Starting phenix.real_space_refine on Fri Jun 27 13:43:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glw_40221/06_2025/8glw_40221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glw_40221/06_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_40221/06_2025/8glw_40221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glw_40221/06_2025/8glw_40221.map" model { file = "/net/cci-nas-00/data/ceres_data/8glw_40221/06_2025/8glw_40221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glw_40221/06_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 20.92, per 1000 atoms: 0.65 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: 8.63 Conformation dependent library (CDL) restraints added in 4.2 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: 10.06 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: 11.03 Time building geometry restraints manager: 10.14 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: 18.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.440 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 84.860 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.460 ------------------------------------------------------------------------------- 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 : 3.420 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: 0.5354 time to fit residues: 317.8815 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 : 4.273 ------------------------------------------------------------------------------- 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 = 0.231651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.213195 restraints weight = 39956.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.209614 restraints weight = 66835.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.207458 restraints weight = 71083.819| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4374 r_free = 0.4374 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4374 r_free = 0.4374 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 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 : 16.888 172.830 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 4.62167 ( 3544) metal coordination : bond 0.00364 ( 8) metal coordination : angle 1.35734 ( 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 : 3.447 Fit side-chains revert: symmetry clash REVERT: A 417 LEU cc_start: 0.5372 (mt) cc_final: 0.5088 (tp) REVERT: B 64 ARG cc_start: 0.6824 (ttm170) cc_final: 0.6508 (ptp-170) REVERT: B 470 MET cc_start: -0.0716 (ptp) cc_final: -0.0968 (pmm) REVERT: D 444 TYR cc_start: 0.4974 (t80) cc_final: 0.4652 (t80) REVERT: D 484 MET cc_start: 0.3499 (mpp) cc_final: 0.2241 (tmm) REVERT: E 470 MET cc_start: 0.1798 (OUTLIER) cc_final: 0.1247 (ptt) REVERT: G 357 ARG cc_start: 0.6772 (ttt180) cc_final: 0.6547 (ttt180) outliers start: 20 outliers final: 12 residues processed: 324 average time/residue: 0.4352 time to fit residues: 226.4761 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 : 3.428 ------------------------------------------------------------------------------- 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: 10.0000 chunk 44 optimal weight: 30.0000 chunk 218 optimal weight: 4.9990 chunk 301 optimal weight: 3.9990 chunk 379 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 146 optimal weight: 0.0270 chunk 74 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 335 optimal weight: 1.9990 overall best weight: 1.7044 ------------------------------------------------------------------------------- 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 B 208 HIS 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** E 355 GLN F 341 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.236840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.217795 restraints weight = 41057.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.214407 restraints weight = 69618.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.212383 restraints weight = 59696.826| |-----------------------------------------------------------------------------| r_work (final): 0.4570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4570 r_free = 0.4570 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4570 r_free = 0.4570 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33010 Z= 0.164 Angle : 0.613 12.775 45146 Z= 0.307 Chirality : 0.041 0.163 5077 Planarity : 0.004 0.062 5440 Dihedral : 16.952 174.627 5355 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 1.70 % Allowed : 10.77 % Favored : 87.53 % 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: -0.78 (0.14), residues: 3712 helix: 0.08 (0.13), residues: 1826 sheet: 0.44 (0.40), residues: 179 loop : -1.24 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 336 HIS 0.009 0.001 HIS Y 239 PHE 0.019 0.002 PHE Y 4 TYR 0.030 0.002 TYR A 91 ARG 0.005 0.000 ARG D 301 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 1275) hydrogen bonds : angle 4.44885 ( 3544) metal coordination : bond 0.01085 ( 8) metal coordination : angle 1.19866 ( 6) covalent geometry : bond 0.00392 (33002) covalent geometry : angle 0.61313 (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 349 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 294 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.4610 (tp) cc_final: 0.4129 (tt) REVERT: Y 96 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7413 (mtp) REVERT: E 470 MET cc_start: 0.1742 (OUTLIER) cc_final: 0.1311 (ptt) REVERT: G 357 ARG cc_start: 0.6809 (ttt180) cc_final: 0.6580 (ttt180) outliers start: 55 outliers final: 35 residues processed: 326 average time/residue: 0.4396 time to fit residues: 230.5473 Evaluate side-chains 313 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 276 time to evaluate : 3.719 ------------------------------------------------------------------------------- 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 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 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 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 403 LEU 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 239 HIS Chi-restraints excluded: chain X residue 265 ASN 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: 0.0980 chunk 232 optimal weight: 4.9990 chunk 328 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 17 optimal weight: 10.0000 chunk 364 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 297 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.234297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.215940 restraints weight = 41006.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.210802 restraints weight = 104228.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.206730 restraints weight = 52523.569| |-----------------------------------------------------------------------------| r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4460 r_free = 0.4460 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 = 0.4460 r_free = 0.4460 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33010 Z= 0.184 Angle : 0.628 12.311 45146 Z= 0.315 Chirality : 0.041 0.158 5077 Planarity : 0.004 0.061 5440 Dihedral : 16.997 176.432 5355 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 1.85 % Allowed : 12.94 % Favored : 85.21 % 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: -0.85 (0.14), residues: 3712 helix: 0.05 (0.13), residues: 1837 sheet: 0.16 (0.38), residues: 195 loop : -1.30 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 336 HIS 0.006 0.001 HIS G 176 PHE 0.018 0.002 PHE Y 4 TYR 0.032 0.002 TYR A 91 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 1275) hydrogen bonds : angle 4.42763 ( 3544) metal coordination : bond 0.01286 ( 8) metal coordination : angle 1.26676 ( 6) covalent geometry : bond 0.00446 (33002) covalent geometry : angle 0.62792 (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 344 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 4.372 Fit side-chains revert: symmetry clash REVERT: A 408 ILE cc_start: 0.5205 (tp) cc_final: 0.4709 (tt) REVERT: B 470 MET cc_start: 0.0313 (pmm) cc_final: -0.0522 (pmm) REVERT: D 61 THR cc_start: 0.4958 (m) cc_final: 0.4655 (m) REVERT: D 220 ILE cc_start: 0.7782 (mt) cc_final: 0.7517 (mt) REVERT: D 484 MET cc_start: 0.4474 (mpp) cc_final: 0.2400 (tpt) REVERT: E 470 MET cc_start: 0.2308 (OUTLIER) cc_final: 0.1802 (ptt) REVERT: G 357 ARG cc_start: 0.6820 (ttt180) cc_final: 0.6601 (ttt180) outliers start: 60 outliers final: 41 residues processed: 325 average time/residue: 0.5377 time to fit residues: 287.5827 Evaluate side-chains 303 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 3.567 ------------------------------------------------------------------------------- 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 15 VAL 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 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 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 401 SER 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 403 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 86 MET 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 45 THR Chi-restraints excluded: chain X residue 60 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 107 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 193 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 321 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 276 optimal weight: 0.8980 chunk 369 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 237 optimal weight: 0.5980 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS C 297 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 GLN ** 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 = 0.4771 r_free = 0.4771 target = 0.235006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.215205 restraints weight = 40902.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.212727 restraints weight = 68782.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.210441 restraints weight = 55652.136| |-----------------------------------------------------------------------------| 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: 0.6776 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33010 Z= 0.152 Angle : 0.606 10.882 45146 Z= 0.302 Chirality : 0.040 0.188 5077 Planarity : 0.004 0.059 5440 Dihedral : 16.899 178.997 5355 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 2.04 % Allowed : 13.95 % Favored : 84.01 % 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: -0.77 (0.14), residues: 3712 helix: 0.12 (0.13), residues: 1839 sheet: 0.13 (0.38), residues: 195 loop : -1.26 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 336 HIS 0.005 0.001 HIS G 383 PHE 0.015 0.001 PHE Y 4 TYR 0.030 0.002 TYR A 91 ARG 0.006 0.000 ARG Y 238 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 1275) hydrogen bonds : angle 4.33174 ( 3544) metal coordination : bond 0.01031 ( 8) metal coordination : angle 1.27083 ( 6) covalent geometry : bond 0.00360 (33002) covalent geometry : angle 0.60562 (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 346 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 280 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.4816 (tp) cc_final: 0.4352 (tt) REVERT: B 61 THR cc_start: 0.7441 (t) cc_final: 0.7083 (m) REVERT: B 470 MET cc_start: -0.0195 (pmm) cc_final: -0.0843 (pmm) REVERT: D 61 THR cc_start: 0.4782 (m) cc_final: 0.4519 (m) REVERT: D 220 ILE cc_start: 0.7836 (mt) cc_final: 0.7587 (mt) REVERT: D 484 MET cc_start: 0.4057 (mpp) cc_final: 0.2166 (tmm) REVERT: E 470 MET cc_start: 0.1797 (OUTLIER) cc_final: 0.1250 (ptt) REVERT: G 357 ARG cc_start: 0.6774 (ttt180) cc_final: 0.6565 (ttt180) outliers start: 66 outliers final: 41 residues processed: 323 average time/residue: 0.4403 time to fit residues: 234.5697 Evaluate side-chains 307 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 3.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 350 LEU 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 15 VAL 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 B residue 343 VAL 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 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 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 F residue 268 THR 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 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 265 ASN 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: 2.9990 chunk 3 optimal weight: 20.0000 chunk 274 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 211 optimal weight: 20.0000 chunk 253 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 353 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 C 222 ASN C 297 GLN C 306 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN E 414 GLN F 208 HIS ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 305 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.232187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.213987 restraints weight = 40775.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.207638 restraints weight = 103241.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.201320 restraints weight = 63677.639| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4397 r_free = 0.4397 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 = 0.4397 r_free = 0.4397 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 33010 Z= 0.252 Angle : 0.705 13.970 45146 Z= 0.354 Chirality : 0.044 0.218 5077 Planarity : 0.005 0.059 5440 Dihedral : 17.118 177.130 5355 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 2.47 % Allowed : 14.91 % Favored : 82.62 % 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: -1.09 (0.13), residues: 3712 helix: -0.08 (0.12), residues: 1833 sheet: -0.21 (0.37), residues: 192 loop : -1.48 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 336 HIS 0.011 0.001 HIS E 442 PHE 0.023 0.002 PHE Y 4 TYR 0.025 0.002 TYR D 337 ARG 0.005 0.000 ARG Y 238 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 1275) hydrogen bonds : angle 4.55195 ( 3544) metal coordination : bond 0.02018 ( 8) metal coordination : angle 2.35084 ( 6) covalent geometry : bond 0.00619 (33002) covalent geometry : angle 0.70501 (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 354 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 274 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.5332 (tp) cc_final: 0.4838 (tt) REVERT: B 50 ASP cc_start: 0.5214 (OUTLIER) cc_final: 0.4886 (t0) REVERT: B 470 MET cc_start: 0.0088 (pmm) cc_final: -0.0477 (pmm) REVERT: C 102 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: C 192 ASP cc_start: 0.7635 (p0) cc_final: 0.7374 (p0) REVERT: C 220 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8093 (tp) REVERT: Y 173 TRP cc_start: 0.7808 (t60) cc_final: 0.7567 (t60) REVERT: D 61 THR cc_start: 0.5182 (m) cc_final: 0.4912 (m) REVERT: E 52 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: E 470 MET cc_start: 0.2185 (OUTLIER) cc_final: 0.1630 (ptt) REVERT: F 361 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6969 (mp) REVERT: G 357 ARG cc_start: 0.6869 (ttt180) cc_final: 0.6639 (ttt180) outliers start: 80 outliers final: 49 residues processed: 330 average time/residue: 0.4268 time to fit residues: 229.4855 Evaluate side-chains 313 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 3.509 ------------------------------------------------------------------------------- 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 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 15 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 144 THR 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 12 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 102 GLN 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 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 159 VAL Chi-restraints excluded: chain D residue 213 MET 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 470 MET 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 361 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 86 MET 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 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 193 THR Chi-restraints excluded: chain X residue 239 HIS 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: 4.9990 chunk 128 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 378 optimal weight: 8.9990 chunk 367 optimal weight: 10.0000 chunk 334 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 272 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 GLN C 306 GLN ** C 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.240258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.218986 restraints weight = 41386.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.215972 restraints weight = 109559.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.211896 restraints weight = 51341.065| |-----------------------------------------------------------------------------| r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4461 r_free = 0.4461 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 = 0.4461 r_free = 0.4461 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33010 Z= 0.164 Angle : 0.623 12.658 45146 Z= 0.313 Chirality : 0.041 0.162 5077 Planarity : 0.004 0.060 5440 Dihedral : 16.899 170.491 5355 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 2.10 % Allowed : 16.09 % Favored : 81.82 % 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: -0.92 (0.14), residues: 3712 helix: 0.03 (0.13), residues: 1833 sheet: -0.06 (0.38), residues: 189 loop : -1.36 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 336 HIS 0.005 0.001 HIS G 176 PHE 0.019 0.002 PHE X 221 TYR 0.026 0.002 TYR B 375 ARG 0.012 0.000 ARG X 245 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 1275) hydrogen bonds : angle 4.40556 ( 3544) metal coordination : bond 0.01027 ( 8) metal coordination : angle 1.52046 ( 6) covalent geometry : bond 0.00394 (33002) covalent geometry : angle 0.62244 (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 346 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 278 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.5386 (tp) cc_final: 0.4888 (tt) REVERT: B 50 ASP cc_start: 0.5304 (OUTLIER) cc_final: 0.5006 (t0) REVERT: B 61 THR cc_start: 0.7770 (t) cc_final: 0.7421 (m) REVERT: B 470 MET cc_start: -0.0055 (pmm) cc_final: -0.0500 (pmm) REVERT: C 102 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7331 (mt0) REVERT: D 61 THR cc_start: 0.5125 (m) cc_final: 0.4865 (m) REVERT: D 268 THR cc_start: 0.7004 (OUTLIER) cc_final: 0.6731 (t) REVERT: D 484 MET cc_start: 0.4665 (mpp) cc_final: 0.2303 (tpt) REVERT: E 52 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7315 (pt0) REVERT: E 446 MET cc_start: 0.5047 (OUTLIER) cc_final: 0.4651 (mtm) REVERT: E 470 MET cc_start: 0.1861 (OUTLIER) cc_final: 0.1446 (ptt) REVERT: F 361 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6782 (mp) REVERT: G 357 ARG cc_start: 0.6799 (ttt180) cc_final: 0.6598 (ttt180) outliers start: 68 outliers final: 51 residues processed: 321 average time/residue: 0.5930 time to fit residues: 308.1402 Evaluate side-chains 324 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 6.439 ------------------------------------------------------------------------------- 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 350 LEU 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 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 102 GLN 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 255 MET Chi-restraints excluded: chain C residue 306 GLN 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 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 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 446 MET Chi-restraints excluded: chain E residue 470 MET 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 361 LEU 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 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 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 215 LEU 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: 0.0870 chunk 307 optimal weight: 0.3980 chunk 370 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.0020 chunk 217 optimal weight: 6.9990 chunk 368 optimal weight: 6.9990 chunk 329 optimal weight: 0.0170 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 40.0000 chunk 223 optimal weight: 0.9990 overall best weight: 0.2404 ------------------------------------------------------------------------------- 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 170 HIS ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.239165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.221335 restraints weight = 40968.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.215718 restraints weight = 102930.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.211235 restraints weight = 60754.406| |-----------------------------------------------------------------------------| r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4508 r_free = 0.4508 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4508 r_free = 0.4508 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33010 Z= 0.103 Angle : 0.571 10.505 45146 Z= 0.287 Chirality : 0.039 0.165 5077 Planarity : 0.004 0.062 5440 Dihedral : 16.523 157.375 5355 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 1.57 % Allowed : 17.07 % Favored : 81.35 % 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: -0.61 (0.14), residues: 3712 helix: 0.25 (0.13), residues: 1838 sheet: 0.20 (0.38), residues: 189 loop : -1.17 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 336 HIS 0.004 0.001 HIS G 383 PHE 0.019 0.001 PHE D 311 TYR 0.023 0.001 TYR B 375 ARG 0.010 0.000 ARG X 245 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 1275) hydrogen bonds : angle 4.23296 ( 3544) metal coordination : bond 0.00313 ( 8) metal coordination : angle 0.82634 ( 6) covalent geometry : bond 0.00222 (33002) covalent geometry : angle 0.57137 (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 345 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 294 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.5150 (tp) cc_final: 0.4785 (tt) REVERT: B 61 THR cc_start: 0.7728 (t) cc_final: 0.7382 (m) REVERT: C 102 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7139 (mt0) REVERT: D 61 THR cc_start: 0.5235 (m) cc_final: 0.4974 (m) REVERT: D 484 MET cc_start: 0.4748 (mpp) cc_final: 0.2704 (tpt) REVERT: E 446 MET cc_start: 0.5102 (OUTLIER) cc_final: 0.4762 (mtm) REVERT: E 470 MET cc_start: 0.1903 (OUTLIER) cc_final: 0.1514 (ptt) outliers start: 51 outliers final: 34 residues processed: 324 average time/residue: 0.4509 time to fit residues: 241.3969 Evaluate side-chains 309 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 272 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 350 LEU 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 144 THR Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 102 GLN 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 96 MET Chi-restraints excluded: chain Y residue 159 VAL 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 446 MET 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 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 48 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 275 optimal weight: 1.9990 chunk 356 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 357 optimal weight: 1.9990 chunk 299 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 377 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 330 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN ** G 198 ASN ** 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 = 0.4753 r_free = 0.4753 target = 0.232606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.212524 restraints weight = 40915.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.208108 restraints weight = 75615.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.205501 restraints weight = 80954.608| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4498 r_free = 0.4498 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4498 r_free = 0.4498 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 33010 Z= 0.238 Angle : 0.695 15.423 45146 Z= 0.348 Chirality : 0.043 0.189 5077 Planarity : 0.005 0.059 5440 Dihedral : 16.858 150.277 5355 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.53 % Rotamer: Outliers : 1.91 % Allowed : 16.98 % Favored : 81.11 % 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: -0.89 (0.14), residues: 3712 helix: 0.06 (0.13), residues: 1830 sheet: -0.07 (0.38), residues: 189 loop : -1.33 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 336 HIS 0.014 0.001 HIS A 383 PHE 0.022 0.002 PHE D 311 TYR 0.022 0.002 TYR D 444 ARG 0.011 0.000 ARG X 245 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 1275) hydrogen bonds : angle 4.46806 ( 3544) metal coordination : bond 0.01958 ( 8) metal coordination : angle 2.32008 ( 6) covalent geometry : bond 0.00583 (33002) covalent geometry : angle 0.69412 (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 326 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 264 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ILE cc_start: 0.4889 (tp) cc_final: 0.4570 (tt) REVERT: B 50 ASP cc_start: 0.4797 (OUTLIER) cc_final: 0.4453 (t0) REVERT: B 61 THR cc_start: 0.7573 (t) cc_final: 0.7233 (m) REVERT: C 102 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7403 (mt0) REVERT: Y 173 TRP cc_start: 0.7664 (t60) cc_final: 0.7442 (t60) REVERT: D 61 THR cc_start: 0.5265 (m) cc_final: 0.5033 (m) REVERT: D 268 THR cc_start: 0.6801 (OUTLIER) cc_final: 0.6561 (t) REVERT: D 484 MET cc_start: 0.4337 (mpp) cc_final: 0.2558 (tpt) REVERT: E 52 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7109 (pt0) REVERT: E 470 MET cc_start: 0.1530 (OUTLIER) cc_final: 0.1267 (ptt) REVERT: F 35 ASN cc_start: 0.7972 (t0) cc_final: 0.7726 (t0) REVERT: F 361 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6957 (mp) outliers start: 62 outliers final: 41 residues processed: 306 average time/residue: 0.4408 time to fit residues: 219.8825 Evaluate side-chains 299 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU 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 237 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain C residue 102 GLN 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 Y residue 162 ASP 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 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 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 13 THR Chi-restraints excluded: chain G residue 24 ILE 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 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 46 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 301 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 380 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 241 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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** ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 287 HIS D 319 GLN E 45 GLN F 198 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.233312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.201502 restraints weight = 40760.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.201806 restraints weight = 98837.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.202024 restraints weight = 35149.792| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4404 r_free = 0.4404 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4404 r_free = 0.4404 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 33010 Z= 0.197 Angle : 0.667 16.694 45146 Z= 0.335 Chirality : 0.042 0.186 5077 Planarity : 0.004 0.059 5440 Dihedral : 16.813 142.219 5355 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 1.67 % Allowed : 17.88 % Favored : 80.46 % 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: -0.93 (0.14), residues: 3712 helix: 0.05 (0.13), residues: 1823 sheet: -0.08 (0.39), residues: 175 loop : -1.37 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 336 HIS 0.006 0.001 HIS G 176 PHE 0.018 0.002 PHE Y 4 TYR 0.022 0.002 TYR D 444 ARG 0.011 0.000 ARG X 245 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 1275) hydrogen bonds : angle 4.46609 ( 3544) metal coordination : bond 0.01425 ( 8) metal coordination : angle 1.90067 ( 6) covalent geometry : bond 0.00481 (33002) covalent geometry : angle 0.66652 (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 317 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.4706 (mmt) cc_final: 0.3772 (tpp) REVERT: A 408 ILE cc_start: 0.5105 (tp) cc_final: 0.4757 (tt) REVERT: B 50 ASP cc_start: 0.5375 (OUTLIER) cc_final: 0.4990 (t0) REVERT: B 61 THR cc_start: 0.7912 (t) cc_final: 0.7567 (m) REVERT: C 102 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7418 (mt0) REVERT: D 61 THR cc_start: 0.5238 (m) cc_final: 0.4974 (m) REVERT: D 268 THR cc_start: 0.6846 (OUTLIER) cc_final: 0.6600 (t) REVERT: D 484 MET cc_start: 0.5093 (mpp) cc_final: 0.2773 (tpt) REVERT: E 52 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7258 (pt0) REVERT: E 470 MET cc_start: 0.1920 (OUTLIER) cc_final: 0.1693 (ptt) REVERT: F 35 ASN cc_start: 0.7975 (t0) cc_final: 0.7735 (t0) REVERT: F 361 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6831 (mp) outliers start: 54 outliers final: 44 residues processed: 299 average time/residue: 0.4282 time to fit residues: 206.8356 Evaluate side-chains 307 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU 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 A residue 484 MET 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 102 GLN 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 Y residue 162 ASP 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 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 470 MET 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 13 THR Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 56 VAL 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 177 HIS Chi-restraints excluded: chain X residue 193 THR 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: 0.9990 chunk 242 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 323 optimal weight: 0.6980 chunk 305 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** ** Y 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.236245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.216929 restraints weight = 40746.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.214180 restraints weight = 70648.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.212356 restraints weight = 60410.246| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4566 r_free = 0.4566 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4566 r_free = 0.4566 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.4566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 33010 Z= 0.128 Angle : 0.615 15.967 45146 Z= 0.308 Chirality : 0.040 0.169 5077 Planarity : 0.004 0.060 5440 Dihedral : 16.509 143.207 5355 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 1.57 % Allowed : 18.25 % Favored : 80.18 % 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: -0.73 (0.14), residues: 3712 helix: 0.19 (0.13), residues: 1839 sheet: 0.10 (0.39), residues: 175 loop : -1.26 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 336 HIS 0.004 0.001 HIS G 383 PHE 0.017 0.001 PHE X 221 TYR 0.026 0.001 TYR D 444 ARG 0.011 0.000 ARG B 272 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 1275) hydrogen bonds : angle 4.32043 ( 3544) metal coordination : bond 0.00600 ( 8) metal coordination : angle 1.25079 ( 6) covalent geometry : bond 0.00298 (33002) covalent geometry : angle 0.61469 (45140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11608.98 seconds wall clock time: 208 minutes 27.71 seconds (12507.71 seconds total)