Starting phenix.real_space_refine on Thu May 29 08:26:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glw_40221/05_2025/8glw_40221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glw_40221/05_2025/8glw_40221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8glw_40221/05_2025/8glw_40221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glw_40221/05_2025/8glw_40221.map" model { file = "/net/cci-nas-00/data/ceres_data/8glw_40221/05_2025/8glw_40221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glw_40221/05_2025/8glw_40221.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 116 5.49 5 Mg 7 5.21 5 S 110 5.16 5 C 20032 2.51 5 N 5763 2.21 5 O 6144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32174 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "B" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "C" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3116 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain breaks: 1 Chain: "Y" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2515 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain: "D" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "E" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3860 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "F" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3203 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 14, 'TRANS': 388} Chain: "G" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3106 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 1 Chain: "X" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2523 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "H" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1029 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "I" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1021 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "A" 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: "B" 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: "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: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" 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: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11841 SG CYS Y 124 22.426 82.153 113.979 1.00 30.69 S ATOM 11862 SG CYS Y 127 21.756 85.923 114.327 1.00 28.39 S ATOM 12080 SG CYS Y 152 21.386 83.567 117.422 1.00 37.35 S ATOM 28390 SG CYS X 124 56.103 58.710 57.504 1.00 23.91 S ATOM 28411 SG CYS X 127 59.005 56.222 57.959 1.00 17.16 S ATOM 28629 SG CYS X 152 59.380 59.097 55.468 1.00 19.28 S Time building chain proxies: 19.68, per 1000 atoms: 0.61 Number of scatterers: 32174 At special positions: 0 Unit cell: (182.97, 169.29, 197.505, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 110 16.00 P 116 15.00 Mg 7 11.99 O 6144 8.00 N 5763 7.00 C 20032 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: 7.44 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" ND1 HIS X 155 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 127 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 152 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 124 " pdb=" ZN Y 601 " pdb="ZN ZN Y 601 " - pdb=" NE2 HIS Y 155 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 124 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 152 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 127 " Number of angles added : 6 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7030 Finding SS restraints... Secondary structure from input PDB file: 205 helices and 19 sheets defined 55.3% alpha, 4.2% beta 48 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 9.59 Creating SS restraints... Processing helix chain 'A' and resid 15 through 19 removed outlier: 3.627A pdb=" N TYR A 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 35 through 40 removed outlier: 3.663A pdb=" N SER A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 73 through 90 removed outlier: 3.728A pdb=" N LEU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.952A pdb=" N ARG A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 209 through 225 removed outlier: 3.609A pdb=" N ALA A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.579A pdb=" N LEU A 237 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.691A pdb=" N ASN A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.092A pdb=" N PHE A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.025A pdb=" N GLY A 287 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 3.823A pdb=" N ILE A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.613A pdb=" N GLY A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.710A pdb=" N ALA A 398 " --> pdb=" O PRO A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 420 removed outlier: 3.920A pdb=" N ALA A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 removed outlier: 3.644A pdb=" N LYS A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 447 removed outlier: 4.195A pdb=" N TYR A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 464 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 475 through 482 removed outlier: 4.451A pdb=" N VAL A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 removed outlier: 3.518A pdb=" N TYR B 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.561A pdb=" N LEU B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 74 through 90 removed outlier: 4.256A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 removed outlier: 3.946A pdb=" N HIS B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 removed outlier: 3.599A pdb=" N ILE B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 145 through 150' Processing helix chain 'B' and resid 179 through 196 removed outlier: 3.640A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N PHE B 188 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.557A pdb=" N MET B 217 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 4.003A pdb=" N LEU B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 259 Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.749A pdb=" N PHE B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 305 through 315 Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.843A pdb=" N VAL B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 379 removed outlier: 3.689A pdb=" N LEU B 379 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 392 removed outlier: 3.550A pdb=" N GLY B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.713A pdb=" N TYR B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 423 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.866A pdb=" N LEU B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 455 through 467 removed outlier: 3.665A pdb=" N ILE B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 485 removed outlier: 4.145A pdb=" N LEU B 478 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B 485 " --> pdb=" O GLN B 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 21 through 27 removed outlier: 3.774A pdb=" N LEU C 27 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 41 removed outlier: 4.375A pdb=" N SER C 39 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 removed outlier: 3.522A pdb=" N GLN C 52 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.505A pdb=" N ILE C 62 " --> pdb=" O ARG C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 90 removed outlier: 4.159A pdb=" N LEU C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C 78 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 removed outlier: 4.094A pdb=" N ASN C 95 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 3.764A pdb=" N HIS C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 106 " --> pdb=" O GLN C 102 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.549A pdb=" N ASP C 192 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 209 through 224 removed outlier: 4.252A pdb=" N ALA C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.704A pdb=" N HIS C 236 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 238 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 removed outlier: 4.673A pdb=" N MET C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 Processing helix chain 'C' and resid 305 through 317 Processing helix chain 'C' and resid 329 through 341 Processing helix chain 'C' and resid 343 through 362 removed outlier: 3.642A pdb=" N PHE C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.610A pdb=" N GLY C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 399 Processing helix chain 'Y' and resid 12 through 24 removed outlier: 3.730A pdb=" N GLN Y 24 " --> pdb=" O ALA Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 37 removed outlier: 3.574A pdb=" N LEU Y 32 " --> pdb=" O SER Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 59 removed outlier: 4.079A pdb=" N ILE Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 73 removed outlier: 3.901A pdb=" N LEU Y 70 " --> pdb=" O ALA Y 66 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 80 removed outlier: 3.545A pdb=" N LEU Y 79 " --> pdb=" O LEU Y 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 98 removed outlier: 3.681A pdb=" N GLU Y 91 " --> pdb=" O GLU Y 87 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR Y 98 " --> pdb=" O ARG Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 109 removed outlier: 3.905A pdb=" N HIS Y 105 " --> pdb=" O GLN Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 114 Processing helix chain 'Y' and resid 124 through 135 removed outlier: 3.743A pdb=" N ALA Y 129 " --> pdb=" O PRO Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 204 Proline residue: Y 201 - end of helix removed outlier: 3.875A pdb=" N ASP Y 204 " --> pdb=" O ALA Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 205 through 210 removed outlier: 3.839A pdb=" N GLN Y 209 " --> pdb=" O PRO Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 229 Processing helix chain 'Y' and resid 240 through 250 Processing helix chain 'Y' and resid 251 through 258 Processing helix chain 'Y' and resid 269 through 275 removed outlier: 3.509A pdb=" N SER Y 273 " --> pdb=" O CYS Y 269 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE Y 275 " --> pdb=" O LEU Y 271 " (cutoff:3.500A) Processing helix chain 'Y' and resid 283 through 295 Processing helix chain 'Y' and resid 299 through 309 Processing helix chain 'D' and resid 15 through 19 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 32 through 37 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.591A pdb=" N ARG D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 3.768A pdb=" N LEU D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.780A pdb=" N HIS D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 129 Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 179 through 196 removed outlier: 3.648A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE D 188 " --> pdb=" O CYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.997A pdb=" N ARG D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.529A pdb=" N MET D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 273 removed outlier: 3.698A pdb=" N GLU D 273 " --> pdb=" O PRO D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 281 Processing helix chain 'D' and resid 305 through 317 Processing helix chain 'D' and resid 329 through 339 removed outlier: 3.692A pdb=" N TRP D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 362 removed outlier: 3.833A pdb=" N LEU D 350 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN D 355 " --> pdb=" O PHE D 351 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 356 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'D' and resid 382 through 392 Processing helix chain 'D' and resid 393 through 400 Processing helix chain 'D' and resid 407 through 421 removed outlier: 3.970A pdb=" N ARG D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 435 removed outlier: 3.863A pdb=" N LEU D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 448 removed outlier: 3.846A pdb=" N TYR D 444 " --> pdb=" O GLN D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 471 through 485 Proline residue: D 477 - end of helix Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.771A pdb=" N ARG E 19 " --> pdb=" O GLU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.651A pdb=" N LEU E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 75 through 90 removed outlier: 4.009A pdb=" N LEU E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 90 " --> pdb=" O MET E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.987A pdb=" N ASN E 95 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 113 removed outlier: 4.097A pdb=" N HIS E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN E 113 " --> pdb=" O TYR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 151 removed outlier: 3.785A pdb=" N ARG E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 182 removed outlier: 3.703A pdb=" N GLU E 182 " --> pdb=" O SER E 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 179 through 182' Processing helix chain 'E' and resid 183 through 195 removed outlier: 3.802A pdb=" N PHE E 188 " --> pdb=" O CYS E 184 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E 193 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'E' and resid 209 through 224 removed outlier: 4.205A pdb=" N SER E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 253 through 257 Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 305 through 317 removed outlier: 3.883A pdb=" N ILE E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 343 through 362 removed outlier: 3.675A pdb=" N VAL E 348 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU E 359 " --> pdb=" O GLN E 355 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 378 Processing helix chain 'E' and resid 382 through 392 removed outlier: 3.541A pdb=" N LEU E 386 " --> pdb=" O VAL E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 400 Processing helix chain 'E' and resid 407 through 422 removed outlier: 4.090A pdb=" N ARG E 411 " --> pdb=" O GLU E 407 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 422 " --> pdb=" O ASP E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 435 Processing helix chain 'E' and resid 437 through 448 Processing helix chain 'E' and resid 455 through 467 Processing helix chain 'E' and resid 471 through 485 removed outlier: 3.804A pdb=" N LEU E 476 " --> pdb=" O ARG E 472 " (cutoff:3.500A) Proline residue: E 477 - end of helix Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 34 through 38 removed outlier: 3.613A pdb=" N ALA F 37 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA F 38 " --> pdb=" O ASN F 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 34 through 38' Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 64 through 69 Processing helix chain 'F' and resid 73 through 76 removed outlier: 3.673A pdb=" N HIS F 76 " --> pdb=" O LEU F 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 73 through 76' Processing helix chain 'F' and resid 77 through 90 removed outlier: 3.642A pdb=" N ARG F 88 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY F 90 " --> pdb=" O MET F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 114 Processing helix chain 'F' and resid 143 through 150 Processing helix chain 'F' and resid 151 through 153 No H-bonds generated for 'chain 'F' and resid 151 through 153' Processing helix chain 'F' and resid 185 through 192 Processing helix chain 'F' and resid 199 through 204 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 234 through 238 removed outlier: 3.511A pdb=" N LEU F 237 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER F 238 " --> pdb=" O GLN F 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 234 through 238' Processing helix chain 'F' and resid 248 through 260 removed outlier: 3.862A pdb=" N VAL F 253 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY F 260 " --> pdb=" O VAL F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.774A pdb=" N PHE F 275 " --> pdb=" O ALA F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 286 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.944A pdb=" N ASN F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 315 " --> pdb=" O PHE F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 329 through 341 Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 362 Processing helix chain 'F' and resid 367 through 379 Processing helix chain 'F' and resid 382 through 392 Processing helix chain 'F' and resid 393 through 398 Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.694A pdb=" N LEU G 51 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 61 Processing helix chain 'G' and resid 64 through 69 Processing helix chain 'G' and resid 73 through 89 removed outlier: 4.077A pdb=" N LEU G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU G 78 " --> pdb=" O GLY G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 95 removed outlier: 3.966A pdb=" N ASN G 95 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.572A pdb=" N GLN G 106 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY G 108 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU G 110 " --> pdb=" O GLN G 106 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 192 Processing helix chain 'G' and resid 209 through 224 removed outlier: 3.690A pdb=" N MET G 217 " --> pdb=" O MET G 213 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER G 218 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 243 through 258 removed outlier: 3.593A pdb=" N MET G 248 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU G 249 " --> pdb=" O SER G 245 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 253 " --> pdb=" O LEU G 249 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL G 256 " --> pdb=" O PHE G 252 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN G 257 " --> pdb=" O VAL G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 273 removed outlier: 3.982A pdb=" N GLU G 273 " --> pdb=" O LYS G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 316 Processing helix chain 'G' and resid 329 through 341 Processing helix chain 'G' and resid 343 through 362 Processing helix chain 'G' and resid 367 through 379 Processing helix chain 'G' and resid 382 through 392 Processing helix chain 'G' and resid 393 through 399 removed outlier: 4.143A pdb=" N ARG G 399 " --> pdb=" O GLU G 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 23 Processing helix chain 'X' and resid 28 through 37 Processing helix chain 'X' and resid 54 through 59 Processing helix chain 'X' and resid 66 through 74 Processing helix chain 'X' and resid 80 through 85 removed outlier: 4.202A pdb=" N GLY X 85 " --> pdb=" O ALA X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 98 removed outlier: 3.928A pdb=" N GLU X 97 " --> pdb=" O ILE X 93 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR X 98 " --> pdb=" O ARG X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 108 removed outlier: 3.896A pdb=" N VAL X 104 " --> pdb=" O ALA X 100 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU X 108 " --> pdb=" O VAL X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 135 removed outlier: 3.775A pdb=" N ALA X 129 " --> pdb=" O PRO X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 201 through 203 No H-bonds generated for 'chain 'X' and resid 201 through 203' Processing helix chain 'X' and resid 205 through 209 Processing helix chain 'X' and resid 214 through 230 Processing helix chain 'X' and resid 240 through 250 Processing helix chain 'X' and resid 251 through 258 Processing helix chain 'X' and resid 271 through 276 removed outlier: 4.022A pdb=" N PHE X 275 " --> pdb=" O LEU X 271 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG X 276 " --> pdb=" O LYS X 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 271 through 276' Processing helix chain 'X' and resid 283 through 295 removed outlier: 3.593A pdb=" N HIS X 287 " --> pdb=" O SER X 283 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 310 removed outlier: 3.517A pdb=" N LEU X 310 " --> pdb=" O GLN X 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 5.940A pdb=" N ILE A 6 " --> pdb=" O TYR A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 173 removed outlier: 7.008A pdb=" N LEU A 170 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASP A 232 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 172 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 229 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE A 266 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 231 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 133 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TRP A 293 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE A 135 " --> pdb=" O TRP A 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.753A pdb=" N ILE B 172 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU B 132 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLY B 267 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU B 134 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B 133 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N TRP B 293 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE B 135 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 6 through 7 removed outlier: 6.235A pdb=" N ILE C 6 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 170 through 173 removed outlier: 6.529A pdb=" N LEU C 170 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASP C 232 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 172 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C 229 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE C 266 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 231 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 136 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N SER C 131 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ILE C 291 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 133 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TRP C 293 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE C 135 " --> pdb=" O TRP C 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 151 through 152 Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 7 removed outlier: 6.774A pdb=" N ILE D 6 " --> pdb=" O TYR D 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 170 through 172 removed outlier: 5.755A pdb=" N LEU D 132 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY D 267 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU D 134 " --> pdb=" O GLY D 267 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 291 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 299 through 300 Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 7 removed outlier: 6.393A pdb=" N ILE E 6 " --> pdb=" O TYR E 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 132 through 135 removed outlier: 6.115A pdb=" N LEU E 132 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLY E 267 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU E 134 " --> pdb=" O GLY E 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 6 through 7 removed outlier: 5.979A pdb=" N ILE F 6 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 170 through 173 removed outlier: 6.262A pdb=" N LEU F 229 " --> pdb=" O MET F 264 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE F 266 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE F 231 " --> pdb=" O ILE F 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 299 through 300 Processing sheet with id=AB8, first strand: chain 'G' and resid 6 through 7 removed outlier: 6.495A pdb=" N ILE G 6 " --> pdb=" O TYR G 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'G' and resid 169 through 173 removed outlier: 6.490A pdb=" N LEU G 229 " --> pdb=" O MET G 264 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE G 266 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE G 231 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY G 136 " --> pdb=" O GLY G 267 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N SER G 131 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE G 291 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU G 133 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TRP G 293 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE G 135 " --> pdb=" O TRP G 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 232 through 233 1153 hydrogen bonds defined for protein. 3300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 122 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 10.85 Time building geometry restraints manager: 8.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9304 1.34 - 1.45: 5645 1.45 - 1.57: 17645 1.57 - 1.69: 224 1.69 - 1.81: 184 Bond restraints: 33002 Sorted by residual: bond pdb=" C HIS A 383 " pdb=" N PRO A 384 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.38e-02 5.25e+03 5.85e+00 bond pdb=" CB PRO X 125 " pdb=" CG PRO X 125 " ideal model delta sigma weight residual 1.492 1.587 -0.095 5.00e-02 4.00e+02 3.64e+00 bond pdb=" CA GLN A 52 " pdb=" CB GLN A 52 " ideal model delta sigma weight residual 1.528 1.577 -0.049 2.61e-02 1.47e+03 3.55e+00 bond pdb=" CA ASN G 198 " pdb=" CB ASN G 198 " ideal model delta sigma weight residual 1.531 1.585 -0.055 3.12e-02 1.03e+03 3.05e+00 bond pdb=" C HIS F 383 " pdb=" N PRO F 384 " ideal model delta sigma weight residual 1.335 1.358 -0.022 1.30e-02 5.92e+03 2.99e+00 ... (remaining 32997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 44472 2.36 - 4.72: 536 4.72 - 7.08: 120 7.08 - 9.43: 10 9.43 - 11.79: 2 Bond angle restraints: 45140 Sorted by residual: angle pdb=" CA PRO X 125 " pdb=" N PRO X 125 " pdb=" CD PRO X 125 " ideal model delta sigma weight residual 112.00 105.90 6.10 1.40e+00 5.10e-01 1.90e+01 angle pdb=" N ASP B 313 " pdb=" CA ASP B 313 " pdb=" C ASP B 313 " ideal model delta sigma weight residual 113.18 108.00 5.18 1.33e+00 5.65e-01 1.52e+01 angle pdb=" C SER D 401 " pdb=" N ASP D 402 " pdb=" CA ASP D 402 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" C GLY B 267 " pdb=" N THR B 268 " pdb=" CA THR B 268 " ideal model delta sigma weight residual 121.03 126.78 -5.75 1.60e+00 3.91e-01 1.29e+01 angle pdb=" N GLN E 414 " pdb=" CA GLN E 414 " pdb=" CB GLN E 414 " ideal model delta sigma weight residual 110.28 115.58 -5.30 1.55e+00 4.16e-01 1.17e+01 ... (remaining 45135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.45: 18729 32.45 - 64.90: 980 64.90 - 97.35: 53 97.35 - 129.80: 3 129.80 - 162.25: 6 Dihedral angle restraints: 19771 sinusoidal: 8887 harmonic: 10884 Sorted by residual: dihedral pdb=" C5' ADP D 601 " pdb=" O5' ADP D 601 " pdb=" PA ADP D 601 " pdb=" O2A ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 102.26 -162.25 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C5' ADP B 601 " pdb=" O5' ADP B 601 " pdb=" PA ADP B 601 " pdb=" O2A ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 102.20 -162.19 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C5' ADP E 601 " pdb=" O5' ADP E 601 " pdb=" PA ADP E 601 " pdb=" O2A ADP E 601 " ideal model delta sinusoidal sigma weight residual 300.00 143.69 156.32 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 19768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3722 0.043 - 0.086: 1041 0.086 - 0.129: 273 0.129 - 0.172: 35 0.172 - 0.215: 6 Chirality restraints: 5077 Sorted by residual: chirality pdb=" CA HIS B 383 " pdb=" N HIS B 383 " pdb=" C HIS B 383 " pdb=" CB HIS B 383 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE F 346 " pdb=" CA ILE F 346 " pdb=" CG1 ILE F 346 " pdb=" CG2 ILE F 346 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CA ARG X 114 " pdb=" N ARG X 114 " pdb=" C ARG X 114 " pdb=" CB ARG X 114 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 5074 not shown) Planarity restraints: 5440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS X 124 " 0.081 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO X 125 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO X 125 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO X 125 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU X 149 " 0.055 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO X 150 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO X 150 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO X 150 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 402 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" CG ASP D 402 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP D 402 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP D 402 " 0.015 2.00e-02 2.50e+03 ... (remaining 5437 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 215 2.60 - 3.18: 26217 3.18 - 3.75: 48666 3.75 - 4.33: 64961 4.33 - 4.90: 107377 Nonbonded interactions: 247436 Sorted by model distance: nonbonded pdb="MG MG E 603 " pdb=" O1B ADP F 601 " model vdw 2.028 2.170 nonbonded pdb=" OG1 THR C 143 " pdb="MG MG C 602 " model vdw 2.029 2.170 nonbonded pdb=" O1B ADP E 601 " pdb="MG MG E 602 " model vdw 2.038 2.170 nonbonded pdb=" O3B ADP B 601 " pdb="MG MG B 602 " model vdw 2.045 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 2.054 2.170 ... (remaining 247431 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 4 through 485 or resid 601 through 602)) selection = (chain 'B' and (resid 4 through 485 or resid 601 through 602)) selection = (chain 'D' and (resid 4 through 485 or resid 601 through 602)) selection = (chain 'E' and (resid 4 through 485 or resid 601 through 602)) } ncs_group { reference = (chain 'C' and resid 3 through 403) selection = (chain 'F' and (resid 3 through 275 or resid 288 through 403)) selection = (chain 'G' and resid 3 through 403) } ncs_group { reference = (chain 'X' and (resid 1 through 309 or resid 601)) selection = chain 'Y' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.400 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 80.550 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.160 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 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 : 0.004 0.095 33010 Z= 0.159 Angle : 0.682 11.792 45146 Z= 0.342 Chirality : 0.043 0.215 5077 Planarity : 0.005 0.119 5440 Dihedral : 17.624 162.253 12741 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 0.03 % Allowed : 0.43 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 3712 helix: -0.30 (0.12), residues: 1821 sheet: 0.67 (0.38), residues: 199 loop : -1.32 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 336 HIS 0.011 0.001 HIS C 383 PHE 0.030 0.002 PHE B 351 TYR 0.018 0.001 TYR D 337 ARG 0.010 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.16621 ( 1275) hydrogen bonds : angle 6.07692 ( 3544) metal coordination : bond 0.00900 ( 8) metal coordination : angle 1.29786 ( 6) covalent geometry : bond 0.00364 (33002) covalent geometry : angle 0.68169 (45140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 4.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 ARG cc_start: 0.7037 (ttm170) cc_final: 0.6644 (ttm170) REVERT: B 446 MET cc_start: 0.4426 (mpp) cc_final: 0.3673 (mpp) REVERT: D 31 GLN cc_start: 0.8035 (mp10) cc_final: 0.7827 (mp10) REVERT: E 213 MET cc_start: 0.7900 (mtm) cc_final: 0.7683 (mtm) REVERT: F 255 MET cc_start: 0.8250 (ttp) cc_final: 0.8048 (ttm) REVERT: G 357 ARG cc_start: 0.6719 (ttt180) cc_final: 0.6502 (ttt180) outliers start: 1 outliers final: 0 residues processed: 370 average time/residue: 0.4199 time to fit residues: 248.9600 Evaluate side-chains 264 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 2.9990 chunk 288 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 98 optimal weight: 0.0000 chunk 194 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 298 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 222 optimal weight: 0.0980 chunk 345 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 GLN C 306 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS Y 61 GLN ** Y 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN D 440 GLN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 HIS X 305 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.231650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.213194 restraints weight = 39956.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.210079 restraints weight = 66832.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.208050 restraints weight = 66362.314| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4380 r_free = 0.4380 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4380 r_free = 0.4380 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33010 Z= 0.114 Angle : 0.591 9.361 45146 Z= 0.296 Chirality : 0.040 0.191 5077 Planarity : 0.004 0.068 5440 Dihedral : 16.888 172.834 5355 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 0.62 % Allowed : 8.00 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3712 helix: 0.08 (0.13), residues: 1825 sheet: 0.68 (0.39), residues: 191 loop : -1.17 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 336 HIS 0.008 0.001 HIS B 383 PHE 0.019 0.001 PHE B 351 TYR 0.029 0.001 TYR E 337 ARG 0.006 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 1275) hydrogen bonds : angle 4.62157 ( 3544) metal coordination : bond 0.00364 ( 8) metal coordination : angle 1.35714 ( 6) covalent geometry : bond 0.00244 (33002) covalent geometry : angle 0.59079 (45140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 312 time to evaluate : 3.160 Fit side-chains revert: symmetry clash REVERT: A 417 LEU cc_start: 0.5355 (mt) cc_final: 0.5082 (tp) REVERT: B 64 ARG cc_start: 0.6825 (ttm170) cc_final: 0.6509 (ptp-170) REVERT: B 470 MET cc_start: -0.0714 (ptp) cc_final: -0.0966 (pmm) REVERT: D 444 TYR cc_start: 0.4965 (t80) cc_final: 0.4643 (t80) REVERT: D 484 MET cc_start: 0.3482 (mpp) cc_final: 0.2240 (tmm) REVERT: E 470 MET cc_start: 0.1781 (OUTLIER) cc_final: 0.1232 (ptt) REVERT: G 357 ARG cc_start: 0.6778 (ttt180) cc_final: 0.6549 (ttt180) outliers start: 20 outliers final: 12 residues processed: 324 average time/residue: 0.4276 time to fit residues: 222.3822 Evaluate side-chains 284 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 271 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 295 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 370 optimal weight: 9.9990 chunk 44 optimal weight: 30.0000 chunk 218 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 379 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 335 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 236 HIS C 222 ASN C 236 HIS C 297 GLN C 306 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 GLN E 355 GLN F 208 HIS F 341 GLN ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.220592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.199283 restraints weight = 40036.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.195706 restraints weight = 73288.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.193987 restraints weight = 76719.078| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 33010 Z= 0.291 Angle : 0.743 14.814 45146 Z= 0.374 Chirality : 0.046 0.240 5077 Planarity : 0.005 0.072 5440 Dihedral : 17.275 173.955 5355 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.23 % Favored : 94.67 % Rotamer: Outliers : 1.76 % Allowed : 11.42 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3712 helix: -0.20 (0.12), residues: 1842 sheet: 0.10 (0.39), residues: 171 loop : -1.49 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 336 HIS 0.011 0.002 HIS G 176 PHE 0.027 0.003 PHE Y 4 TYR 0.032 0.002 TYR A 91 ARG 0.006 0.001 ARG F 58 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 1275) hydrogen bonds : angle 4.72582 ( 3544) metal coordination : bond 0.02128 ( 8) metal coordination : angle 2.10464 ( 6) covalent geometry : bond 0.00717 (33002) covalent geometry : angle 0.74310 (45140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 192 ASP cc_start: 0.7562 (p0) cc_final: 0.7329 (p0) REVERT: C 344 MET cc_start: 0.6447 (mmm) cc_final: 0.6240 (mmt) REVERT: E 470 MET cc_start: 0.1773 (OUTLIER) cc_final: 0.1334 (ptt) REVERT: F 35 ASN cc_start: 0.7997 (t0) cc_final: 0.7712 (t0) REVERT: F 161 GLU cc_start: 0.7642 (pt0) cc_final: 0.7438 (pt0) REVERT: G 161 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7626 (mm-30) REVERT: G 357 ARG cc_start: 0.6802 (ttt180) cc_final: 0.6569 (ttt180) outliers start: 57 outliers final: 39 residues processed: 322 average time/residue: 0.4157 time to fit residues: 216.3630 Evaluate side-chains 305 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 446 MET Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 86 MET Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 193 THR Chi-restraints excluded: chain X residue 239 HIS Chi-restraints excluded: chain X residue 295 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 294 optimal weight: 4.9990 chunk 232 optimal weight: 0.8980 chunk 328 optimal weight: 0.9980 chunk 204 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 364 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN B 208 HIS C 222 ASN C 297 GLN C 306 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN E 355 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.235838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.216117 restraints weight = 40897.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.212819 restraints weight = 72934.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.210317 restraints weight = 73404.439| |-----------------------------------------------------------------------------| r_work (final): 0.4547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4547 r_free = 0.4547 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4547 r_free = 0.4547 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33010 Z= 0.141 Angle : 0.607 10.973 45146 Z= 0.304 Chirality : 0.040 0.210 5077 Planarity : 0.004 0.058 5440 Dihedral : 17.025 172.107 5355 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 1.70 % Allowed : 13.99 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3712 helix: -0.01 (0.13), residues: 1835 sheet: 0.01 (0.38), residues: 194 loop : -1.38 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 336 HIS 0.006 0.001 HIS G 383 PHE 0.016 0.001 PHE Y 4 TYR 0.030 0.002 TYR A 91 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 1275) hydrogen bonds : angle 4.46210 ( 3544) metal coordination : bond 0.00830 ( 8) metal coordination : angle 1.03131 ( 6) covalent geometry : bond 0.00330 (33002) covalent geometry : angle 0.60656 (45140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.4901 (tp) cc_final: 0.4362 (tt) REVERT: B 470 MET cc_start: -0.0145 (pmm) cc_final: -0.0519 (pmm) REVERT: D 61 THR cc_start: 0.4850 (m) cc_final: 0.4556 (m) REVERT: D 220 ILE cc_start: 0.7808 (mt) cc_final: 0.7568 (mt) REVERT: D 484 MET cc_start: 0.3849 (mpp) cc_final: 0.2216 (tpt) REVERT: E 470 MET cc_start: 0.1958 (OUTLIER) cc_final: 0.1467 (ptt) REVERT: F 35 ASN cc_start: 0.7906 (t0) cc_final: 0.7676 (t0) REVERT: G 357 ARG cc_start: 0.6778 (ttt180) cc_final: 0.6548 (ttt180) outliers start: 55 outliers final: 36 residues processed: 322 average time/residue: 0.4173 time to fit residues: 216.6220 Evaluate side-chains 298 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 446 MET Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain G residue 86 MET Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 239 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 107 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 chunk 211 optimal weight: 30.0000 chunk 362 optimal weight: 9.9990 chunk 276 optimal weight: 0.0470 chunk 369 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 314 ASN B 208 HIS C 222 ASN C 297 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.232424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.214277 restraints weight = 40587.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.208477 restraints weight = 104161.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.204738 restraints weight = 52419.568| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4444 r_free = 0.4444 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4444 r_free = 0.4444 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 33010 Z= 0.237 Angle : 0.690 13.623 45146 Z= 0.346 Chirality : 0.043 0.199 5077 Planarity : 0.005 0.058 5440 Dihedral : 17.137 170.141 5355 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 2.50 % Allowed : 14.42 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 3712 helix: -0.14 (0.12), residues: 1843 sheet: -0.10 (0.39), residues: 171 loop : -1.50 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 336 HIS 0.010 0.001 HIS Y 239 PHE 0.022 0.002 PHE Y 4 TYR 0.031 0.002 TYR A 91 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 1275) hydrogen bonds : angle 4.57625 ( 3544) metal coordination : bond 0.01744 ( 8) metal coordination : angle 2.09167 ( 6) covalent geometry : bond 0.00580 (33002) covalent geometry : angle 0.68961 (45140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 274 time to evaluate : 3.239 Fit side-chains revert: symmetry clash REVERT: A 408 ILE cc_start: 0.5236 (tp) cc_final: 0.4707 (tt) REVERT: B 50 ASP cc_start: 0.5144 (OUTLIER) cc_final: 0.4821 (t0) REVERT: B 470 MET cc_start: 0.0283 (pmm) cc_final: -0.0166 (pmm) REVERT: C 192 ASP cc_start: 0.7572 (p0) cc_final: 0.7283 (p0) REVERT: C 220 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8188 (tp) REVERT: D 61 THR cc_start: 0.4971 (m) cc_final: 0.4685 (m) REVERT: D 220 ILE cc_start: 0.7883 (mt) cc_final: 0.7625 (mt) REVERT: E 52 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7282 (pt0) REVERT: E 470 MET cc_start: 0.2230 (OUTLIER) cc_final: 0.1783 (ptt) REVERT: E 475 LEU cc_start: 0.2557 (OUTLIER) cc_final: 0.2051 (tp) REVERT: F 35 ASN cc_start: 0.7998 (t0) cc_final: 0.7694 (t0) REVERT: F 361 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6943 (mp) REVERT: G 357 ARG cc_start: 0.6826 (ttt180) cc_final: 0.6598 (ttt180) outliers start: 81 outliers final: 45 residues processed: 330 average time/residue: 0.4206 time to fit residues: 226.3141 Evaluate side-chains 312 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 261 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain G residue 86 MET Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 239 HIS Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 122 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 274 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 211 optimal weight: 0.0980 chunk 253 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 354 optimal weight: 1.9990 chunk 353 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS C 222 ASN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.237291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.217387 restraints weight = 40987.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.213210 restraints weight = 74401.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.210328 restraints weight = 79337.941| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4545 r_free = 0.4545 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4545 r_free = 0.4545 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33010 Z= 0.115 Angle : 0.582 10.814 45146 Z= 0.292 Chirality : 0.039 0.148 5077 Planarity : 0.004 0.058 5440 Dihedral : 16.795 177.285 5355 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 1.85 % Allowed : 15.71 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3712 helix: 0.09 (0.13), residues: 1844 sheet: 0.05 (0.38), residues: 190 loop : -1.31 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 336 HIS 0.005 0.001 HIS G 383 PHE 0.017 0.001 PHE X 221 TYR 0.022 0.001 TYR A 375 ARG 0.005 0.000 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 1275) hydrogen bonds : angle 4.31651 ( 3544) metal coordination : bond 0.00329 ( 8) metal coordination : angle 0.86585 ( 6) covalent geometry : bond 0.00261 (33002) covalent geometry : angle 0.58235 (45140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 299 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.3401 (t80) cc_final: 0.2757 (t80) REVERT: A 408 ILE cc_start: 0.4993 (tp) cc_final: 0.4565 (tt) REVERT: B 50 ASP cc_start: 0.4677 (OUTLIER) cc_final: 0.4415 (t0) REVERT: D 61 THR cc_start: 0.4811 (m) cc_final: 0.4548 (m) REVERT: E 470 MET cc_start: 0.1963 (OUTLIER) cc_final: 0.1401 (ptt) REVERT: E 475 LEU cc_start: 0.2076 (OUTLIER) cc_final: 0.1730 (tp) REVERT: F 385 MET cc_start: 0.3541 (OUTLIER) cc_final: 0.3276 (ptp) REVERT: G 357 ARG cc_start: 0.6759 (ttt180) cc_final: 0.6557 (ttt180) outliers start: 60 outliers final: 37 residues processed: 336 average time/residue: 0.4214 time to fit residues: 229.3801 Evaluate side-chains 313 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 162 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 239 HIS Chi-restraints excluded: chain X residue 265 ASN Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 378 optimal weight: 8.9990 chunk 367 optimal weight: 8.9990 chunk 334 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS C 222 ASN C 306 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.233003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.200947 restraints weight = 40871.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.201339 restraints weight = 100136.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.201285 restraints weight = 37091.547| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4391 r_free = 0.4391 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4391 r_free = 0.4391 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 33010 Z= 0.199 Angle : 0.655 13.592 45146 Z= 0.327 Chirality : 0.042 0.173 5077 Planarity : 0.004 0.058 5440 Dihedral : 16.933 178.548 5355 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.59 % Rotamer: Outliers : 2.07 % Allowed : 16.46 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3712 helix: 0.02 (0.13), residues: 1833 sheet: -0.02 (0.39), residues: 175 loop : -1.38 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 336 HIS 0.013 0.001 HIS A 383 PHE 0.020 0.002 PHE Y 4 TYR 0.026 0.002 TYR D 337 ARG 0.010 0.000 ARG X 245 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 1275) hydrogen bonds : angle 4.43202 ( 3544) metal coordination : bond 0.01428 ( 8) metal coordination : angle 1.99794 ( 6) covalent geometry : bond 0.00485 (33002) covalent geometry : angle 0.65471 (45140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.4138 (t80) cc_final: 0.3414 (t80) REVERT: A 408 ILE cc_start: 0.5395 (tp) cc_final: 0.4897 (tt) REVERT: B 50 ASP cc_start: 0.5342 (OUTLIER) cc_final: 0.4991 (t0) REVERT: D 61 THR cc_start: 0.5139 (m) cc_final: 0.4864 (m) REVERT: D 268 THR cc_start: 0.7019 (OUTLIER) cc_final: 0.6747 (t) REVERT: D 484 MET cc_start: 0.5124 (mpp) cc_final: 0.2666 (tpt) REVERT: E 52 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: E 470 MET cc_start: 0.2390 (OUTLIER) cc_final: 0.1666 (ptt) REVERT: E 475 LEU cc_start: 0.2765 (OUTLIER) cc_final: 0.2262 (tp) REVERT: F 361 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6945 (mp) REVERT: F 385 MET cc_start: 0.3833 (OUTLIER) cc_final: 0.3597 (ptp) REVERT: G 357 ARG cc_start: 0.6877 (ttt180) cc_final: 0.6671 (ttt180) outliers start: 67 outliers final: 51 residues processed: 318 average time/residue: 0.4338 time to fit residues: 223.4541 Evaluate side-chains 318 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 86 MET Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 239 HIS Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 46 optimal weight: 30.0000 chunk 307 optimal weight: 0.6980 chunk 370 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.3980 chunk 217 optimal weight: 0.0170 chunk 368 optimal weight: 6.9990 chunk 329 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 223 optimal weight: 0.8980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.237604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.218693 restraints weight = 41004.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.215373 restraints weight = 67147.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.213523 restraints weight = 62713.100| |-----------------------------------------------------------------------------| r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4577 r_free = 0.4577 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4577 r_free = 0.4577 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33010 Z= 0.107 Angle : 0.585 11.617 45146 Z= 0.292 Chirality : 0.039 0.150 5077 Planarity : 0.004 0.060 5440 Dihedral : 16.629 171.632 5355 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 1.70 % Allowed : 17.38 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3712 helix: 0.16 (0.13), residues: 1843 sheet: 0.12 (0.38), residues: 190 loop : -1.21 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 336 HIS 0.005 0.001 HIS G 383 PHE 0.016 0.001 PHE X 221 TYR 0.028 0.001 TYR B 375 ARG 0.011 0.000 ARG X 245 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 1275) hydrogen bonds : angle 4.26462 ( 3544) metal coordination : bond 0.00240 ( 8) metal coordination : angle 0.89858 ( 6) covalent geometry : bond 0.00235 (33002) covalent geometry : angle 0.58465 (45140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 280 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.3468 (t80) cc_final: 0.3093 (t80) REVERT: A 408 ILE cc_start: 0.4816 (tp) cc_final: 0.4474 (tt) REVERT: B 50 ASP cc_start: 0.4625 (OUTLIER) cc_final: 0.4378 (t0) REVERT: D 61 THR cc_start: 0.4898 (m) cc_final: 0.4657 (m) REVERT: D 484 MET cc_start: 0.4078 (mpp) cc_final: 0.2351 (tpt) REVERT: E 470 MET cc_start: 0.1941 (OUTLIER) cc_final: 0.1373 (ptt) REVERT: F 385 MET cc_start: 0.3421 (OUTLIER) cc_final: 0.3130 (ptp) outliers start: 55 outliers final: 39 residues processed: 315 average time/residue: 0.4163 time to fit residues: 213.5338 Evaluate side-chains 313 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 239 HIS Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 275 optimal weight: 0.5980 chunk 356 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 357 optimal weight: 1.9990 chunk 299 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 377 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 280 optimal weight: 0.0570 chunk 330 optimal weight: 2.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN X 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.235991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.217109 restraints weight = 41031.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.213490 restraints weight = 68836.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.211110 restraints weight = 69058.837| |-----------------------------------------------------------------------------| r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4554 r_free = 0.4554 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4554 r_free = 0.4554 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 33010 Z= 0.141 Angle : 0.601 11.561 45146 Z= 0.301 Chirality : 0.040 0.158 5077 Planarity : 0.004 0.058 5440 Dihedral : 16.648 165.186 5355 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 1.73 % Allowed : 17.66 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3712 helix: 0.19 (0.13), residues: 1834 sheet: 0.20 (0.39), residues: 175 loop : -1.20 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 336 HIS 0.004 0.001 HIS G 176 PHE 0.015 0.001 PHE X 221 TYR 0.023 0.001 TYR B 375 ARG 0.011 0.000 ARG X 245 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 1275) hydrogen bonds : angle 4.28760 ( 3544) metal coordination : bond 0.00909 ( 8) metal coordination : angle 1.49995 ( 6) covalent geometry : bond 0.00335 (33002) covalent geometry : angle 0.60127 (45140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.4788 (tp) cc_final: 0.4483 (tt) REVERT: B 50 ASP cc_start: 0.4735 (OUTLIER) cc_final: 0.4471 (t0) REVERT: D 61 THR cc_start: 0.4963 (m) cc_final: 0.4721 (m) REVERT: D 268 THR cc_start: 0.6870 (OUTLIER) cc_final: 0.6609 (t) REVERT: D 484 MET cc_start: 0.4462 (mpp) cc_final: 0.2696 (tpt) REVERT: E 52 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.7025 (pt0) REVERT: E 470 MET cc_start: 0.1897 (OUTLIER) cc_final: 0.1411 (ptt) REVERT: E 475 LEU cc_start: 0.1804 (OUTLIER) cc_final: 0.1558 (tp) REVERT: F 361 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6849 (mp) REVERT: F 385 MET cc_start: 0.3459 (OUTLIER) cc_final: 0.3194 (mtt) outliers start: 56 outliers final: 44 residues processed: 305 average time/residue: 0.4183 time to fit residues: 207.2456 Evaluate side-chains 311 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 260 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 239 HIS Chi-restraints excluded: chain X residue 265 ASN Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 46 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 205 optimal weight: 0.9990 chunk 380 optimal weight: 10.0000 chunk 94 optimal weight: 0.2980 chunk 241 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.236475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.218702 restraints weight = 40893.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.212125 restraints weight = 105689.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.206809 restraints weight = 63926.020| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4458 r_free = 0.4458 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4458 r_free = 0.4458 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33010 Z= 0.128 Angle : 0.598 11.272 45146 Z= 0.299 Chirality : 0.040 0.160 5077 Planarity : 0.004 0.059 5440 Dihedral : 16.595 158.382 5355 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 1.67 % Allowed : 17.91 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3712 helix: 0.19 (0.13), residues: 1845 sheet: 0.24 (0.39), residues: 175 loop : -1.18 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 336 HIS 0.004 0.001 HIS G 383 PHE 0.016 0.001 PHE X 221 TYR 0.024 0.001 TYR B 375 ARG 0.012 0.000 ARG X 245 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 1275) hydrogen bonds : angle 4.25593 ( 3544) metal coordination : bond 0.00713 ( 8) metal coordination : angle 1.31180 ( 6) covalent geometry : bond 0.00300 (33002) covalent geometry : angle 0.59799 (45140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7424 Ramachandran restraints generated. 3712 Oldfield, 0 Emsley, 3712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 260 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.5011 (tp) cc_final: 0.4676 (tt) REVERT: B 50 ASP cc_start: 0.5342 (OUTLIER) cc_final: 0.5036 (t0) REVERT: D 61 THR cc_start: 0.5082 (m) cc_final: 0.4804 (m) REVERT: D 484 MET cc_start: 0.5106 (mpp) cc_final: 0.2796 (tpt) REVERT: E 52 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7210 (pt0) REVERT: E 470 MET cc_start: 0.2332 (OUTLIER) cc_final: 0.1587 (ptt) REVERT: E 475 LEU cc_start: 0.2534 (OUTLIER) cc_final: 0.2111 (tp) REVERT: F 361 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6751 (mp) REVERT: F 385 MET cc_start: 0.3524 (OUTLIER) cc_final: 0.3293 (mtt) outliers start: 54 outliers final: 45 residues processed: 296 average time/residue: 0.4156 time to fit residues: 201.0489 Evaluate side-chains 306 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 60 HIS Chi-restraints excluded: chain X residue 177 HIS Chi-restraints excluded: chain X residue 215 LEU Chi-restraints excluded: chain X residue 239 HIS Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 150 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 242 optimal weight: 0.0470 chunk 73 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 293 optimal weight: 7.9990 chunk 323 optimal weight: 1.9990 chunk 305 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 287 HIS ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.235658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.217047 restraints weight = 40825.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.214059 restraints weight = 67740.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.211685 restraints weight = 54257.411| |-----------------------------------------------------------------------------| r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4560 r_free = 0.4560 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4560 r_free = 0.4560 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 33010 Z= 0.147 Angle : 0.616 14.147 45146 Z= 0.308 Chirality : 0.040 0.194 5077 Planarity : 0.004 0.059 5440 Dihedral : 16.598 147.199 5355 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.61 % Favored : 95.34 % Rotamer: Outliers : 1.82 % Allowed : 17.97 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3712 helix: 0.18 (0.13), residues: 1842 sheet: 0.19 (0.39), residues: 175 loop : -1.22 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 336 HIS 0.007 0.001 HIS C 383 PHE 0.015 0.001 PHE X 221 TYR 0.025 0.001 TYR D 444 ARG 0.012 0.000 ARG X 245 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 1275) hydrogen bonds : angle 4.29054 ( 3544) metal coordination : bond 0.00964 ( 8) metal coordination : angle 1.54751 ( 6) covalent geometry : bond 0.00351 (33002) covalent geometry : angle 0.61614 (45140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9307.29 seconds wall clock time: 164 minutes 38.52 seconds (9878.52 seconds total)