (ptpt) cc_final: 0.8319 (ptpp) REVERT: D 384 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7185 (ttt) REVERT: F 19 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7669 (tm-30) REVERT: F 446 GLN cc_start: 0.8562 (tp40) cc_final: 0.7977 (tm-30) REVERT: g 49 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.6802 (mtp) REVERT: g 112 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6700 (tm-30) REVERT: g 128 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7178 (m110) REVERT: g 139 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: g 146 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8290 (tm) REVERT: g 278 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8134 (mp0) REVERT: E 47 ASP cc_start: 0.8630 (t0) cc_final: 0.8352 (t0) REVERT: E 123 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8251 (p0) REVERT: E 238 LYS cc_start: 0.8424 (mmmm) cc_final: 0.8163 (mmmm) REVERT: E 376 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8322 (mptm) REVERT: A 133 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7834 (p) REVERT: A 298 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9035 (tp) outliers start: 112 outliers final: 59 residues processed: 264 average time/residue: 0.6327 time to fit residues: 194.2299 Evaluate side-chains 240 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 165 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 319 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 358 THR 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 274 ILE 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 414 LEU Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 165 ILE 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 384 MET Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain F residue 53 ILE 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 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 99 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 157 LEU Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 ASP 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 E residue 414 VAL 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 171 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 291 VAL 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 147 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 193 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.111717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.079701 restraints weight = 45444.227| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.88 r_work: 0.2931 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25052 Z= 0.126 Angle : 0.542 11.084 33962 Z= 0.277 Chirality : 0.043 0.155 3916 Planarity : 0.004 0.047 4418 Dihedral : 6.808 79.498 3642 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.09 % Allowed : 18.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3210 helix: 1.60 (0.15), residues: 1252 sheet: 0.19 (0.23), residues: 492 loop : -1.13 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 140 TYR 0.017 0.001 TYR E 252 PHE 0.030 0.001 PHE C 508 TRP 0.004 0.001 TRP C 139 HIS 0.006 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00289 (25052) covalent geometry : angle 0.54218 (33962) hydrogen bonds : bond 0.04620 ( 1097) hydrogen bonds : angle 4.62637 ( 3120) *********************** 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 257 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 177 time to evaluate : 0.890 Fit side-chains REVERT: e 22 MET cc_start: 0.5845 (tmm) cc_final: 0.5026 (ppp) REVERT: e 60 GLU cc_start: 0.2077 (OUTLIER) cc_final: 0.1720 (tm-30) REVERT: B 28 ASN cc_start: 0.7913 (p0) cc_final: 0.7043 (p0) REVERT: B 103 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: B 324 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8415 (m) REVERT: B 332 GLU cc_start: 0.8620 (tt0) cc_final: 0.8393 (tt0) REVERT: C 34 MET cc_start: 0.7808 (ttp) cc_final: 0.7231 (ttm) REVERT: C 68 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8469 (mm-30) REVERT: C 110 ASP cc_start: 0.8591 (t0) cc_final: 0.8216 (t0) REVERT: C 457 MET cc_start: 0.6856 (pmm) cc_final: 0.5774 (ptp) REVERT: C 479 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: C 489 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: D 182 THR cc_start: 0.7981 (p) cc_final: 0.7755 (p) REVERT: D 189 TYR cc_start: 0.8012 (t80) cc_final: 0.7743 (t80) REVERT: D 238 LYS cc_start: 0.8581 (ptpt) cc_final: 0.8343 (ptpp) REVERT: F 19 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7607 (tm-30) REVERT: F 87 MET cc_start: 0.8566 (mtt) cc_final: 0.8335 (mtt) REVERT: F 446 GLN cc_start: 0.8512 (tp40) cc_final: 0.7927 (tm-30) REVERT: g 49 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6829 (mtp) REVERT: g 139 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: g 146 LEU cc_start: 0.8628 (mm) cc_final: 0.8393 (tm) REVERT: g 278 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8099 (mp0) REVERT: E 25 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8217 (mtmm) REVERT: E 47 ASP cc_start: 0.8543 (t0) cc_final: 0.8183 (t0) REVERT: E 123 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8262 (p0) REVERT: E 238 LYS cc_start: 0.8436 (mmmm) cc_final: 0.8114 (mmmm) REVERT: E 376 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8295 (mptm) REVERT: A 63 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7817 (ptm) REVERT: A 133 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7821 (p) REVERT: A 298 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9016 (tp) outliers start: 80 outliers final: 39 residues processed: 243 average time/residue: 0.6391 time to fit residues: 180.2643 Evaluate side-chains 217 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 24 ILE 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 100 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 204 SER 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 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 C residue 493 TYR 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 385 ASP Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 152 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 157 LEU Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 123 ASP 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 316 THR Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain A residue 63 MET 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 493 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 63 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 216 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 191 optimal weight: 0.0000 chunk 24 optimal weight: 6.9990 chunk 284 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 chunk 305 optimal weight: 7.9990 overall best weight: 0.5702 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.112791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.080823 restraints weight = 45247.720| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.86 r_work: 0.2957 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25052 Z= 0.104 Angle : 0.527 11.329 33962 Z= 0.268 Chirality : 0.043 0.182 3916 Planarity : 0.003 0.045 4418 Dihedral : 6.556 75.424 3642 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.75 % Allowed : 19.45 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.15), residues: 3210 helix: 1.81 (0.15), residues: 1240 sheet: 0.32 (0.23), residues: 491 loop : -1.03 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 140 TYR 0.016 0.001 TYR E 252 PHE 0.029 0.001 PHE C 508 TRP 0.003 0.000 TRP C 139 HIS 0.006 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00224 (25052) covalent geometry : angle 0.52730 (33962) hydrogen bonds : bond 0.04213 ( 1097) hydrogen bonds : angle 4.48733 ( 3120) *********************** 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 247 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 1.028 Fit side-chains REVERT: e 22 MET cc_start: 0.5784 (tmm) cc_final: 0.5040 (ppp) REVERT: e 60 GLU cc_start: 0.1971 (OUTLIER) cc_final: 0.1572 (tm-30) REVERT: B 28 ASN cc_start: 0.7921 (p0) cc_final: 0.7061 (p0) REVERT: B 94 ARG cc_start: 0.7767 (mtm110) cc_final: 0.7397 (mtm110) REVERT: B 103 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: B 324 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8413 (m) REVERT: B 332 GLU cc_start: 0.8605 (tt0) cc_final: 0.8368 (tt0) REVERT: C 34 MET cc_start: 0.7771 (ttp) cc_final: 0.7219 (ttm) REVERT: C 68 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8465 (mm-30) REVERT: C 110 ASP cc_start: 0.8500 (t0) cc_final: 0.8218 (t0) REVERT: C 403 GLU cc_start: 0.8472 (pp20) cc_final: 0.8219 (mm-30) REVERT: C 457 MET cc_start: 0.6895 (pmm) cc_final: 0.5870 (ptp) REVERT: C 479 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7100 (mm-30) REVERT: C 489 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: D 55 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7567 (mtm) REVERT: D 189 TYR cc_start: 0.8039 (t80) cc_final: 0.7732 (t80) REVERT: D 238 LYS cc_start: 0.8565 (ptpt) cc_final: 0.8330 (ptpp) REVERT: F 19 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7571 (tm-30) REVERT: F 446 GLN cc_start: 0.8492 (tp40) cc_final: 0.7891 (tm-30) REVERT: g 49 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6854 (mtp) REVERT: g 139 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: g 146 LEU cc_start: 0.8573 (mm) cc_final: 0.8368 (tm) REVERT: g 278 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8067 (mp0) REVERT: E 47 ASP cc_start: 0.8543 (t0) cc_final: 0.8173 (t0) REVERT: E 123 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8247 (p0) REVERT: E 238 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8163 (mmmm) REVERT: E 376 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8314 (mptm) REVERT: A 63 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7828 (ptm) REVERT: A 133 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7805 (p) REVERT: A 298 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8935 (tp) outliers start: 71 outliers final: 40 residues processed: 236 average time/residue: 0.6614 time to fit residues: 180.0052 Evaluate side-chains 216 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 291 VAL 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 C residue 29 GLU Chi-restraints excluded: chain C residue 204 SER 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 414 LEU Chi-restraints excluded: chain C residue 479 GLU 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 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 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 157 LEU Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 270 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 263 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 54 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 267 optimal weight: 0.1980 chunk 176 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 247 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 204 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 chunk 271 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.109909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.078251 restraints weight = 45643.999| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.78 r_work: 0.2907 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25052 Z= 0.208 Angle : 0.610 12.034 33962 Z= 0.311 Chirality : 0.046 0.225 3916 Planarity : 0.004 0.045 4418 Dihedral : 6.895 80.097 3642 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.05 % Allowed : 19.22 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.15), residues: 3210 helix: 1.63 (0.15), residues: 1248 sheet: 0.11 (0.23), residues: 496 loop : -1.10 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 347 TYR 0.019 0.001 TYR E 252 PHE 0.033 0.001 PHE C 508 TRP 0.007 0.001 TRP C 139 HIS 0.005 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00512 (25052) covalent geometry : angle 0.60965 (33962) hydrogen bonds : bond 0.05535 ( 1097) hydrogen bonds : angle 4.70075 ( 3120) *********************** 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 248 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 169 time to evaluate : 0.812 Fit side-chains REVERT: e 22 MET cc_start: 0.5762 (tmm) cc_final: 0.5125 (ppp) REVERT: e 60 GLU cc_start: 0.1952 (OUTLIER) cc_final: 0.1568 (tm-30) REVERT: B 28 ASN cc_start: 0.7924 (p0) cc_final: 0.7115 (p0) REVERT: B 42 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8635 (mp) REVERT: B 94 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7457 (mtm110) REVERT: B 103 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: B 324 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8414 (m) REVERT: B 332 GLU cc_start: 0.8682 (tt0) cc_final: 0.8449 (tt0) REVERT: B 365 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8206 (mm) REVERT: C 34 MET cc_start: 0.7831 (ttp) cc_final: 0.7263 (ttm) REVERT: C 68 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8536 (mm-30) REVERT: C 110 ASP cc_start: 0.8604 (t0) cc_final: 0.8265 (t0) REVERT: C 479 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: C 489 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: D 55 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7675 (mtm) REVERT: D 189 TYR cc_start: 0.8075 (t80) cc_final: 0.7791 (t80) REVERT: D 238 LYS cc_start: 0.8549 (ptpt) cc_final: 0.8311 (ptpp) REVERT: F 19 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7609 (tm-30) REVERT: F 446 GLN cc_start: 0.8517 (tp40) cc_final: 0.7913 (tm-30) REVERT: g 49 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6842 (mtp) REVERT: g 112 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6672 (tm-30) REVERT: g 139 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: g 146 LEU cc_start: 0.8527 (mm) cc_final: 0.8307 (tm) REVERT: g 278 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8092 (mp0) REVERT: E 25 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8129 (mtmm) REVERT: E 47 ASP cc_start: 0.8628 (t0) cc_final: 0.8298 (t0) REVERT: E 123 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8225 (p0) REVERT: E 238 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8172 (mmmm) REVERT: E 376 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8311 (mptm) REVERT: A 133 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7837 (p) REVERT: A 298 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9009 (tp) outliers start: 79 outliers final: 45 residues processed: 236 average time/residue: 0.6366 time to fit residues: 173.7664 Evaluate side-chains 224 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 204 SER 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 414 LEU Chi-restraints excluded: chain C residue 479 GLU 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 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 D residue 416 THR 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 100 VAL Chi-restraints excluded: chain g residue 102 HIS Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 ASP 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 298 LEU 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 291 optimal weight: 4.9990 chunk 254 optimal weight: 0.0270 chunk 65 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 308 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 202 optimal weight: 0.5980 chunk 252 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.111516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.079739 restraints weight = 45412.833| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.83 r_work: 0.2931 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25052 Z= 0.134 Angle : 0.555 11.400 33962 Z= 0.282 Chirality : 0.044 0.189 3916 Planarity : 0.004 0.046 4418 Dihedral : 6.672 77.250 3642 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.90 % Allowed : 19.64 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 3210 helix: 1.68 (0.15), residues: 1254 sheet: 0.25 (0.23), residues: 482 loop : -1.07 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 140 TYR 0.018 0.001 TYR E 252 PHE 0.030 0.001 PHE C 508 TRP 0.004 0.001 TRP C 139 HIS 0.005 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00316 (25052) covalent geometry : angle 0.55513 (33962) hydrogen bonds : bond 0.04645 ( 1097) hydrogen bonds : angle 4.54525 ( 3120) *********************** 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 241 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 166 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: e 22 MET cc_start: 0.5793 (tmm) cc_final: 0.5103 (ppp) REVERT: e 60 GLU cc_start: 0.1852 (OUTLIER) cc_final: 0.1475 (tm-30) REVERT: B 28 ASN cc_start: 0.7934 (p0) cc_final: 0.7125 (p0) REVERT: B 94 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7455 (mtm110) REVERT: B 103 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: B 324 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8418 (m) REVERT: B 332 GLU cc_start: 0.8643 (tt0) cc_final: 0.8406 (tt0) REVERT: B 365 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8209 (mm) REVERT: C 34 MET cc_start: 0.7840 (ttp) cc_final: 0.7257 (ttm) REVERT: C 68 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8474 (mm-30) REVERT: C 110 ASP cc_start: 0.8563 (t0) cc_final: 0.8284 (t0) REVERT: C 403 GLU cc_start: 0.8529 (pp20) cc_final: 0.8222 (mm-30) REVERT: C 457 MET cc_start: 0.6934 (pmm) cc_final: 0.5891 (ptp) REVERT: C 479 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7118 (mm-30) REVERT: C 489 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: D 55 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7646 (mtm) REVERT: D 189 TYR cc_start: 0.8052 (t80) cc_final: 0.7757 (t80) REVERT: D 238 LYS cc_start: 0.8552 (ptpt) cc_final: 0.8316 (ptpp) REVERT: F 19 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7480 (tm-30) REVERT: F 446 GLN cc_start: 0.8506 (tp40) cc_final: 0.7919 (tm-30) REVERT: g 49 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6841 (mtp) REVERT: g 139 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: g 146 LEU cc_start: 0.8610 (mm) cc_final: 0.8400 (tm) REVERT: g 278 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8146 (mp0) REVERT: E 25 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8115 (mtmm) REVERT: E 47 ASP cc_start: 0.8555 (t0) cc_final: 0.8199 (t0) REVERT: E 123 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8241 (p0) REVERT: E 167 LYS cc_start: 0.7632 (mmpt) cc_final: 0.7332 (mmpt) REVERT: E 238 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8179 (mmmm) REVERT: E 376 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8303 (mptm) REVERT: A 63 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7837 (ptm) REVERT: A 133 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7828 (p) REVERT: A 298 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9004 (tp) outliers start: 75 outliers final: 41 residues processed: 232 average time/residue: 0.6887 time to fit residues: 184.7805 Evaluate side-chains 221 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 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 204 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 331 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 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 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 100 VAL Chi-restraints excluded: chain g residue 102 HIS Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 270 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 298 LEU 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 70 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 276 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.110185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.078439 restraints weight = 45709.010| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.80 r_work: 0.2910 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25052 Z= 0.192 Angle : 0.612 15.338 33962 Z= 0.311 Chirality : 0.045 0.224 3916 Planarity : 0.004 0.047 4418 Dihedral : 6.815 79.492 3642 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.63 % Allowed : 19.84 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3210 helix: 1.60 (0.15), residues: 1254 sheet: 0.16 (0.23), residues: 485 loop : -1.12 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 347 TYR 0.018 0.001 TYR D 252 PHE 0.034 0.001 PHE C 508 TRP 0.005 0.001 TRP C 139 HIS 0.005 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00469 (25052) covalent geometry : angle 0.61219 (33962) hydrogen bonds : bond 0.05308 ( 1097) hydrogen bonds : angle 4.65693 ( 3120) ********************** 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 233 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 1.026 Fit side-chains REVERT: e 22 MET cc_start: 0.5786 (tmm) cc_final: 0.5085 (ppp) REVERT: e 60 GLU cc_start: 0.1960 (OUTLIER) cc_final: 0.1558 (tm-30) REVERT: B 28 ASN cc_start: 0.7941 (p0) cc_final: 0.7161 (p0) REVERT: B 94 ARG cc_start: 0.7858 (mtm110) cc_final: 0.7466 (mtm110) REVERT: B 103 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: B 324 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8404 (m) REVERT: B 332 GLU cc_start: 0.8665 (tt0) cc_final: 0.8433 (tt0) REVERT: B 365 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8198 (mm) REVERT: C 34 MET cc_start: 0.7830 (ttp) cc_final: 0.7262 (ttm) REVERT: C 68 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8474 (mm-30) REVERT: C 110 ASP cc_start: 0.8612 (t0) cc_final: 0.8297 (t0) REVERT: C 457 MET cc_start: 0.7004 (pmm) cc_final: 0.6071 (ptp) REVERT: C 479 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: C 489 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: D 55 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7672 (mtm) REVERT: D 189 TYR cc_start: 0.8041 (t80) cc_final: 0.7752 (t80) REVERT: D 238 LYS cc_start: 0.8542 (ptpt) cc_final: 0.8301 (ptpp) REVERT: F 19 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7650 (tm-30) REVERT: F 446 GLN cc_start: 0.8510 (tp40) cc_final: 0.7927 (tm-30) REVERT: g 49 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6811 (mtp) REVERT: g 139 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: g 146 LEU cc_start: 0.8599 (mm) cc_final: 0.8392 (tm) REVERT: g 278 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8104 (mp0) REVERT: E 25 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8248 (mtmm) REVERT: E 47 ASP cc_start: 0.8640 (t0) cc_final: 0.8309 (t0) REVERT: E 123 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8197 (p0) REVERT: E 167 LYS cc_start: 0.7604 (mmpt) cc_final: 0.7320 (mmpt) REVERT: E 238 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8186 (mmmm) REVERT: E 376 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8303 (mptm) REVERT: A 133 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7842 (p) REVERT: A 278 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8321 (mp) REVERT: A 298 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9021 (tp) outliers start: 68 outliers final: 44 residues processed: 224 average time/residue: 0.7174 time to fit residues: 184.5557 Evaluate side-chains 219 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 204 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 331 ILE 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 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 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 100 VAL Chi-restraints excluded: chain g residue 102 HIS Chi-restraints excluded: chain g residue 139 GLN Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 270 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 278 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 293 optimal weight: 0.9980 chunk 160 optimal weight: 0.0870 chunk 267 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 106 optimal weight: 0.0470 chunk 71 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 overall best weight: 0.6056 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.112433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.080207 restraints weight = 45342.059| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.90 r_work: 0.2949 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25052 Z= 0.106 Angle : 0.541 11.450 33962 Z= 0.274 Chirality : 0.043 0.172 3916 Planarity : 0.003 0.046 4418 Dihedral : 6.353 74.514 3642 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.44 % Allowed : 20.34 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.15), residues: 3210 helix: 1.77 (0.15), residues: 1252 sheet: 0.31 (0.23), residues: 495 loop : -1.00 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 419 TYR 0.016 0.001 TYR E 252 PHE 0.029 0.001 PHE C 508 TRP 0.003 0.000 TRP C 139 HIS 0.006 0.001 HIS g 55 Details of bonding type rmsd covalent geometry : bond 0.00235 (25052) covalent geometry : angle 0.54102 (33962) hydrogen bonds : bond 0.04066 ( 1097) hydrogen bonds : angle 4.42526 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7116.61 seconds wall clock time: 122 minutes 13.86 seconds (7333.86 seconds total)