Starting phenix.real_space_refine on Tue Aug 26 15:16:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki3_37251/08_2025/8ki3_37251.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki3_37251/08_2025/8ki3_37251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ki3_37251/08_2025/8ki3_37251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki3_37251/08_2025/8ki3_37251.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ki3_37251/08_2025/8ki3_37251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki3_37251/08_2025/8ki3_37251.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.120 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 Br 1 7.06 5 P 13 5.49 5 Mg 5 5.21 5 S 159 5.16 5 C 24671 2.51 5 N 6549 2.21 5 O 7264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 272 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38662 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3830 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 484} Chain breaks: 1 Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3714 Classifications: {'peptide': 487} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3458 Classifications: {'peptide': 456} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3529 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "G" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2103 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 5, 'TRANS': 265} Chain: "J" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "3" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.04, per 1000 atoms: 0.23 Number of scatterers: 38662 At special positions: 0 Unit cell: (142.35, 130.67, 243.09, 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) Br 1 34.99 S 159 16.00 P 13 15.00 Mg 5 11.99 O 7264 8.00 N 6549 7.00 C 24671 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: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9208 Finding SS restraints... Secondary structure from input PDB file: 230 helices and 24 sheets defined 58.9% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 4 through 7 removed outlier: 3.540A pdb=" N GLU A 7 " --> pdb=" O GLY A 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4 through 7' Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.938A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.887A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.550A pdb=" N GLY A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 239 through 259 Proline residue: A 247 - end of helix removed outlier: 3.930A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.738A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.740A pdb=" N GLY A 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.520A pdb=" N GLY A 360 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.750A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 removed outlier: 3.867A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.652A pdb=" N LEU A 410 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.644A pdb=" N LYS A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 490 through 508 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.517A pdb=" N LEU B 81 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.555A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.901A pdb=" N GLY B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.519A pdb=" N LYS B 198 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 239 through 259 Proline residue: B 247 - end of helix removed outlier: 4.064A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.557A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 297 through 307 removed outlier: 4.006A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 380 through 401 removed outlier: 4.073A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 429 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 476 Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.621A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 507 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.787A pdb=" N LEU C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.817A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 239 through 259 Proline residue: C 247 - end of helix removed outlier: 4.006A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 284 removed outlier: 3.744A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.977A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.533A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 4.213A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 400 " --> pdb=" O GLN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 460 through 476 Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 140 through 146 Processing helix chain 'D' and resid 164 through 180 Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 228 through 249 removed outlier: 4.905A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 276 removed outlier: 4.047A pdb=" N THR D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.807A pdb=" N GLY D 283 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 339 through 344 removed outlier: 3.620A pdb=" N ALA D 343 " --> pdb=" O SER D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 394 removed outlier: 4.071A pdb=" N HIS D 370 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 418 removed outlier: 3.668A pdb=" N SER D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 436 through 450 Processing helix chain 'D' and resid 456 through 460 Processing helix chain 'D' and resid 465 through 480 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.542A pdb=" N LEU E 94 " --> pdb=" O PRO E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 129 Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 164 through 180 Processing helix chain 'E' and resid 192 through 205 Processing helix chain 'E' and resid 228 through 249 removed outlier: 5.021A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.580A pdb=" N PHE E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 322 through 329 Processing helix chain 'E' and resid 339 through 345 Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 367 through 391 removed outlier: 3.574A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 417 Processing helix chain 'E' and resid 421 through 423 No H-bonds generated for 'chain 'E' and resid 421 through 423' Processing helix chain 'E' and resid 424 through 429 Processing helix chain 'E' and resid 436 through 450 Processing helix chain 'E' and resid 456 through 460 Processing helix chain 'E' and resid 465 through 474 Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.625A pdb=" N THR F 93 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU F 94 " --> pdb=" O PRO F 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 90 through 94' Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.546A pdb=" N GLU F 128 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 177 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 4.796A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 275 removed outlier: 4.079A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 329 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 339 through 344 Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 367 through 394 removed outlier: 4.583A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.715A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 425 removed outlier: 3.665A pdb=" N GLU F 425 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 450 Processing helix chain 'F' and resid 456 through 460 Processing helix chain 'F' and resid 465 through 477 removed outlier: 3.619A pdb=" N ALA F 469 " --> pdb=" O PRO F 465 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 37 removed outlier: 3.657A pdb=" N ARG G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 48 removed outlier: 3.517A pdb=" N ILE G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 99 removed outlier: 3.549A pdb=" N ILE G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA G 94 " --> pdb=" O LYS G 90 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR G 95 " --> pdb=" O SER G 91 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 117 removed outlier: 3.566A pdb=" N LEU G 116 " --> pdb=" O ILE G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 148 Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 201 through 271 removed outlier: 3.801A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE G 212 " --> pdb=" O ASN G 208 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER G 226 " --> pdb=" O THR G 222 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 19 removed outlier: 3.945A pdb=" N GLY J 19 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 42 removed outlier: 3.600A pdb=" N LYS J 24 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU J 26 " --> pdb=" O PHE J 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 28 removed outlier: 3.511A pdb=" N GLY O 16 " --> pdb=" O TYR O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 47 Processing helix chain 'O' and resid 48 through 56 Processing helix chain 'O' and resid 61 through 76 removed outlier: 3.587A pdb=" N LYS O 65 " --> pdb=" O LYS O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 93 Processing helix chain 'O' and resid 97 through 113 Processing helix chain 'O' and resid 127 through 140 removed outlier: 3.744A pdb=" N SER O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 159 removed outlier: 3.805A pdb=" N LEU O 159 " --> pdb=" O PRO O 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 156 through 159' Processing helix chain 'O' and resid 174 through 188 Processing helix chain '1' and resid 2 through 14 removed outlier: 4.108A pdb=" N PHE 1 8 " --> pdb=" O THR 1 4 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE 1 9 " --> pdb=" O ALA 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 17 through 37 removed outlier: 3.940A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA 1 23 " --> pdb=" O ALA 1 19 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 1 25 " --> pdb=" O SER 1 21 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE 1 33 " --> pdb=" O PHE 1 29 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE 1 34 " --> pdb=" O GLY 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 41 No H-bonds generated for 'chain '1' and resid 39 through 41' Processing helix chain '1' and resid 42 through 69 removed outlier: 3.582A pdb=" N LEU 1 52 " --> pdb=" O SER 1 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET 1 60 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS 1 64 " --> pdb=" O MET 1 60 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 15 removed outlier: 3.737A pdb=" N LYS 2 7 " --> pdb=" O ASP 2 3 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE 2 8 " --> pdb=" O THR 2 4 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE 2 9 " --> pdb=" O ALA 2 5 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA 2 11 " --> pdb=" O LYS 2 7 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR 2 15 " --> pdb=" O ALA 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 30 removed outlier: 3.831A pdb=" N GLY 2 26 " --> pdb=" O GLY 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 30 through 39 removed outlier: 3.752A pdb=" N ILE 2 34 " --> pdb=" O GLY 2 30 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 73 removed outlier: 3.622A pdb=" N SER 2 48 " --> pdb=" O GLN 2 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR 2 49 " --> pdb=" O GLN 2 45 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU 2 52 " --> pdb=" O SER 2 48 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET 2 60 " --> pdb=" O LEU 2 56 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE 2 63 " --> pdb=" O ALA 2 59 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS 2 64 " --> pdb=" O MET 2 60 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 15 removed outlier: 3.592A pdb=" N LYS 3 7 " --> pdb=" O ASP 3 3 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE 3 8 " --> pdb=" O THR 3 4 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE 3 9 " --> pdb=" O ALA 3 5 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 37 removed outlier: 3.978A pdb=" N SER 3 21 " --> pdb=" O GLY 3 17 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY 3 26 " --> pdb=" O GLY 3 22 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR 3 27 " --> pdb=" O ALA 3 23 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE 3 33 " --> pdb=" O PHE 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 39 through 41 No H-bonds generated for 'chain '3' and resid 39 through 41' Processing helix chain '3' and resid 42 through 73 removed outlier: 3.532A pdb=" N TYR 3 49 " --> pdb=" O GLN 3 45 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU 3 52 " --> pdb=" O SER 3 48 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET 3 60 " --> pdb=" O LEU 3 56 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY 3 61 " --> pdb=" O SER 3 57 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N CYS 3 64 " --> pdb=" O MET 3 60 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL 3 67 " --> pdb=" O PHE 3 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 3 72 " --> pdb=" O ALA 3 68 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 13 removed outlier: 3.904A pdb=" N LYS 4 7 " --> pdb=" O ASP 4 3 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE 4 8 " --> pdb=" O THR 4 4 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE 4 9 " --> pdb=" O ALA 4 5 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA 4 13 " --> pdb=" O ILE 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 39 removed outlier: 3.596A pdb=" N GLY 4 26 " --> pdb=" O GLY 4 22 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE 4 33 " --> pdb=" O PHE 4 29 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE 4 34 " --> pdb=" O GLY 4 30 " (cutoff:3.500A) Processing helix chain '4' and resid 42 through 73 removed outlier: 3.717A pdb=" N SER 4 48 " --> pdb=" O GLN 4 44 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR 4 49 " --> pdb=" O GLN 4 45 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER 4 57 " --> pdb=" O GLY 4 53 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET 4 60 " --> pdb=" O LEU 4 56 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N CYS 4 64 " --> pdb=" O MET 4 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU 4 65 " --> pdb=" O GLY 4 61 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL 4 67 " --> pdb=" O PHE 4 63 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU 4 72 " --> pdb=" O ALA 4 68 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 15 removed outlier: 3.582A pdb=" N ALA 5 6 " --> pdb=" O ILE 5 2 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE 5 8 " --> pdb=" O THR 5 4 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE 5 9 " --> pdb=" O ALA 5 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA 5 11 " --> pdb=" O LYS 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 17 through 23 removed outlier: 4.250A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA 5 23 " --> pdb=" O ALA 5 19 " (cutoff:3.500A) Processing helix chain '5' and resid 24 through 39 removed outlier: 3.553A pdb=" N ILE 5 33 " --> pdb=" O PHE 5 29 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 72 removed outlier: 3.682A pdb=" N LEU 5 52 " --> pdb=" O SER 5 48 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET 5 60 " --> pdb=" O LEU 5 56 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS 5 64 " --> pdb=" O MET 5 60 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU 5 72 " --> pdb=" O ALA 5 68 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 15 removed outlier: 3.915A pdb=" N PHE 6 8 " --> pdb=" O THR 6 4 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE 6 9 " --> pdb=" O ALA 6 5 " (cutoff:3.500A) Processing helix chain '6' and resid 16 through 18 No H-bonds generated for 'chain '6' and resid 16 through 18' Processing helix chain '6' and resid 19 through 24 removed outlier: 3.587A pdb=" N ALA 6 23 " --> pdb=" O ALA 6 19 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 39 removed outlier: 3.507A pdb=" N ILE 6 34 " --> pdb=" O GLY 6 30 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG 6 38 " --> pdb=" O ILE 6 34 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN 6 39 " --> pdb=" O GLY 6 35 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 51 removed outlier: 4.379A pdb=" N SER 6 48 " --> pdb=" O GLN 6 44 " (cutoff:3.500A) Processing helix chain '6' and resid 51 through 72 removed outlier: 4.285A pdb=" N MET 6 60 " --> pdb=" O LEU 6 56 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS 6 64 " --> pdb=" O MET 6 60 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU 6 65 " --> pdb=" O GLY 6 61 " (cutoff:3.500A) Processing helix chain '7' and resid 3 through 15 removed outlier: 3.999A pdb=" N PHE 7 8 " --> pdb=" O THR 7 4 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE 7 9 " --> pdb=" O ALA 7 5 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR 7 15 " --> pdb=" O ALA 7 11 " (cutoff:3.500A) Processing helix chain '7' and resid 17 through 25 removed outlier: 3.901A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA 7 23 " --> pdb=" O ALA 7 19 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 37 removed outlier: 4.261A pdb=" N ILE 7 33 " --> pdb=" O PHE 7 29 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE 7 34 " --> pdb=" O GLY 7 30 " (cutoff:3.500A) Processing helix chain '7' and resid 39 through 41 No H-bonds generated for 'chain '7' and resid 39 through 41' Processing helix chain '7' and resid 42 through 48 Processing helix chain '7' and resid 53 through 72 removed outlier: 4.120A pdb=" N ALA 7 59 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET 7 60 " --> pdb=" O LEU 7 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU 7 62 " --> pdb=" O GLU 7 58 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU 7 65 " --> pdb=" O GLY 7 61 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 15 removed outlier: 4.197A pdb=" N PHE 8 8 " --> pdb=" O THR 8 4 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE 8 9 " --> pdb=" O ALA 8 5 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR 8 15 " --> pdb=" O ALA 8 11 " (cutoff:3.500A) Processing helix chain '8' and resid 16 through 21 Processing helix chain '8' and resid 23 through 39 removed outlier: 3.740A pdb=" N ILE 8 33 " --> pdb=" O PHE 8 29 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE 8 34 " --> pdb=" O GLY 8 30 " (cutoff:3.500A) Processing helix chain '8' and resid 42 through 51 removed outlier: 3.568A pdb=" N TYR 8 49 " --> pdb=" O GLN 8 45 " (cutoff:3.500A) Processing helix chain '8' and resid 51 through 72 removed outlier: 3.803A pdb=" N MET 8 60 " --> pdb=" O LEU 8 56 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS 8 64 " --> pdb=" O MET 8 60 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE 8 71 " --> pdb=" O VAL 8 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 121 removed outlier: 3.858A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 removed outlier: 4.127A pdb=" N ILE H 131 " --> pdb=" O THR H 127 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 38 removed outlier: 4.095A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS I 37 " --> pdb=" O ALA I 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 removed outlier: 3.559A pdb=" N PHE K 24 " --> pdb=" O GLU K 20 " (cutoff:3.500A) Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 46 Processing helix chain 'K' and resid 54 through 120 removed outlier: 4.248A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER K 62 " --> pdb=" O PHE K 58 " (cutoff:3.500A) Proline residue: K 76 - end of helix removed outlier: 3.960A pdb=" N ASP K 83 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA K 91 " --> pdb=" O GLU K 87 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA K 96 " --> pdb=" O GLN K 92 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE K 101 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE K 104 " --> pdb=" O SER K 100 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA K 107 " --> pdb=" O HIS K 103 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU K 111 " --> pdb=" O ALA K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 152 removed outlier: 3.899A pdb=" N GLN K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA K 135 " --> pdb=" O ASN K 131 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR K 148 " --> pdb=" O LEU K 144 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU K 150 " --> pdb=" O ARG K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 182 removed outlier: 4.256A pdb=" N HIS K 158 " --> pdb=" O ARG K 154 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN K 162 " --> pdb=" O HIS K 158 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU K 178 " --> pdb=" O ILE K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 206 removed outlier: 3.527A pdb=" N ILE K 198 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS K 206 " --> pdb=" O LYS K 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 18 removed outlier: 3.847A pdb=" N GLU M 17 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 22 No H-bonds generated for 'chain 'M' and resid 20 through 22' Processing helix chain 'M' and resid 23 through 43 removed outlier: 3.601A pdb=" N THR M 36 " --> pdb=" O SER M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 60 removed outlier: 3.625A pdb=" N ALA M 58 " --> pdb=" O ALA M 54 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN M 59 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL M 60 " --> pdb=" O TYR M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 75 removed outlier: 4.105A pdb=" N GLU M 70 " --> pdb=" O VAL M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 123 removed outlier: 3.658A pdb=" N GLU M 92 " --> pdb=" O GLN M 88 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU M 95 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP M 103 " --> pdb=" O SER M 99 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR M 114 " --> pdb=" O ARG M 110 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS M 120 " --> pdb=" O LYS M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 Processing helix chain 'M' and resid 131 through 139 removed outlier: 4.044A pdb=" N GLU M 137 " --> pdb=" O GLU M 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 10 Processing helix chain 'N' and resid 20 through 25 removed outlier: 3.606A pdb=" N ILE N 24 " --> pdb=" O ALA N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 31 Processing helix chain 'N' and resid 40 through 58 Processing helix chain 'N' and resid 64 through 69 Processing helix chain 'N' and resid 75 through 85 removed outlier: 3.597A pdb=" N LEU N 84 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 118 Proline residue: N 107 - end of helix removed outlier: 3.529A pdb=" N THR N 112 " --> pdb=" O LEU N 108 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET N 115 " --> pdb=" O GLY N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 125 Processing helix chain 'N' and resid 137 through 148 removed outlier: 3.679A pdb=" N LEU N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE N 143 " --> pdb=" O PRO N 139 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE N 144 " --> pdb=" O MET N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 181 removed outlier: 3.602A pdb=" N ALA N 157 " --> pdb=" O PRO N 153 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA N 166 " --> pdb=" O ALA N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 182 through 184 No H-bonds generated for 'chain 'N' and resid 182 through 184' Processing helix chain 'N' and resid 185 through 224 removed outlier: 3.521A pdb=" N THR N 189 " --> pdb=" O ASN N 185 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE N 191 " --> pdb=" O PRO N 187 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA N 211 " --> pdb=" O ALA N 207 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE N 214 " --> pdb=" O GLN N 210 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER N 219 " --> pdb=" O THR N 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 19 removed outlier: 3.714A pdb=" N LYS P 19 " --> pdb=" O PRO P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 41 removed outlier: 3.543A pdb=" N ILE P 26 " --> pdb=" O GLN P 22 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1 through 8 removed outlier: 3.745A pdb=" N LEU Q 4 " --> pdb=" O MET Q 1 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR Q 6 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR Q 7 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 21 removed outlier: 3.704A pdb=" N THR Q 14 " --> pdb=" O PRO Q 10 " (cutoff:3.500A) Proline residue: Q 15 - end of helix removed outlier: 3.516A pdb=" N THR Q 19 " --> pdb=" O PRO Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 29 removed outlier: 3.534A pdb=" N LEU Q 26 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 32 removed outlier: 4.247A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG R 32 " --> pdb=" O TRP R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 55 removed outlier: 3.613A pdb=" N TYR R 50 " --> pdb=" O GLY R 46 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS R 53 " --> pdb=" O ARG R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 65 Processing helix chain 'R' and resid 69 through 79 removed outlier: 3.612A pdb=" N LEU R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE R 75 " --> pdb=" O CYS R 71 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 27 through 37 removed outlier: 5.066A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU S 36 " --> pdb=" O TYR S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 61 removed outlier: 4.634A pdb=" N ARG S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 67 Processing helix chain 'S' and resid 68 through 93 removed outlier: 3.898A pdb=" N LEU S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP S 85 " --> pdb=" O GLU S 81 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR S 87 " --> pdb=" O LEU S 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 44 removed outlier: 4.454A pdb=" N TYR T 16 " --> pdb=" O LYS T 12 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR T 30 " --> pdb=" O GLY T 26 " (cutoff:3.500A) Proline residue: T 35 - end of helix removed outlier: 3.803A pdb=" N GLU T 38 " --> pdb=" O LYS T 34 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU T 39 " --> pdb=" O PRO T 35 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU T 40 " --> pdb=" O ARG T 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 54 removed outlier: 3.547A pdb=" N ILE L 47 " --> pdb=" O PHE L 43 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR L 50 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 83 removed outlier: 3.535A pdb=" N GLU L 72 " --> pdb=" O GLN L 68 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.732A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 91 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL E 19 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP E 25 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.233A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 8.522A pdb=" N ILE A 230 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.165A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA F 18 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLN F 27 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE F 16 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.485A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.873A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 147 through 154 removed outlier: 3.664A pdb=" N LYS O 149 " --> pdb=" O VAL O 116 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU C 27 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 91 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N MET C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU C 51 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.187A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 8.672A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.609A pdb=" N ILE C 159 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 13 through 20 removed outlier: 6.432A pdb=" N ASP D 25 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL D 19 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.435A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.113A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU D 157 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE D 158 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.263A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.340A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.106A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLN E 224 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL E 254 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL E 310 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU E 256 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA E 312 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE E 258 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS E 154 " --> pdb=" O ASP E 333 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR E 335 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY E 156 " --> pdb=" O THR E 335 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL E 337 " --> pdb=" O GLY E 156 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE E 158 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.223A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.544A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.122A pdb=" N MET F 98 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL F 254 " --> pdb=" O THR F 308 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL F 310 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU F 256 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA F 312 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE F 258 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR F 314 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS F 154 " --> pdb=" O ALA F 334 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR F 336 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY F 156 " --> pdb=" O THR F 336 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.092A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 171 through 178 removed outlier: 6.543A pdb=" N LEU G 67 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE G 161 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE G 69 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ASN G 163 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N VAL G 71 " --> pdb=" O ASN G 163 " (cutoff:3.500A) removed outlier: 10.899A pdb=" N PHE G 165 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU G 125 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU G 105 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA G 127 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLY G 107 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LYS G 129 " --> pdb=" O GLY G 107 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS I 44 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 26 through 31 removed outlier: 6.416A pdb=" N PHE H 20 " --> pdb=" O PHE H 27 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN H 29 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE H 18 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU H 93 " --> pdb=" O SER H 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.526A pdb=" N GLN H 35 " --> pdb=" O HIS H 66 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY H 61 " --> pdb=" O VAL H 77 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 12 through 13 2102 hydrogen bonds defined for protein. 6045 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.14 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 12620 1.34 - 1.49: 9325 1.49 - 1.64: 17032 1.64 - 1.79: 127 1.79 - 1.94: 193 Bond restraints: 39297 Sorted by residual: bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.461 -0.124 1.10e-02 8.26e+03 1.28e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.461 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.461 -0.124 1.10e-02 8.26e+03 1.26e+02 bond pdb=" C4 ATP A 601 " pdb=" N9 ATP A 601 " ideal model delta sigma weight residual 1.374 1.287 0.087 1.00e-02 1.00e+04 7.55e+01 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.288 0.086 1.00e-02 1.00e+04 7.46e+01 ... (remaining 39292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 52933 3.41 - 6.83: 202 6.83 - 10.24: 25 10.24 - 13.66: 8 13.66 - 17.07: 3 Bond angle restraints: 53171 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 122.80 17.07 1.00e+00 1.00e+00 2.92e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.88 15.99 1.00e+00 1.00e+00 2.56e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 125.34 14.53 1.00e+00 1.00e+00 2.11e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 123.67 13.16 1.00e+00 1.00e+00 1.73e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 123.94 12.89 1.00e+00 1.00e+00 1.66e+02 ... (remaining 53166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 23351 33.74 - 67.49: 419 67.49 - 101.23: 52 101.23 - 134.97: 0 134.97 - 168.72: 3 Dihedral angle restraints: 23825 sinusoidal: 9435 harmonic: 14390 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 108.72 -168.72 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 99.57 -159.57 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 75.54 -135.54 1 2.00e+01 2.50e-03 4.11e+01 ... (remaining 23822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4696 0.048 - 0.097: 1235 0.097 - 0.145: 248 0.145 - 0.194: 10 0.194 - 0.242: 4 Chirality restraints: 6193 Sorted by residual: chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.44 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.44 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.45 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 6190 not shown) Planarity restraints: 6780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 174 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C ASN D 174 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN D 174 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN D 175 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 240 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 241 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 322 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO E 323 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO E 323 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 323 " 0.021 5.00e-02 4.00e+02 ... (remaining 6777 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 242 2.51 - 3.10: 28828 3.10 - 3.70: 58286 3.70 - 4.30: 89987 4.30 - 4.90: 148157 Nonbonded interactions: 325500 Sorted by model distance: nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 1.907 2.170 nonbonded pdb=" O1B ATP A 601 " pdb="MG MG A 602 " model vdw 1.933 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 1.980 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 1.996 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 2.027 2.170 ... (remaining 325495 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 '1' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '2' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '3' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '4' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '5' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '6' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '7' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '8' and (resid 1 through 37 or resid 39 through 75)) } ncs_group { reference = (chain 'A' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'C' and resid 24 through 602) } ncs_group { reference = (chain 'D' and (resid 12 through 391 or resid 400 through 475)) selection = chain 'E' selection = (chain 'F' and (resid 12 through 391 or resid 400 through 475)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.340 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: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 35.790 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.006 0.145 39297 Z= 0.326 Angle : 0.675 17.075 53171 Z= 0.424 Chirality : 0.044 0.242 6193 Planarity : 0.003 0.042 6780 Dihedral : 13.760 168.718 14617 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.09 % Rotamer: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.80 (0.10), residues: 4982 helix: -2.56 (0.08), residues: 2699 sheet: -2.04 (0.21), residues: 505 loop : -2.24 (0.13), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 49 TYR 0.014 0.001 TYR O 170 PHE 0.021 0.001 PHE D 329 TRP 0.014 0.001 TRP M 33 HIS 0.004 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00586 (39297) covalent geometry : angle 0.67494 (53171) hydrogen bonds : bond 0.22473 ( 2102) hydrogen bonds : angle 8.85729 ( 6045) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 768 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8354 (mt-10) REVERT: A 80 LYS cc_start: 0.8570 (pttp) cc_final: 0.7871 (ptmm) REVERT: A 89 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7226 (mmmt) REVERT: A 429 LYS cc_start: 0.8317 (mttt) cc_final: 0.8108 (mtpm) REVERT: A 492 GLN cc_start: 0.7742 (mt0) cc_final: 0.7308 (mp10) REVERT: B 426 GLU cc_start: 0.8190 (mp0) cc_final: 0.7897 (mp0) REVERT: B 492 GLN cc_start: 0.6969 (tm-30) cc_final: 0.6622 (tp40) REVERT: B 499 GLU cc_start: 0.8159 (tt0) cc_final: 0.7943 (tt0) REVERT: C 381 ARG cc_start: 0.7432 (tpp-160) cc_final: 0.7219 (mmp-170) REVERT: D 203 MET cc_start: 0.8221 (mtt) cc_final: 0.7975 (mtt) REVERT: D 295 MET cc_start: 0.8602 (tmm) cc_final: 0.7907 (ttm) REVERT: D 433 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7500 (mmtp) REVERT: E 79 LEU cc_start: 0.8145 (tp) cc_final: 0.7714 (mm) REVERT: E 382 GLN cc_start: 0.7576 (mt0) cc_final: 0.7170 (mm-40) REVERT: E 458 GLN cc_start: 0.7880 (mm110) cc_final: 0.7153 (tm-30) REVERT: F 430 HIS cc_start: 0.7773 (m90) cc_final: 0.7220 (m-70) REVERT: G 11 LYS cc_start: 0.7942 (mttm) cc_final: 0.7605 (mtmt) REVERT: G 75 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7249 (mmm160) REVERT: G 229 MET cc_start: 0.7795 (ttp) cc_final: 0.7594 (ttp) REVERT: O 128 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7058 (tm-30) REVERT: 2 44 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7642 (tm-30) REVERT: 5 75 MET cc_start: 0.5363 (ptp) cc_final: 0.4233 (pp-130) REVERT: 6 44 GLN cc_start: 0.7440 (mm-40) cc_final: 0.6888 (tm-30) REVERT: 7 69 PHE cc_start: 0.8130 (m-10) cc_final: 0.7734 (t80) REVERT: H 134 ARG cc_start: 0.7693 (ttp-110) cc_final: 0.7477 (ttm-80) REVERT: I 7 GLN cc_start: 0.8329 (mm110) cc_final: 0.7968 (mt0) REVERT: I 21 LYS cc_start: 0.8813 (tttm) cc_final: 0.8564 (tttm) REVERT: I 32 LYS cc_start: 0.8111 (tttt) cc_final: 0.7747 (ttmt) REVERT: K 165 MET cc_start: 0.8880 (tpp) cc_final: 0.8656 (mmm) REVERT: K 166 ARG cc_start: 0.8230 (ttt90) cc_final: 0.7794 (ttp-110) REVERT: P 11 ILE cc_start: 0.9190 (mm) cc_final: 0.8962 (mm) REVERT: Q 5 ASN cc_start: 0.8526 (t0) cc_final: 0.8180 (t0) REVERT: R 49 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7523 (tmt170) REVERT: R 85 LYS cc_start: 0.8377 (ptmt) cc_final: 0.8096 (pttp) REVERT: R 87 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7713 (tm-30) REVERT: S 90 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8444 (tm-30) REVERT: L 47 ILE cc_start: 0.8667 (pt) cc_final: 0.8325 (mm) REVERT: L 68 GLN cc_start: 0.8638 (tp40) cc_final: 0.7888 (tp-100) outliers start: 3 outliers final: 2 residues processed: 770 average time/residue: 0.6634 time to fit residues: 611.5073 Evaluate side-chains 569 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 567 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain 2 residue 71 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 470 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 503 ASN B 432 GLN B 466 ASN C 42 HIS C 208 GLN C 385 GLN C 477 GLN D 175 ASN D 180 HIS D 210 ASN D 266 GLN D 364 ASN D 458 GLN E 37 ASN E 174 ASN E 296 GLN E 311 GLN F 42 GLN F 133 GLN F 249 GLN J 37 GLN O 34 GLN O 99 GLN 1 39 ASN I 7 GLN K 88 GLN K 115 GLN K 130 ASN M 74 ASN M 136 ASN M 155 GLN N 46 GLN N 47 GLN N 61 HIS N 225 ASN Q 3 GLN R 83 HIS S 57 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100570 restraints weight = 60747.704| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.36 r_work: 0.3100 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 39297 Z= 0.147 Angle : 0.600 10.653 53171 Z= 0.310 Chirality : 0.043 0.156 6193 Planarity : 0.004 0.059 6780 Dihedral : 7.639 177.237 5572 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % Rotamer: Outliers : 2.21 % Allowed : 11.69 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.11), residues: 4982 helix: -0.92 (0.09), residues: 2632 sheet: -1.56 (0.20), residues: 587 loop : -1.56 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 381 TYR 0.018 0.001 TYR T 25 PHE 0.017 0.001 PHE R 79 TRP 0.015 0.001 TRP M 53 HIS 0.003 0.001 HIS F 120 Details of bonding type rmsd covalent geometry : bond 0.00307 (39297) covalent geometry : angle 0.60036 (53171) hydrogen bonds : bond 0.05094 ( 2102) hydrogen bonds : angle 5.35124 ( 6045) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 613 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8597 (mt-10) REVERT: A 80 LYS cc_start: 0.8322 (pttp) cc_final: 0.7437 (ptmm) REVERT: A 89 LYS cc_start: 0.7407 (mmtm) cc_final: 0.6840 (mmmt) REVERT: A 349 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7807 (pm20) REVERT: A 390 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7774 (tpp) REVERT: A 450 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7551 (mmt-90) REVERT: A 463 LYS cc_start: 0.8398 (mmmm) cc_final: 0.8112 (mmmm) REVERT: A 484 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6426 (ttm110) REVERT: A 492 GLN cc_start: 0.7558 (mt0) cc_final: 0.7104 (mp10) REVERT: B 426 GLU cc_start: 0.8064 (mp0) cc_final: 0.7701 (mp0) REVERT: B 484 ARG cc_start: 0.7109 (tmm160) cc_final: 0.6103 (ttm170) REVERT: B 492 GLN cc_start: 0.6854 (tm-30) cc_final: 0.6429 (tp40) REVERT: C 194 ASP cc_start: 0.6942 (t70) cc_final: 0.6694 (p0) REVERT: C 353 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7410 (mt-10) REVERT: C 381 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.6857 (mmp-170) REVERT: C 445 ILE cc_start: 0.7817 (mp) cc_final: 0.7529 (mp) REVERT: D 203 MET cc_start: 0.7881 (mtt) cc_final: 0.7578 (mtt) REVERT: D 210 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8182 (t0) REVERT: D 433 LYS cc_start: 0.7534 (mmtt) cc_final: 0.7072 (mmtp) REVERT: E 79 LEU cc_start: 0.8086 (tp) cc_final: 0.7525 (mm) REVERT: E 205 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6580 (mp0) REVERT: E 342 ILE cc_start: 0.7725 (mm) cc_final: 0.7428 (mp) REVERT: E 382 GLN cc_start: 0.7266 (mt0) cc_final: 0.6786 (mm-40) REVERT: E 438 LYS cc_start: 0.8166 (mmtp) cc_final: 0.7834 (pttp) REVERT: F 58 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8141 (tt0) REVERT: F 115 GLN cc_start: 0.7904 (pm20) cc_final: 0.7619 (pm20) REVERT: F 430 HIS cc_start: 0.7966 (m90) cc_final: 0.7225 (m-70) REVERT: G 11 LYS cc_start: 0.7342 (mttm) cc_final: 0.7003 (mtmt) REVERT: G 87 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7664 (pttp) REVERT: G 188 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8159 (t0) REVERT: G 229 MET cc_start: 0.7410 (ttp) cc_final: 0.7188 (ttp) REVERT: O 128 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7296 (tm-30) REVERT: O 133 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8102 (pt0) REVERT: 5 75 MET cc_start: 0.5364 (ptp) cc_final: 0.3660 (pp-130) REVERT: 6 44 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7232 (tm-30) REVERT: 7 69 PHE cc_start: 0.8465 (m-10) cc_final: 0.7509 (t80) REVERT: 8 7 LYS cc_start: 0.8512 (mtmm) cc_final: 0.7955 (mttp) REVERT: 8 44 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8048 (mm110) REVERT: 8 47 PHE cc_start: 0.8480 (t80) cc_final: 0.8270 (t80) REVERT: 8 66 MET cc_start: 0.8454 (tpp) cc_final: 0.7869 (tmm) REVERT: I 7 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7880 (mt0) REVERT: I 21 LYS cc_start: 0.8917 (tttm) cc_final: 0.8565 (tttm) REVERT: I 25 ASP cc_start: 0.9080 (m-30) cc_final: 0.8827 (m-30) REVERT: I 44 LYS cc_start: 0.8611 (mtpm) cc_final: 0.8022 (mttp) REVERT: K 158 HIS cc_start: 0.8169 (m-70) cc_final: 0.7957 (m-70) REVERT: K 165 MET cc_start: 0.9172 (tpp) cc_final: 0.8955 (mmm) REVERT: K 166 ARG cc_start: 0.8340 (ttt90) cc_final: 0.7777 (ttp-110) REVERT: K 171 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8701 (tm-30) REVERT: K 175 ASN cc_start: 0.9017 (t0) cc_final: 0.8738 (m-40) REVERT: M 116 LYS cc_start: 0.9358 (tmmt) cc_final: 0.9127 (tmmt) REVERT: N 140 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.6174 (tmm) REVERT: N 185 ASN cc_start: 0.7445 (m-40) cc_final: 0.7160 (p0) REVERT: N 199 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8729 (mp) REVERT: Q 5 ASN cc_start: 0.8280 (t0) cc_final: 0.7768 (t0) REVERT: R 31 MET cc_start: 0.7821 (mtt) cc_final: 0.7423 (mtt) REVERT: R 32 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7226 (mmp80) REVERT: R 49 ARG cc_start: 0.8589 (ttm110) cc_final: 0.7355 (tmt170) REVERT: R 85 LYS cc_start: 0.8403 (ptmt) cc_final: 0.7994 (pttm) REVERT: R 87 GLU cc_start: 0.8778 (mt-10) cc_final: 0.7992 (tm-30) REVERT: S 30 TRP cc_start: 0.7590 (OUTLIER) cc_final: 0.6997 (t-100) REVERT: S 90 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8317 (tm-30) REVERT: T 16 TYR cc_start: 0.8229 (m-80) cc_final: 0.7991 (m-80) REVERT: L 47 ILE cc_start: 0.8728 (pt) cc_final: 0.8465 (mp) REVERT: L 48 ARG cc_start: 0.8538 (ptm-80) cc_final: 0.8270 (ptm-80) REVERT: L 49 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8293 (mm-30) REVERT: L 54 ARG cc_start: 0.8506 (tpp80) cc_final: 0.8181 (tpp80) REVERT: L 68 GLN cc_start: 0.8419 (tp40) cc_final: 0.7847 (tp-100) outliers start: 90 outliers final: 36 residues processed: 652 average time/residue: 0.6331 time to fit residues: 501.2296 Evaluate side-chains 585 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 539 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 4 residue 21 SER Chi-restraints excluded: chain 7 residue 48 SER Chi-restraints excluded: chain 8 residue 44 GLN Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 134 ASP Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain S residue 31 TYR Chi-restraints excluded: chain S residue 97 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 451 optimal weight: 0.0020 chunk 237 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 chunk 422 optimal weight: 0.9990 chunk 50 optimal weight: 0.0470 chunk 58 optimal weight: 0.9980 chunk 252 optimal weight: 0.8980 chunk 339 optimal weight: 5.9990 chunk 406 optimal weight: 8.9990 overall best weight: 0.5888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 ASN D 175 ASN D 364 ASN F 174 ASN 1 39 ASN 7 45 GLN M 23 GLN L 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102114 restraints weight = 57788.899| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.25 r_work: 0.3132 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 39297 Z= 0.119 Angle : 0.547 10.074 53171 Z= 0.279 Chirality : 0.042 0.175 6193 Planarity : 0.004 0.048 6780 Dihedral : 7.096 168.620 5572 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.99 % Favored : 97.97 % Rotamer: Outliers : 2.24 % Allowed : 14.07 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.12), residues: 4982 helix: -0.08 (0.10), residues: 2639 sheet: -1.13 (0.21), residues: 588 loop : -1.16 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 167 TYR 0.035 0.001 TYR S 31 PHE 0.016 0.001 PHE 1 69 TRP 0.013 0.001 TRP M 53 HIS 0.004 0.001 HIS K 172 Details of bonding type rmsd covalent geometry : bond 0.00250 (39297) covalent geometry : angle 0.54741 (53171) hydrogen bonds : bond 0.04135 ( 2102) hydrogen bonds : angle 4.81639 ( 6045) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 584 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8541 (mt-10) REVERT: A 52 MET cc_start: 0.8139 (ttp) cc_final: 0.7492 (tpp) REVERT: A 80 LYS cc_start: 0.8299 (pttp) cc_final: 0.7441 (ptmm) REVERT: A 89 LYS cc_start: 0.7450 (mmtm) cc_final: 0.7115 (mttt) REVERT: A 390 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7796 (tpp) REVERT: A 463 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8113 (mmmm) REVERT: A 492 GLN cc_start: 0.7492 (mt0) cc_final: 0.7076 (mp10) REVERT: B 143 ARG cc_start: 0.8270 (ptp-170) cc_final: 0.7832 (ptp-110) REVERT: B 297 ASP cc_start: 0.8907 (p0) cc_final: 0.8645 (p0) REVERT: B 353 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7923 (mt-10) REVERT: B 426 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: B 484 ARG cc_start: 0.7129 (tmm160) cc_final: 0.6157 (ttm170) REVERT: B 492 GLN cc_start: 0.6858 (tm-30) cc_final: 0.6467 (tp40) REVERT: C 353 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7401 (mt-10) REVERT: C 381 ARG cc_start: 0.7461 (tpp-160) cc_final: 0.6860 (mmp-170) REVERT: D 58 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7890 (mm-30) REVERT: D 203 MET cc_start: 0.7888 (mtt) cc_final: 0.7597 (mtt) REVERT: D 210 ASN cc_start: 0.8587 (t0) cc_final: 0.7643 (t0) REVERT: D 433 LYS cc_start: 0.7520 (mmtt) cc_final: 0.7073 (mmtp) REVERT: E 79 LEU cc_start: 0.8117 (tp) cc_final: 0.7550 (mm) REVERT: E 205 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: E 340 ARG cc_start: 0.7302 (tpt90) cc_final: 0.6866 (tpm-80) REVERT: E 382 GLN cc_start: 0.7289 (mt0) cc_final: 0.6761 (mm-40) REVERT: E 438 LYS cc_start: 0.8193 (mmtp) cc_final: 0.7837 (pttp) REVERT: F 40 GLU cc_start: 0.8692 (mp0) cc_final: 0.8440 (mp0) REVERT: F 58 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8167 (tm-30) REVERT: F 115 GLN cc_start: 0.7926 (pm20) cc_final: 0.7464 (pm20) REVERT: G 11 LYS cc_start: 0.7341 (mttm) cc_final: 0.7035 (mtmt) REVERT: G 155 PHE cc_start: 0.7839 (p90) cc_final: 0.7186 (p90) REVERT: O 126 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5560 (pp) REVERT: O 128 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7397 (tm-30) REVERT: 5 75 MET cc_start: 0.5448 (ptp) cc_final: 0.3714 (pp-130) REVERT: 6 44 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7181 (tm-30) REVERT: 7 45 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7144 (tp40) REVERT: 7 69 PHE cc_start: 0.8489 (m-10) cc_final: 0.7501 (t80) REVERT: 8 7 LYS cc_start: 0.8498 (mtmm) cc_final: 0.7998 (mttp) REVERT: 8 39 ASN cc_start: 0.8340 (t0) cc_final: 0.8029 (t0) REVERT: 8 44 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8021 (mm110) REVERT: 8 47 PHE cc_start: 0.8490 (t80) cc_final: 0.8264 (t80) REVERT: 8 66 MET cc_start: 0.8456 (tpp) cc_final: 0.7952 (tmm) REVERT: 8 69 PHE cc_start: 0.8119 (m-10) cc_final: 0.7234 (t80) REVERT: H 69 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8282 (p0) REVERT: I 7 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7878 (mt0) REVERT: I 21 LYS cc_start: 0.8968 (tttm) cc_final: 0.8521 (tttp) REVERT: I 25 ASP cc_start: 0.9063 (m-30) cc_final: 0.8812 (m-30) REVERT: I 44 LYS cc_start: 0.8670 (mtpm) cc_final: 0.8078 (mttm) REVERT: K 134 MET cc_start: 0.8795 (ptp) cc_final: 0.8450 (ppp) REVERT: K 158 HIS cc_start: 0.8131 (m-70) cc_final: 0.7852 (m-70) REVERT: K 166 ARG cc_start: 0.8405 (ttt90) cc_final: 0.7802 (ptp-110) REVERT: K 167 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8419 (tmm-80) REVERT: K 171 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8484 (tm-30) REVERT: K 175 ASN cc_start: 0.8970 (t0) cc_final: 0.8654 (m-40) REVERT: M 133 GLU cc_start: 0.8654 (tt0) cc_final: 0.8452 (tm-30) REVERT: N 140 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.6011 (tmm) REVERT: N 185 ASN cc_start: 0.7399 (m-40) cc_final: 0.7161 (p0) REVERT: Q 5 ASN cc_start: 0.8152 (t0) cc_final: 0.7602 (t0) REVERT: Q 16 MET cc_start: 0.8827 (tmm) cc_final: 0.8480 (tmm) REVERT: R 49 ARG cc_start: 0.8544 (ttm110) cc_final: 0.7396 (tmt170) REVERT: R 85 LYS cc_start: 0.8399 (ptmt) cc_final: 0.8013 (pttm) REVERT: R 87 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8014 (tm-30) REVERT: S 30 TRP cc_start: 0.7560 (OUTLIER) cc_final: 0.6912 (t-100) REVERT: S 90 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8205 (tm-30) REVERT: S 94 LYS cc_start: 0.7477 (ptmm) cc_final: 0.7216 (ptmm) REVERT: T 32 TYR cc_start: 0.7601 (m-80) cc_final: 0.7210 (m-80) REVERT: L 47 ILE cc_start: 0.8766 (pt) cc_final: 0.8511 (mp) REVERT: L 54 ARG cc_start: 0.8606 (tpp80) cc_final: 0.8145 (tpp80) REVERT: L 68 GLN cc_start: 0.8464 (tp40) cc_final: 0.7885 (tp-100) REVERT: L 78 LEU cc_start: 0.9115 (tp) cc_final: 0.8081 (tm) REVERT: L 81 MET cc_start: 0.8759 (tmt) cc_final: 0.8405 (ppp) REVERT: L 82 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7166 (m-10) outliers start: 91 outliers final: 31 residues processed: 624 average time/residue: 0.6526 time to fit residues: 492.3090 Evaluate side-chains 577 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 536 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 2 residue 67 VAL Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 7 residue 45 GLN Chi-restraints excluded: chain 8 residue 44 GLN Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain L residue 82 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 173 optimal weight: 3.9990 chunk 487 optimal weight: 0.8980 chunk 478 optimal weight: 5.9990 chunk 358 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 445 optimal weight: 0.6980 chunk 217 optimal weight: 2.9990 chunk 452 optimal weight: 0.8980 chunk 479 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN D 180 HIS D 364 ASN 7 45 GLN H 85 ASN Q 3 GLN L 80 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098710 restraints weight = 65063.974| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.36 r_work: 0.3082 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 39297 Z= 0.181 Angle : 0.576 10.058 53171 Z= 0.292 Chirality : 0.044 0.161 6193 Planarity : 0.004 0.043 6780 Dihedral : 7.003 175.433 5572 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 2.83 % Allowed : 15.13 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.12), residues: 4982 helix: 0.12 (0.10), residues: 2663 sheet: -0.96 (0.21), residues: 601 loop : -1.07 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 48 TYR 0.028 0.001 TYR T 32 PHE 0.021 0.001 PHE 5 69 TRP 0.008 0.001 TRP S 30 HIS 0.005 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00428 (39297) covalent geometry : angle 0.57627 (53171) hydrogen bonds : bond 0.04328 ( 2102) hydrogen bonds : angle 4.71983 ( 6045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 545 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8603 (mt-10) REVERT: A 52 MET cc_start: 0.8135 (ttp) cc_final: 0.7492 (tpp) REVERT: A 80 LYS cc_start: 0.8332 (pttp) cc_final: 0.7478 (ptmm) REVERT: A 89 LYS cc_start: 0.7434 (mmtm) cc_final: 0.7058 (mtpt) REVERT: A 463 LYS cc_start: 0.8453 (mmmm) cc_final: 0.8155 (mmmm) REVERT: A 492 GLN cc_start: 0.7540 (mt0) cc_final: 0.7155 (mp10) REVERT: B 143 ARG cc_start: 0.8284 (ptp-170) cc_final: 0.7931 (ptp-170) REVERT: B 297 ASP cc_start: 0.8946 (p0) cc_final: 0.8686 (p0) REVERT: B 304 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7904 (ptp-170) REVERT: B 426 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: B 484 ARG cc_start: 0.7050 (tmm160) cc_final: 0.6066 (ttm170) REVERT: B 492 GLN cc_start: 0.6873 (tm-30) cc_final: 0.6486 (tp40) REVERT: C 353 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7411 (mt-10) REVERT: C 381 ARG cc_start: 0.7489 (tpp-160) cc_final: 0.6879 (mmp-170) REVERT: D 58 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7910 (mm-30) REVERT: D 203 MET cc_start: 0.7872 (mtt) cc_final: 0.7602 (mtt) REVERT: D 210 ASN cc_start: 0.8664 (t0) cc_final: 0.7547 (t0) REVERT: D 433 LYS cc_start: 0.7506 (mmtt) cc_final: 0.7049 (mmtp) REVERT: E 79 LEU cc_start: 0.8099 (tp) cc_final: 0.7524 (mm) REVERT: E 205 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: E 340 ARG cc_start: 0.7388 (tpt90) cc_final: 0.6956 (tpm-80) REVERT: E 382 GLN cc_start: 0.7281 (mt0) cc_final: 0.6753 (mm-40) REVERT: E 438 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7867 (pttp) REVERT: F 40 GLU cc_start: 0.8724 (mp0) cc_final: 0.8444 (mp0) REVERT: F 58 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8166 (tm-30) REVERT: F 115 GLN cc_start: 0.7870 (pm20) cc_final: 0.7643 (pm20) REVERT: G 11 LYS cc_start: 0.7356 (mttm) cc_final: 0.7068 (mtmt) REVERT: G 155 PHE cc_start: 0.7826 (p90) cc_final: 0.7100 (p90) REVERT: G 188 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8048 (t0) REVERT: O 126 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5581 (pp) REVERT: O 128 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7392 (tm-30) REVERT: 5 75 MET cc_start: 0.5299 (ptp) cc_final: 0.3627 (pp-130) REVERT: 6 44 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7224 (tm-30) REVERT: 7 69 PHE cc_start: 0.8472 (m-10) cc_final: 0.7497 (t80) REVERT: 7 75 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7249 (mtp) REVERT: 8 7 LYS cc_start: 0.8462 (mtmm) cc_final: 0.8181 (mtpp) REVERT: 8 44 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8053 (mm110) REVERT: 8 66 MET cc_start: 0.8466 (tpp) cc_final: 0.7932 (tmm) REVERT: 8 69 PHE cc_start: 0.8107 (m-10) cc_final: 0.7242 (t80) REVERT: H 69 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8283 (p0) REVERT: I 7 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7857 (mt0) REVERT: I 21 LYS cc_start: 0.8987 (tttm) cc_final: 0.8599 (tttm) REVERT: I 25 ASP cc_start: 0.9133 (m-30) cc_final: 0.8884 (m-30) REVERT: I 36 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8425 (mm-30) REVERT: I 44 LYS cc_start: 0.8659 (mtpm) cc_final: 0.8065 (mttm) REVERT: K 158 HIS cc_start: 0.8120 (m-70) cc_final: 0.7886 (m-70) REVERT: K 166 ARG cc_start: 0.8382 (ttt90) cc_final: 0.7831 (ptp-110) REVERT: K 171 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8470 (tm-30) REVERT: K 175 ASN cc_start: 0.8997 (t0) cc_final: 0.8656 (m-40) REVERT: N 185 ASN cc_start: 0.7392 (m-40) cc_final: 0.7161 (p0) REVERT: N 199 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8771 (mp) REVERT: P 23 GLU cc_start: 0.8931 (pm20) cc_final: 0.8456 (mp0) REVERT: P 39 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8042 (mtm180) REVERT: Q 5 ASN cc_start: 0.8204 (t0) cc_final: 0.7553 (t0) REVERT: Q 6 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8546 (m) REVERT: R 31 MET cc_start: 0.7933 (mtt) cc_final: 0.7625 (ptp) REVERT: R 49 ARG cc_start: 0.8572 (ttm110) cc_final: 0.7395 (tmt170) REVERT: R 85 LYS cc_start: 0.8423 (ptmt) cc_final: 0.8017 (pttm) REVERT: R 87 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8032 (tm-30) REVERT: S 30 TRP cc_start: 0.7554 (OUTLIER) cc_final: 0.6921 (t-100) REVERT: S 90 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8211 (tm-30) REVERT: S 94 LYS cc_start: 0.7566 (ptmm) cc_final: 0.7234 (ptmm) REVERT: T 32 TYR cc_start: 0.7649 (m-80) cc_final: 0.7318 (m-80) REVERT: L 68 GLN cc_start: 0.8463 (tp40) cc_final: 0.8060 (tp-100) REVERT: L 78 LEU cc_start: 0.9138 (tp) cc_final: 0.8240 (tm) REVERT: L 81 MET cc_start: 0.8876 (tmt) cc_final: 0.8538 (ppp) REVERT: L 82 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7175 (m-10) outliers start: 115 outliers final: 54 residues processed: 590 average time/residue: 0.7077 time to fit residues: 505.0018 Evaluate side-chains 591 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 524 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 60 MET Chi-restraints excluded: chain 1 residue 67 VAL Chi-restraints excluded: chain 2 residue 67 VAL Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 4 residue 21 SER Chi-restraints excluded: chain 7 residue 75 MET Chi-restraints excluded: chain 8 residue 44 GLN Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 121 MET Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 39 ARG Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 268 optimal weight: 0.1980 chunk 407 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 320 optimal weight: 0.8980 chunk 441 optimal weight: 0.7980 chunk 480 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 481 optimal weight: 0.0070 chunk 249 optimal weight: 1.9990 chunk 460 optimal weight: 4.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 180 HIS D 364 ASN F 331 HIS 7 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103358 restraints weight = 57877.748| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.34 r_work: 0.3138 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 39297 Z= 0.108 Angle : 0.530 10.367 53171 Z= 0.268 Chirality : 0.042 0.243 6193 Planarity : 0.004 0.055 6780 Dihedral : 6.515 179.611 5570 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.89 % Favored : 98.09 % Rotamer: Outliers : 2.44 % Allowed : 16.17 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.12), residues: 4982 helix: 0.51 (0.10), residues: 2649 sheet: -0.73 (0.22), residues: 571 loop : -0.84 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 32 TYR 0.021 0.001 TYR E 384 PHE 0.027 0.001 PHE A 464 TRP 0.010 0.001 TRP R 28 HIS 0.005 0.000 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00233 (39297) covalent geometry : angle 0.53029 (53171) hydrogen bonds : bond 0.03746 ( 2102) hydrogen bonds : angle 4.49784 ( 6045) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 570 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8577 (mt-10) REVERT: A 52 MET cc_start: 0.8112 (ttp) cc_final: 0.7465 (tpp) REVERT: A 80 LYS cc_start: 0.8297 (pttp) cc_final: 0.7567 (ptmm) REVERT: A 89 LYS cc_start: 0.7471 (mmtm) cc_final: 0.7033 (mtpt) REVERT: A 463 LYS cc_start: 0.8418 (mmmm) cc_final: 0.8127 (mmmm) REVERT: A 492 GLN cc_start: 0.7532 (mt0) cc_final: 0.7149 (mp10) REVERT: B 143 ARG cc_start: 0.8267 (ptp-170) cc_final: 0.8006 (ptp-170) REVERT: B 196 LYS cc_start: 0.8436 (ptmm) cc_final: 0.7612 (mmmt) REVERT: B 297 ASP cc_start: 0.8880 (p0) cc_final: 0.8631 (p0) REVERT: B 426 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: B 484 ARG cc_start: 0.6944 (tmm160) cc_final: 0.6015 (ttm170) REVERT: B 492 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6392 (tp40) REVERT: C 353 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7259 (mt-10) REVERT: C 381 ARG cc_start: 0.7451 (tpp-160) cc_final: 0.6708 (mmp-170) REVERT: C 385 GLN cc_start: 0.7530 (mt0) cc_final: 0.7223 (mt0) REVERT: D 58 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7922 (mm-30) REVERT: D 203 MET cc_start: 0.7839 (mtt) cc_final: 0.7572 (mtt) REVERT: D 210 ASN cc_start: 0.8681 (t0) cc_final: 0.7608 (t0) REVERT: D 433 LYS cc_start: 0.7519 (mmtt) cc_final: 0.7043 (mmtp) REVERT: E 79 LEU cc_start: 0.8113 (tp) cc_final: 0.7546 (mm) REVERT: E 205 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: E 340 ARG cc_start: 0.7376 (tpt90) cc_final: 0.6977 (tpm-80) REVERT: E 355 ASP cc_start: 0.8382 (m-30) cc_final: 0.7793 (m-30) REVERT: E 382 GLN cc_start: 0.7279 (mt0) cc_final: 0.6736 (mm-40) REVERT: E 438 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7838 (pttp) REVERT: F 40 GLU cc_start: 0.8696 (mp0) cc_final: 0.8464 (mp0) REVERT: F 58 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8167 (tm-30) REVERT: F 115 GLN cc_start: 0.7839 (pm20) cc_final: 0.7594 (pm20) REVERT: F 128 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7920 (mt-10) REVERT: F 431 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7236 (ttt) REVERT: G 11 LYS cc_start: 0.7368 (mttm) cc_final: 0.7024 (mtmt) REVERT: G 155 PHE cc_start: 0.7744 (p90) cc_final: 0.7096 (p90) REVERT: O 64 ILE cc_start: 0.6847 (mm) cc_final: 0.6535 (mt) REVERT: O 126 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5642 (pp) REVERT: O 128 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7344 (tm-30) REVERT: 5 75 MET cc_start: 0.5456 (ptp) cc_final: 0.3628 (pp-130) REVERT: 6 44 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7156 (tm-30) REVERT: 7 69 PHE cc_start: 0.8412 (m-10) cc_final: 0.7436 (t80) REVERT: 8 39 ASN cc_start: 0.8486 (t0) cc_final: 0.8058 (t0) REVERT: 8 44 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8003 (mm110) REVERT: 8 66 MET cc_start: 0.8476 (tpp) cc_final: 0.7966 (tmm) REVERT: 8 69 PHE cc_start: 0.8045 (m-10) cc_final: 0.7183 (t80) REVERT: H 69 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8230 (p0) REVERT: I 7 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7828 (mt0) REVERT: I 21 LYS cc_start: 0.8971 (tttm) cc_final: 0.8544 (tttp) REVERT: I 25 ASP cc_start: 0.9090 (m-30) cc_final: 0.8838 (m-30) REVERT: I 36 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8477 (mm-30) REVERT: I 44 LYS cc_start: 0.8698 (mtpm) cc_final: 0.8160 (mttm) REVERT: K 158 HIS cc_start: 0.8020 (m-70) cc_final: 0.7766 (m-70) REVERT: K 166 ARG cc_start: 0.8405 (ttt90) cc_final: 0.7843 (ptp-110) REVERT: K 171 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8459 (tm-30) REVERT: K 175 ASN cc_start: 0.8974 (t0) cc_final: 0.8641 (m-40) REVERT: K 180 HIS cc_start: 0.8583 (t70) cc_final: 0.8299 (t70) REVERT: M 71 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8820 (pptt) REVERT: N 56 GLN cc_start: 0.8945 (tp40) cc_final: 0.8728 (mm-40) REVERT: N 140 MET cc_start: 0.6417 (OUTLIER) cc_final: 0.6141 (tmm) REVERT: N 150 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8942 (mp) REVERT: N 185 ASN cc_start: 0.7442 (m-40) cc_final: 0.7115 (p0) REVERT: N 199 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8758 (mp) REVERT: P 23 GLU cc_start: 0.8909 (pm20) cc_final: 0.8501 (mp0) REVERT: Q 5 ASN cc_start: 0.8145 (t0) cc_final: 0.7536 (t0) REVERT: Q 6 THR cc_start: 0.8791 (p) cc_final: 0.8504 (m) REVERT: R 31 MET cc_start: 0.7891 (mtt) cc_final: 0.7599 (ptm) REVERT: R 49 ARG cc_start: 0.8528 (ttm110) cc_final: 0.7373 (tmt170) REVERT: R 85 LYS cc_start: 0.8404 (ptmt) cc_final: 0.8002 (pttm) REVERT: R 87 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8027 (tm-30) REVERT: S 30 TRP cc_start: 0.7546 (OUTLIER) cc_final: 0.6887 (t-100) REVERT: S 32 TYR cc_start: 0.8672 (m-80) cc_final: 0.8451 (m-80) REVERT: S 90 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8151 (tm-30) REVERT: T 13 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8422 (pp) REVERT: T 32 TYR cc_start: 0.7652 (m-80) cc_final: 0.7350 (m-80) REVERT: L 48 ARG cc_start: 0.8505 (ptm-80) cc_final: 0.8234 (ptm-80) REVERT: L 68 GLN cc_start: 0.8485 (tp40) cc_final: 0.8091 (tp40) REVERT: L 78 LEU cc_start: 0.9136 (tp) cc_final: 0.8787 (tm) REVERT: L 82 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7376 (m-10) outliers start: 99 outliers final: 37 residues processed: 615 average time/residue: 0.6236 time to fit residues: 465.7467 Evaluate side-chains 584 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 535 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 431 MET Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 7 residue 45 GLN Chi-restraints excluded: chain 8 residue 44 GLN Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 301 optimal weight: 1.9990 chunk 202 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 240 optimal weight: 0.8980 chunk 214 optimal weight: 0.7980 chunk 290 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 457 optimal weight: 2.9990 chunk 415 optimal weight: 0.9990 chunk 342 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN B 65 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 364 ASN 7 45 GLN Q 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.100048 restraints weight = 66872.897| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.41 r_work: 0.3099 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39297 Z= 0.156 Angle : 0.557 10.035 53171 Z= 0.281 Chirality : 0.043 0.172 6193 Planarity : 0.004 0.047 6780 Dihedral : 6.423 176.423 5570 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.85 % Allowed : 16.49 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.12), residues: 4982 helix: 0.57 (0.10), residues: 2660 sheet: -0.69 (0.22), residues: 587 loop : -0.80 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 373 TYR 0.022 0.001 TYR E 384 PHE 0.016 0.001 PHE 5 69 TRP 0.011 0.001 TRP R 28 HIS 0.004 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00371 (39297) covalent geometry : angle 0.55706 (53171) hydrogen bonds : bond 0.03965 ( 2102) hydrogen bonds : angle 4.49488 ( 6045) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 547 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8583 (mt-10) REVERT: A 52 MET cc_start: 0.8106 (ttp) cc_final: 0.7428 (tpt) REVERT: A 80 LYS cc_start: 0.8314 (pttp) cc_final: 0.7587 (ptmm) REVERT: A 89 LYS cc_start: 0.7462 (mmtm) cc_final: 0.7048 (mtpt) REVERT: A 463 LYS cc_start: 0.8410 (mmmm) cc_final: 0.8104 (mmmm) REVERT: A 492 GLN cc_start: 0.7563 (mt0) cc_final: 0.7187 (mp10) REVERT: B 52 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8093 (tpp) REVERT: B 143 ARG cc_start: 0.8293 (ptp-170) cc_final: 0.8026 (ptp-170) REVERT: B 196 LYS cc_start: 0.8427 (ptmm) cc_final: 0.7630 (mmmt) REVERT: B 304 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7803 (ptp-170) REVERT: B 426 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: B 484 ARG cc_start: 0.6956 (tmm160) cc_final: 0.6059 (ttm170) REVERT: B 492 GLN cc_start: 0.6892 (tm-30) cc_final: 0.6474 (tp40) REVERT: C 353 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7236 (mt-10) REVERT: C 381 ARG cc_start: 0.7491 (tpp-160) cc_final: 0.6735 (mmp-170) REVERT: C 385 GLN cc_start: 0.7522 (mt0) cc_final: 0.7199 (mt0) REVERT: D 58 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7954 (mm-30) REVERT: D 64 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8601 (mt) REVERT: D 180 HIS cc_start: 0.7394 (t-170) cc_final: 0.7123 (t-170) REVERT: D 203 MET cc_start: 0.7907 (mtt) cc_final: 0.7641 (mtt) REVERT: D 210 ASN cc_start: 0.8665 (t0) cc_final: 0.8164 (t0) REVERT: D 433 LYS cc_start: 0.7502 (mmtt) cc_final: 0.7060 (mmtp) REVERT: D 467 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: E 79 LEU cc_start: 0.8091 (tp) cc_final: 0.7514 (mm) REVERT: E 205 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: E 340 ARG cc_start: 0.7317 (tpt90) cc_final: 0.6930 (tpm-80) REVERT: E 355 ASP cc_start: 0.8372 (m-30) cc_final: 0.7766 (m-30) REVERT: E 382 GLN cc_start: 0.7290 (mt0) cc_final: 0.6755 (mm-40) REVERT: E 438 LYS cc_start: 0.8247 (mmtp) cc_final: 0.7874 (pttp) REVERT: F 40 GLU cc_start: 0.8714 (mp0) cc_final: 0.8445 (mp0) REVERT: F 58 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8160 (tm-30) REVERT: F 115 GLN cc_start: 0.7850 (pm20) cc_final: 0.7510 (pm20) REVERT: F 128 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7940 (mt-10) REVERT: F 431 MET cc_start: 0.7447 (ttt) cc_final: 0.7220 (ttt) REVERT: G 11 LYS cc_start: 0.7423 (mttm) cc_final: 0.7100 (mtmt) REVERT: G 155 PHE cc_start: 0.7786 (p90) cc_final: 0.7182 (p90) REVERT: O 128 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7328 (tm-30) REVERT: 5 75 MET cc_start: 0.5335 (ptp) cc_final: 0.3558 (pp-130) REVERT: 6 44 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7214 (tm-30) REVERT: 7 69 PHE cc_start: 0.8446 (m-10) cc_final: 0.7468 (t80) REVERT: 8 44 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8038 (mm110) REVERT: 8 66 MET cc_start: 0.8474 (tpp) cc_final: 0.7942 (tmm) REVERT: 8 69 PHE cc_start: 0.8023 (m-10) cc_final: 0.7106 (t80) REVERT: H 69 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8198 (p0) REVERT: I 7 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7854 (mt0) REVERT: I 21 LYS cc_start: 0.8962 (tttm) cc_final: 0.8555 (tttm) REVERT: I 25 ASP cc_start: 0.9095 (m-30) cc_final: 0.8833 (m-30) REVERT: I 36 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8505 (mm-30) REVERT: I 37 LYS cc_start: 0.9084 (tmtt) cc_final: 0.8530 (pttm) REVERT: K 134 MET cc_start: 0.9074 (ttm) cc_final: 0.8774 (tmm) REVERT: K 158 HIS cc_start: 0.8024 (m-70) cc_final: 0.7786 (m-70) REVERT: K 166 ARG cc_start: 0.8424 (ttt90) cc_final: 0.7845 (ptp-110) REVERT: K 171 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8457 (tm-30) REVERT: K 175 ASN cc_start: 0.8974 (t0) cc_final: 0.8643 (m-40) REVERT: K 180 HIS cc_start: 0.8616 (t70) cc_final: 0.8326 (t70) REVERT: M 71 LYS cc_start: 0.9167 (mmmt) cc_final: 0.8835 (pptt) REVERT: M 133 GLU cc_start: 0.8744 (tt0) cc_final: 0.8502 (tm-30) REVERT: N 140 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.6089 (tmm) REVERT: N 150 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8938 (mp) REVERT: N 185 ASN cc_start: 0.7351 (m-40) cc_final: 0.7110 (p0) REVERT: N 199 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8766 (mp) REVERT: P 23 GLU cc_start: 0.8907 (pm20) cc_final: 0.8552 (mp0) REVERT: Q 5 ASN cc_start: 0.8108 (t0) cc_final: 0.7533 (t0) REVERT: R 31 MET cc_start: 0.7951 (mtt) cc_final: 0.7663 (ptm) REVERT: R 49 ARG cc_start: 0.8561 (ttm110) cc_final: 0.7404 (tmt170) REVERT: R 85 LYS cc_start: 0.8431 (ptmt) cc_final: 0.8013 (pttm) REVERT: R 87 GLU cc_start: 0.8730 (mt-10) cc_final: 0.7981 (tm-30) REVERT: S 30 TRP cc_start: 0.7543 (OUTLIER) cc_final: 0.6899 (t-100) REVERT: S 90 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8161 (tm-30) REVERT: T 13 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8472 (pp) REVERT: T 32 TYR cc_start: 0.7678 (m-80) cc_final: 0.7272 (m-80) REVERT: L 48 ARG cc_start: 0.8496 (ptm-80) cc_final: 0.8273 (ptm-80) REVERT: L 68 GLN cc_start: 0.8495 (tp40) cc_final: 0.8083 (tp40) REVERT: L 78 LEU cc_start: 0.9155 (tp) cc_final: 0.8540 (tm) REVERT: L 81 MET cc_start: 0.8889 (tmt) cc_final: 0.8572 (ppp) REVERT: L 82 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7345 (m-10) outliers start: 116 outliers final: 52 residues processed: 610 average time/residue: 0.6207 time to fit residues: 459.2028 Evaluate side-chains 600 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 534 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 60 MET Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 45 GLN Chi-restraints excluded: chain 8 residue 44 GLN Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 170 optimal weight: 0.5980 chunk 246 optimal weight: 0.0000 chunk 64 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 42 optimal weight: 0.0770 chunk 77 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 356 optimal weight: 0.9980 chunk 487 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN D 364 ASN 7 45 GLN Q 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102380 restraints weight = 64136.977| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.38 r_work: 0.3135 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 39297 Z= 0.109 Angle : 0.542 10.650 53171 Z= 0.272 Chirality : 0.042 0.164 6193 Planarity : 0.004 0.056 6780 Dihedral : 6.149 173.472 5570 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.53 % Allowed : 16.93 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.12), residues: 4982 helix: 0.78 (0.10), residues: 2656 sheet: -0.51 (0.22), residues: 568 loop : -0.68 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 41 TYR 0.023 0.001 TYR E 384 PHE 0.025 0.001 PHE 1 69 TRP 0.012 0.001 TRP R 28 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00237 (39297) covalent geometry : angle 0.54199 (53171) hydrogen bonds : bond 0.03652 ( 2102) hydrogen bonds : angle 4.38363 ( 6045) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 557 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8557 (mt-10) REVERT: A 52 MET cc_start: 0.8122 (ttp) cc_final: 0.7452 (tpt) REVERT: A 80 LYS cc_start: 0.8282 (pttp) cc_final: 0.7555 (ptmm) REVERT: A 89 LYS cc_start: 0.7466 (mmtm) cc_final: 0.7083 (mtpt) REVERT: A 390 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7790 (tpp) REVERT: A 463 LYS cc_start: 0.8429 (mmmm) cc_final: 0.8125 (mmmm) REVERT: A 492 GLN cc_start: 0.7522 (mt0) cc_final: 0.7169 (mp10) REVERT: B 65 ASN cc_start: 0.8592 (m-40) cc_final: 0.8391 (m110) REVERT: B 143 ARG cc_start: 0.8280 (ptp-170) cc_final: 0.8017 (ptp-170) REVERT: B 196 LYS cc_start: 0.8377 (ptmm) cc_final: 0.7559 (mmmt) REVERT: B 304 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7784 (ptp-170) REVERT: B 426 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: B 484 ARG cc_start: 0.6890 (ttm170) cc_final: 0.6018 (ttm170) REVERT: B 492 GLN cc_start: 0.6874 (tm-30) cc_final: 0.6379 (tp40) REVERT: C 188 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7604 (ptp-110) REVERT: C 353 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7197 (mt-10) REVERT: C 381 ARG cc_start: 0.7461 (tpp-160) cc_final: 0.6685 (mmp-170) REVERT: C 385 GLN cc_start: 0.7416 (mt0) cc_final: 0.7095 (mt0) REVERT: C 426 GLU cc_start: 0.7053 (mp0) cc_final: 0.6847 (mp0) REVERT: D 58 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7901 (mm-30) REVERT: D 64 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8617 (mt) REVERT: D 173 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8343 (mt) REVERT: D 203 MET cc_start: 0.7875 (mtt) cc_final: 0.7607 (mtt) REVERT: D 433 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7025 (mmtp) REVERT: E 79 LEU cc_start: 0.8116 (tp) cc_final: 0.7537 (mm) REVERT: E 205 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: E 340 ARG cc_start: 0.7301 (tpt90) cc_final: 0.6920 (tpm-80) REVERT: E 345 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6914 (tt) REVERT: E 355 ASP cc_start: 0.8351 (m-30) cc_final: 0.7752 (m-30) REVERT: E 382 GLN cc_start: 0.7271 (mt0) cc_final: 0.6748 (mm-40) REVERT: F 40 GLU cc_start: 0.8699 (mp0) cc_final: 0.8465 (mp0) REVERT: F 58 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8159 (tm-30) REVERT: F 115 GLN cc_start: 0.7777 (pm20) cc_final: 0.7456 (pm20) REVERT: F 128 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7922 (mt-10) REVERT: F 431 MET cc_start: 0.7384 (ttt) cc_final: 0.7135 (ttt) REVERT: G 11 LYS cc_start: 0.7440 (mttm) cc_final: 0.7112 (mtmt) REVERT: G 46 LEU cc_start: 0.8720 (mt) cc_final: 0.8295 (mt) REVERT: O 64 ILE cc_start: 0.6909 (mm) cc_final: 0.6595 (mt) REVERT: O 128 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7354 (tm-30) REVERT: O 169 LYS cc_start: 0.8065 (mmtm) cc_final: 0.7708 (mppt) REVERT: 5 75 MET cc_start: 0.5416 (ptp) cc_final: 0.3578 (pp-130) REVERT: 7 69 PHE cc_start: 0.8392 (m-10) cc_final: 0.7407 (t80) REVERT: 8 39 ASN cc_start: 0.8549 (t0) cc_final: 0.8058 (t0) REVERT: 8 44 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8009 (mm110) REVERT: 8 66 MET cc_start: 0.8494 (tpp) cc_final: 0.8001 (tmm) REVERT: H 69 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8157 (p0) REVERT: I 7 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7856 (mt0) REVERT: I 21 LYS cc_start: 0.8939 (tttm) cc_final: 0.8383 (ttpt) REVERT: I 25 ASP cc_start: 0.9059 (m-30) cc_final: 0.8786 (m-30) REVERT: I 36 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8491 (mm-30) REVERT: I 37 LYS cc_start: 0.9081 (tmtt) cc_final: 0.8488 (pttm) REVERT: I 44 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8142 (mttp) REVERT: K 132 ILE cc_start: 0.9129 (mm) cc_final: 0.8789 (tp) REVERT: K 134 MET cc_start: 0.9033 (ttm) cc_final: 0.8769 (tmm) REVERT: K 158 HIS cc_start: 0.7998 (m-70) cc_final: 0.7782 (m-70) REVERT: K 166 ARG cc_start: 0.8427 (ttt90) cc_final: 0.7825 (ptp-110) REVERT: K 167 ARG cc_start: 0.8577 (ttp80) cc_final: 0.8220 (tmm-80) REVERT: K 171 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8443 (tm-30) REVERT: K 175 ASN cc_start: 0.8975 (t0) cc_final: 0.8623 (m-40) REVERT: K 180 HIS cc_start: 0.8629 (t70) cc_final: 0.8344 (t70) REVERT: M 71 LYS cc_start: 0.9158 (mmmt) cc_final: 0.8831 (pptt) REVERT: M 133 GLU cc_start: 0.8716 (tt0) cc_final: 0.8462 (tm-30) REVERT: N 56 GLN cc_start: 0.8946 (tp40) cc_final: 0.8728 (mm-40) REVERT: N 114 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7642 (mp) REVERT: N 140 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.6072 (tmm) REVERT: N 150 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8955 (mp) REVERT: N 185 ASN cc_start: 0.7345 (m-40) cc_final: 0.7100 (p0) REVERT: N 199 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8758 (mp) REVERT: P 23 GLU cc_start: 0.8893 (pm20) cc_final: 0.8578 (mp0) REVERT: Q 5 ASN cc_start: 0.8072 (t0) cc_final: 0.7557 (t0) REVERT: R 49 ARG cc_start: 0.8522 (ttm110) cc_final: 0.7411 (tmt170) REVERT: R 67 MET cc_start: 0.8903 (ttm) cc_final: 0.8646 (mtp) REVERT: R 85 LYS cc_start: 0.8394 (ptmt) cc_final: 0.7980 (pttm) REVERT: R 87 GLU cc_start: 0.8683 (mt-10) cc_final: 0.7964 (tm-30) REVERT: S 30 TRP cc_start: 0.7548 (OUTLIER) cc_final: 0.6844 (t-100) REVERT: S 90 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8129 (tm-30) REVERT: T 13 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8447 (pp) REVERT: T 32 TYR cc_start: 0.7655 (m-80) cc_final: 0.7244 (m-80) REVERT: L 68 GLN cc_start: 0.8516 (tp40) cc_final: 0.8085 (tp40) REVERT: L 78 LEU cc_start: 0.9147 (tp) cc_final: 0.8668 (tm) REVERT: L 81 MET cc_start: 0.8941 (tmt) cc_final: 0.8736 (ppp) REVERT: L 82 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7402 (m-10) outliers start: 103 outliers final: 50 residues processed: 612 average time/residue: 0.6109 time to fit residues: 453.6728 Evaluate side-chains 594 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 527 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 60 MET Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 44 GLN Chi-restraints excluded: chain 8 residue 44 GLN Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 82 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 403 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 226 optimal weight: 0.0970 chunk 458 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 132 optimal weight: 0.0870 chunk 217 optimal weight: 2.9990 overall best weight: 0.9558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN D 210 ASN D 364 ASN 7 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103741 restraints weight = 60197.047| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.23 r_work: 0.3128 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39297 Z= 0.124 Angle : 0.555 10.552 53171 Z= 0.278 Chirality : 0.042 0.169 6193 Planarity : 0.004 0.048 6780 Dihedral : 6.050 170.701 5570 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.51 % Allowed : 17.30 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.12), residues: 4982 helix: 0.84 (0.10), residues: 2669 sheet: -0.47 (0.22), residues: 570 loop : -0.64 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 359 TYR 0.022 0.001 TYR E 384 PHE 0.014 0.001 PHE 5 69 TRP 0.016 0.001 TRP R 28 HIS 0.019 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00284 (39297) covalent geometry : angle 0.55529 (53171) hydrogen bonds : bond 0.03719 ( 2102) hydrogen bonds : angle 4.35893 ( 6045) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 553 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8581 (mt-10) REVERT: A 52 MET cc_start: 0.8136 (ttp) cc_final: 0.7482 (tpt) REVERT: A 80 LYS cc_start: 0.8307 (pttp) cc_final: 0.7595 (ptmm) REVERT: A 89 LYS cc_start: 0.7528 (mmtm) cc_final: 0.7300 (mtpt) REVERT: A 463 LYS cc_start: 0.8451 (mmmm) cc_final: 0.8144 (mmmm) REVERT: A 492 GLN cc_start: 0.7531 (mt0) cc_final: 0.7178 (mp10) REVERT: B 89 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7769 (mtpp) REVERT: B 143 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8037 (ptp-170) REVERT: B 196 LYS cc_start: 0.8401 (ptmm) cc_final: 0.7584 (mmmt) REVERT: B 304 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7825 (ptp-170) REVERT: B 426 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: B 484 ARG cc_start: 0.6900 (ttm170) cc_final: 0.5998 (ttm170) REVERT: B 492 GLN cc_start: 0.6890 (tm-30) cc_final: 0.6399 (tp40) REVERT: C 353 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7238 (mt-10) REVERT: C 381 ARG cc_start: 0.7487 (tpp-160) cc_final: 0.6759 (mmp-170) REVERT: C 385 GLN cc_start: 0.7458 (mt0) cc_final: 0.7242 (mt0) REVERT: C 426 GLU cc_start: 0.7068 (mp0) cc_final: 0.6864 (mp0) REVERT: D 58 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7943 (mm-30) REVERT: D 64 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8612 (mt) REVERT: D 173 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8380 (mt) REVERT: D 203 MET cc_start: 0.7945 (mtt) cc_final: 0.7677 (mtt) REVERT: D 433 LYS cc_start: 0.7517 (mmtt) cc_final: 0.7052 (mmtp) REVERT: E 79 LEU cc_start: 0.8149 (tp) cc_final: 0.7566 (mm) REVERT: E 205 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: E 340 ARG cc_start: 0.7335 (tpt90) cc_final: 0.6960 (tpm-80) REVERT: E 345 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6953 (tt) REVERT: E 355 ASP cc_start: 0.8355 (m-30) cc_final: 0.7750 (m-30) REVERT: E 382 GLN cc_start: 0.7313 (mt0) cc_final: 0.6785 (mm-40) REVERT: E 438 LYS cc_start: 0.8268 (mmtp) cc_final: 0.7894 (pttp) REVERT: F 40 GLU cc_start: 0.8722 (mp0) cc_final: 0.8486 (mp0) REVERT: F 58 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8186 (tm-30) REVERT: F 115 GLN cc_start: 0.7840 (pm20) cc_final: 0.7633 (pm20) REVERT: F 128 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7944 (mt-10) REVERT: F 431 MET cc_start: 0.7386 (ttt) cc_final: 0.7141 (ttt) REVERT: G 11 LYS cc_start: 0.7495 (mttm) cc_final: 0.7169 (mtmt) REVERT: G 46 LEU cc_start: 0.8737 (mt) cc_final: 0.8345 (mt) REVERT: O 64 ILE cc_start: 0.6937 (mm) cc_final: 0.6650 (mt) REVERT: O 128 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7434 (tm-30) REVERT: O 169 LYS cc_start: 0.8118 (mmtm) cc_final: 0.7744 (mppt) REVERT: 1 7 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7919 (mttt) REVERT: 4 65 LEU cc_start: 0.8257 (mt) cc_final: 0.7927 (mp) REVERT: 5 75 MET cc_start: 0.5402 (ptp) cc_final: 0.3568 (pp-130) REVERT: 7 69 PHE cc_start: 0.8404 (m-10) cc_final: 0.7432 (t80) REVERT: 8 44 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7989 (mm110) REVERT: 8 66 MET cc_start: 0.8476 (tpp) cc_final: 0.8002 (tmm) REVERT: H 69 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8163 (p0) REVERT: I 7 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7880 (mt0) REVERT: I 21 LYS cc_start: 0.8967 (tttm) cc_final: 0.8404 (ttpt) REVERT: I 25 ASP cc_start: 0.9051 (m-30) cc_final: 0.8784 (m-30) REVERT: I 36 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8506 (mm-30) REVERT: I 44 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8173 (mttm) REVERT: K 134 MET cc_start: 0.9017 (ttm) cc_final: 0.8755 (tmm) REVERT: K 166 ARG cc_start: 0.8437 (ttt90) cc_final: 0.7842 (ptp-110) REVERT: K 171 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8450 (tm-30) REVERT: K 175 ASN cc_start: 0.8975 (t0) cc_final: 0.8621 (m-40) REVERT: K 180 HIS cc_start: 0.8639 (t70) cc_final: 0.8345 (t70) REVERT: M 71 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8836 (pptt) REVERT: M 133 GLU cc_start: 0.8720 (tt0) cc_final: 0.8498 (tm-30) REVERT: N 56 GLN cc_start: 0.8939 (tp40) cc_final: 0.8729 (mm-40) REVERT: N 114 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7436 (mp) REVERT: N 140 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.6078 (tmm) REVERT: N 185 ASN cc_start: 0.7374 (m-40) cc_final: 0.7107 (p0) REVERT: N 199 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8696 (mm) REVERT: P 23 GLU cc_start: 0.8924 (pm20) cc_final: 0.8641 (mp0) REVERT: P 34 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8377 (mp) REVERT: Q 5 ASN cc_start: 0.8073 (t0) cc_final: 0.7458 (t0) REVERT: Q 6 THR cc_start: 0.8594 (p) cc_final: 0.8327 (m) REVERT: R 28 TRP cc_start: 0.8069 (t60) cc_final: 0.7787 (t60) REVERT: R 31 MET cc_start: 0.7674 (ptp) cc_final: 0.6631 (tmm) REVERT: R 49 ARG cc_start: 0.8526 (ttm110) cc_final: 0.7438 (tmt170) REVERT: R 67 MET cc_start: 0.8906 (ttm) cc_final: 0.8673 (mtp) REVERT: R 85 LYS cc_start: 0.8413 (ptmt) cc_final: 0.8003 (pttm) REVERT: R 87 GLU cc_start: 0.8686 (mt-10) cc_final: 0.7914 (tm-30) REVERT: S 30 TRP cc_start: 0.7539 (OUTLIER) cc_final: 0.6220 (t-100) REVERT: S 34 LYS cc_start: 0.8712 (mmpt) cc_final: 0.8144 (mmpt) REVERT: S 52 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8295 (pp) REVERT: S 53 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7697 (pttm) REVERT: S 90 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8150 (tm-30) REVERT: T 13 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8455 (pp) REVERT: T 32 TYR cc_start: 0.7560 (m-10) cc_final: 0.7154 (m-80) REVERT: L 68 GLN cc_start: 0.8545 (tp40) cc_final: 0.8145 (tp40) REVERT: L 78 LEU cc_start: 0.9166 (tp) cc_final: 0.8668 (tm) REVERT: L 82 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7419 (m-10) outliers start: 102 outliers final: 56 residues processed: 606 average time/residue: 0.6153 time to fit residues: 454.3683 Evaluate side-chains 607 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 533 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 60 MET Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 6 residue 21 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 45 GLN Chi-restraints excluded: chain 8 residue 44 GLN Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain R residue 33 ASP Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 161 optimal weight: 0.9990 chunk 456 optimal weight: 0.6980 chunk 488 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 404 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 319 optimal weight: 9.9990 chunk 446 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN D 210 ASN D 364 ASN 7 45 GLN Q 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099906 restraints weight = 64672.474| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.38 r_work: 0.3098 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39297 Z= 0.170 Angle : 0.594 13.794 53171 Z= 0.296 Chirality : 0.044 0.186 6193 Planarity : 0.004 0.063 6780 Dihedral : 6.095 167.541 5570 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.49 % Allowed : 17.74 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.12), residues: 4982 helix: 0.79 (0.10), residues: 2666 sheet: -0.56 (0.22), residues: 602 loop : -0.64 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 48 TYR 0.022 0.001 TYR E 384 PHE 0.028 0.001 PHE A 464 TRP 0.012 0.001 TRP R 28 HIS 0.014 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00407 (39297) covalent geometry : angle 0.59369 (53171) hydrogen bonds : bond 0.03997 ( 2102) hydrogen bonds : angle 4.42483 ( 6045) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 547 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.5960 (mt-10) cc_final: 0.5592 (mp0) REVERT: A 50 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8578 (mt-10) REVERT: A 52 MET cc_start: 0.8137 (ttp) cc_final: 0.7469 (tpt) REVERT: A 80 LYS cc_start: 0.8305 (pttp) cc_final: 0.7593 (ptmm) REVERT: A 89 LYS cc_start: 0.7459 (mmtm) cc_final: 0.7238 (mtpt) REVERT: A 463 LYS cc_start: 0.8414 (mmmm) cc_final: 0.8100 (mmmm) REVERT: A 492 GLN cc_start: 0.7520 (mt0) cc_final: 0.7176 (mp10) REVERT: B 52 MET cc_start: 0.8315 (ttp) cc_final: 0.8017 (tpp) REVERT: B 89 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7711 (mtpp) REVERT: B 196 LYS cc_start: 0.8399 (ptmm) cc_final: 0.7607 (mmmt) REVERT: B 304 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7864 (ptp-170) REVERT: B 426 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: B 484 ARG cc_start: 0.6832 (ttm170) cc_final: 0.5958 (ttm170) REVERT: B 492 GLN cc_start: 0.6908 (tm-30) cc_final: 0.6496 (tp40) REVERT: C 353 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7196 (mt-10) REVERT: C 381 ARG cc_start: 0.7491 (tpp-160) cc_final: 0.7265 (tpp80) REVERT: C 426 GLU cc_start: 0.7100 (mp0) cc_final: 0.6886 (mp0) REVERT: D 58 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7904 (mm-30) REVERT: D 64 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8562 (mt) REVERT: D 173 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8333 (mt) REVERT: D 203 MET cc_start: 0.7880 (mtt) cc_final: 0.7611 (mtt) REVERT: D 433 LYS cc_start: 0.7477 (mmtt) cc_final: 0.7016 (mmtp) REVERT: D 467 GLU cc_start: 0.7474 (mp0) cc_final: 0.6998 (mm-30) REVERT: E 79 LEU cc_start: 0.8087 (tp) cc_final: 0.7490 (mm) REVERT: E 205 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: E 340 ARG cc_start: 0.7319 (tpt90) cc_final: 0.6937 (tpm-80) REVERT: E 355 ASP cc_start: 0.8348 (m-30) cc_final: 0.7728 (m-30) REVERT: E 382 GLN cc_start: 0.7309 (mt0) cc_final: 0.6759 (mm-40) REVERT: E 438 LYS cc_start: 0.8249 (mmtp) cc_final: 0.7879 (pttp) REVERT: F 40 GLU cc_start: 0.8706 (mp0) cc_final: 0.8434 (mp0) REVERT: F 58 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8129 (tm-30) REVERT: F 115 GLN cc_start: 0.7827 (pm20) cc_final: 0.7600 (pm20) REVERT: F 128 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7893 (mt-10) REVERT: F 359 ARG cc_start: 0.8064 (mtm110) cc_final: 0.7698 (ttm-80) REVERT: F 431 MET cc_start: 0.7425 (ttt) cc_final: 0.7160 (ttt) REVERT: F 458 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6986 (tp40) REVERT: G 11 LYS cc_start: 0.7463 (mttm) cc_final: 0.7136 (mtmt) REVERT: G 46 LEU cc_start: 0.8687 (mt) cc_final: 0.8277 (mt) REVERT: O 64 ILE cc_start: 0.6943 (mm) cc_final: 0.6673 (mt) REVERT: O 128 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7407 (tm-30) REVERT: O 169 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7701 (mppt) REVERT: 4 65 LEU cc_start: 0.8211 (mt) cc_final: 0.7873 (mp) REVERT: 4 75 MET cc_start: 0.7012 (mmp) cc_final: 0.5182 (tmt) REVERT: 5 75 MET cc_start: 0.5284 (ptp) cc_final: 0.3523 (pp-130) REVERT: 6 44 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7273 (tm-30) REVERT: 7 69 PHE cc_start: 0.8389 (m-10) cc_final: 0.7433 (t80) REVERT: 7 75 MET cc_start: 0.7675 (mmt) cc_final: 0.7282 (mmt) REVERT: 8 44 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8021 (mm110) REVERT: 8 66 MET cc_start: 0.8473 (tpp) cc_final: 0.7969 (tmm) REVERT: H 69 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8127 (p0) REVERT: I 7 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7913 (mt0) REVERT: I 21 LYS cc_start: 0.8950 (tttm) cc_final: 0.8526 (tttp) REVERT: I 25 ASP cc_start: 0.9067 (m-30) cc_final: 0.8790 (m-30) REVERT: I 36 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8509 (mm-30) REVERT: I 37 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8487 (pttm) REVERT: I 44 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8124 (mttm) REVERT: K 134 MET cc_start: 0.9060 (ttm) cc_final: 0.8800 (tmm) REVERT: K 166 ARG cc_start: 0.8408 (ttt90) cc_final: 0.7837 (ptp-110) REVERT: K 167 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8264 (tmm-80) REVERT: K 171 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8430 (tm-30) REVERT: K 175 ASN cc_start: 0.8966 (t0) cc_final: 0.8587 (m-40) REVERT: K 180 HIS cc_start: 0.8647 (t70) cc_final: 0.8368 (t70) REVERT: M 71 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8836 (pptt) REVERT: M 134 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8402 (m-30) REVERT: N 56 GLN cc_start: 0.8953 (tp40) cc_final: 0.8738 (mm-40) REVERT: N 140 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.6032 (tmm) REVERT: N 185 ASN cc_start: 0.7338 (m-40) cc_final: 0.7068 (p0) REVERT: P 11 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8881 (mm) REVERT: P 23 GLU cc_start: 0.8940 (pm20) cc_final: 0.8683 (mp0) REVERT: Q 5 ASN cc_start: 0.8148 (t0) cc_final: 0.7545 (t0) REVERT: Q 6 THR cc_start: 0.8619 (p) cc_final: 0.8338 (m) REVERT: R 49 ARG cc_start: 0.8561 (ttm170) cc_final: 0.7419 (tmt170) REVERT: R 85 LYS cc_start: 0.8448 (ptmt) cc_final: 0.8020 (pttm) REVERT: R 87 GLU cc_start: 0.8740 (mt-10) cc_final: 0.7967 (tm-30) REVERT: S 30 TRP cc_start: 0.7600 (OUTLIER) cc_final: 0.6310 (t-100) REVERT: S 34 LYS cc_start: 0.8717 (mmpt) cc_final: 0.8134 (mmpt) REVERT: S 90 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8154 (tm-30) REVERT: T 13 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8477 (pp) REVERT: T 32 TYR cc_start: 0.7639 (m-10) cc_final: 0.7204 (m-80) REVERT: L 48 ARG cc_start: 0.8427 (ptm-80) cc_final: 0.8201 (ptm-80) REVERT: L 68 GLN cc_start: 0.8588 (tp40) cc_final: 0.8189 (tp40) REVERT: L 78 LEU cc_start: 0.9048 (tp) cc_final: 0.8787 (tm) REVERT: L 82 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7513 (m-10) outliers start: 101 outliers final: 54 residues processed: 598 average time/residue: 0.5870 time to fit residues: 427.0799 Evaluate side-chains 608 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 539 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 458 GLN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 6 residue 21 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 45 GLN Chi-restraints excluded: chain 8 residue 44 GLN Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 134 ASP Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 142 optimal weight: 8.9990 chunk 274 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 490 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 416 optimal weight: 0.7980 chunk 374 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN B 65 ASN D 210 ASN D 364 ASN 7 45 GLN Q 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.137884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100604 restraints weight = 66333.624| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.41 r_work: 0.3112 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39297 Z= 0.135 Angle : 0.587 13.816 53171 Z= 0.291 Chirality : 0.043 0.195 6193 Planarity : 0.004 0.063 6780 Dihedral : 6.009 165.476 5570 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.04 % Allowed : 18.45 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.12), residues: 4982 helix: 0.86 (0.10), residues: 2671 sheet: -0.49 (0.22), residues: 590 loop : -0.60 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 48 TYR 0.022 0.001 TYR E 384 PHE 0.029 0.001 PHE 1 69 TRP 0.027 0.001 TRP R 28 HIS 0.012 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00316 (39297) covalent geometry : angle 0.58696 (53171) hydrogen bonds : bond 0.03849 ( 2102) hydrogen bonds : angle 4.39361 ( 6045) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9964 Ramachandran restraints generated. 4982 Oldfield, 0 Emsley, 4982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 545 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6041 (mt-10) cc_final: 0.5696 (mp0) REVERT: A 50 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8607 (mt-10) REVERT: A 52 MET cc_start: 0.8101 (ttp) cc_final: 0.7503 (tpp) REVERT: A 80 LYS cc_start: 0.8301 (pttp) cc_final: 0.7594 (ptmm) REVERT: A 89 LYS cc_start: 0.7477 (mmtm) cc_final: 0.7119 (mtpt) REVERT: A 463 LYS cc_start: 0.8421 (mmmm) cc_final: 0.8207 (mmmm) REVERT: A 492 GLN cc_start: 0.7485 (mt0) cc_final: 0.7155 (mp10) REVERT: B 52 MET cc_start: 0.8327 (ttp) cc_final: 0.8039 (tpp) REVERT: B 89 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7725 (mtpp) REVERT: B 196 LYS cc_start: 0.8410 (ptmm) cc_final: 0.7625 (mmmt) REVERT: B 304 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7854 (ptp-170) REVERT: B 426 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: B 484 ARG cc_start: 0.6812 (ttm170) cc_final: 0.5986 (ttm170) REVERT: B 492 GLN cc_start: 0.6956 (tm-30) cc_final: 0.6474 (tp40) REVERT: C 353 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7209 (mt-10) REVERT: D 58 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7931 (mm-30) REVERT: D 64 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8553 (mt) REVERT: D 173 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8352 (mt) REVERT: D 203 MET cc_start: 0.7878 (mtt) cc_final: 0.7612 (mtt) REVERT: D 433 LYS cc_start: 0.7482 (mmtt) cc_final: 0.7023 (mmtp) REVERT: D 467 GLU cc_start: 0.7464 (mp0) cc_final: 0.6984 (mm-30) REVERT: E 79 LEU cc_start: 0.8104 (tp) cc_final: 0.7507 (mm) REVERT: E 205 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: E 340 ARG cc_start: 0.7314 (tpt90) cc_final: 0.6931 (tpm-80) REVERT: E 355 ASP cc_start: 0.8351 (m-30) cc_final: 0.7735 (m-30) REVERT: E 382 GLN cc_start: 0.7313 (mt0) cc_final: 0.6766 (mm-40) REVERT: E 438 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7861 (pttp) REVERT: F 40 GLU cc_start: 0.8706 (mp0) cc_final: 0.8440 (mp0) REVERT: F 58 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8139 (tm-30) REVERT: F 115 GLN cc_start: 0.7818 (pm20) cc_final: 0.7597 (pm20) REVERT: F 128 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7898 (mt-10) REVERT: F 359 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7692 (ttm-80) REVERT: F 458 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6977 (tp40) REVERT: G 11 LYS cc_start: 0.7454 (mttm) cc_final: 0.7129 (mtmt) REVERT: G 46 LEU cc_start: 0.8681 (mt) cc_final: 0.8271 (mt) REVERT: O 64 ILE cc_start: 0.6964 (mm) cc_final: 0.6694 (mt) REVERT: O 128 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7377 (tm-30) REVERT: O 169 LYS cc_start: 0.8101 (mmtm) cc_final: 0.7710 (mppt) REVERT: 4 65 LEU cc_start: 0.8211 (mt) cc_final: 0.7868 (mp) REVERT: 4 75 MET cc_start: 0.6950 (mmp) cc_final: 0.4980 (tmt) REVERT: 5 75 MET cc_start: 0.5274 (ptp) cc_final: 0.3526 (pp-130) REVERT: 6 44 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7198 (tm-30) REVERT: 7 69 PHE cc_start: 0.8361 (m-10) cc_final: 0.7411 (t80) REVERT: 8 44 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7992 (mm110) REVERT: 8 66 MET cc_start: 0.8473 (tpp) cc_final: 0.7984 (tmm) REVERT: H 69 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8163 (p0) REVERT: I 7 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7927 (mt0) REVERT: I 21 LYS cc_start: 0.8942 (tttm) cc_final: 0.8513 (tttp) REVERT: I 25 ASP cc_start: 0.9057 (m-30) cc_final: 0.8796 (m-30) REVERT: I 36 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8540 (mm-30) REVERT: I 37 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8494 (pttm) REVERT: I 44 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8182 (mttm) REVERT: K 132 ILE cc_start: 0.9143 (mm) cc_final: 0.8799 (tp) REVERT: K 134 MET cc_start: 0.9038 (ttm) cc_final: 0.8791 (tmm) REVERT: K 166 ARG cc_start: 0.8422 (ttt90) cc_final: 0.7852 (ptp-110) REVERT: K 167 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8264 (tmm-80) REVERT: K 171 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8403 (tm-30) REVERT: K 175 ASN cc_start: 0.8956 (t0) cc_final: 0.8573 (m-40) REVERT: K 180 HIS cc_start: 0.8656 (t70) cc_final: 0.8393 (t70) REVERT: M 11 ASP cc_start: 0.8338 (t0) cc_final: 0.7881 (m-30) REVERT: M 71 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8824 (pptt) REVERT: N 56 GLN cc_start: 0.8940 (tp40) cc_final: 0.8729 (mm-40) REVERT: N 140 MET cc_start: 0.6301 (OUTLIER) cc_final: 0.6028 (tmm) REVERT: N 185 ASN cc_start: 0.7377 (m-40) cc_final: 0.7115 (p0) REVERT: P 11 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8878 (mm) REVERT: P 23 GLU cc_start: 0.8934 (pm20) cc_final: 0.8690 (mp0) REVERT: P 34 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8328 (mp) REVERT: Q 5 ASN cc_start: 0.8081 (t0) cc_final: 0.7475 (t0) REVERT: Q 6 THR cc_start: 0.8619 (p) cc_final: 0.8351 (m) REVERT: R 49 ARG cc_start: 0.8542 (ttm170) cc_final: 0.7401 (tmt170) REVERT: R 67 MET cc_start: 0.8947 (ttm) cc_final: 0.8703 (mtp) REVERT: R 85 LYS cc_start: 0.8446 (ptmt) cc_final: 0.8020 (pttm) REVERT: R 87 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7947 (tm-30) REVERT: S 30 TRP cc_start: 0.7586 (OUTLIER) cc_final: 0.6304 (t-100) REVERT: S 34 LYS cc_start: 0.8706 (mmpt) cc_final: 0.8121 (mmpt) REVERT: S 90 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8163 (tm-30) REVERT: T 13 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8461 (pp) REVERT: T 32 TYR cc_start: 0.7611 (m-10) cc_final: 0.7263 (m-80) REVERT: L 48 ARG cc_start: 0.8358 (ptm-80) cc_final: 0.8145 (ptm-80) REVERT: L 68 GLN cc_start: 0.8589 (tp40) cc_final: 0.8184 (tp40) REVERT: L 78 LEU cc_start: 0.9076 (tp) cc_final: 0.8805 (tm) REVERT: L 82 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7584 (m-10) outliers start: 83 outliers final: 53 residues processed: 588 average time/residue: 0.6251 time to fit residues: 446.9064 Evaluate side-chains 602 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 534 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 458 GLN Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 177 THR Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 6 residue 21 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 45 GLN Chi-restraints excluded: chain 8 residue 44 GLN Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 103 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 457 optimal weight: 0.9980 chunk 391 optimal weight: 4.9990 chunk 283 optimal weight: 0.0770 chunk 280 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 385 optimal weight: 0.6980 chunk 376 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 307 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN D 210 ASN D 364 ASN 7 45 GLN Q 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101807 restraints weight = 64398.539| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.38 r_work: 0.3131 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39297 Z= 0.118 Angle : 0.586 14.583 53171 Z= 0.290 Chirality : 0.043 0.208 6193 Planarity : 0.004 0.058 6780 Dihedral : 5.915 163.191 5570 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.04 % Allowed : 18.45 % Favored : 79.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.12), residues: 4982 helix: 1.03 (0.10), residues: 2646 sheet: -0.43 (0.22), residues: 582 loop : -0.50 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 48 TYR 0.022 0.001 TYR E 384 PHE 0.029 0.001 PHE 1 69 TRP 0.008 0.001 TRP R 28 HIS 0.010 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00265 (39297) covalent geometry : angle 0.58649 (53171) hydrogen bonds : bond 0.03696 ( 2102) hydrogen bonds : angle 4.34530 ( 6045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17044.97 seconds wall clock time: 289 minutes 31.62 seconds (17371.62 seconds total)