Starting phenix.real_space_refine on Sat Mar 7 04:39:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9u_34582/03_2026/8h9u_34582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9u_34582/03_2026/8h9u_34582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9u_34582/03_2026/8h9u_34582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9u_34582/03_2026/8h9u_34582.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9u_34582/03_2026/8h9u_34582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9u_34582/03_2026/8h9u_34582.cif" } resolution = 2.61 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= 0.007 sd= 1.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 159 5.16 5 C 24558 2.51 5 N 6524 2.21 5 O 7222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 319 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38481 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3706 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 467} 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: 3587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3587 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 451} Chain breaks: 1 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: "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: "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: "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: "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: "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: "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: "3" 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: "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: "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: "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: "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: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 422 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 8, 'TRANS': 42} 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: "J" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} 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: "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: "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} Time building chain proxies: 8.67, per 1000 atoms: 0.23 Number of scatterers: 38481 At special positions: 0 Unit cell: (144.54, 135.05, 247.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 159 16.00 P 13 15.00 Mg 5 11.99 O 7222 8.00 N 6524 7.00 C 24558 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: 3.32 Conformation dependent library (CDL) restraints added in 1.4 seconds 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9170 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 21 sheets defined 60.3% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.574A 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: 3.762A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.551A pdb=" N GLY A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.953A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.690A 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 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.761A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 401 removed outlier: 3.970A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.642A 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 507 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.602A 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 191 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 239 through 259 Proline residue: B 247 - end of helix removed outlier: 4.053A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.626A 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 295 through 296 No H-bonds generated for 'chain 'B' and resid 295 through 296' Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.857A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.518A pdb=" N GLY B 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) 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 removed outlier: 3.516A pdb=" N GLN B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 401 removed outlier: 4.498A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 429 removed outlier: 3.534A pdb=" N GLN B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 475 removed outlier: 3.714A pdb=" N ILE B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.505A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 507 removed outlier: 3.641A pdb=" N GLY B 507 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.580A 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: 3.732A 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 209 through 223 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 239 through 259 Proline residue: C 247 - end of helix removed outlier: 3.998A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.573A 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: 4.008A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.607A pdb=" N GLY C 317 " --> pdb=" O ASP C 314 " (cutoff:3.500A) 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: 3.770A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 3.599A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 400 " --> pdb=" O GLN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 429 removed outlier: 3.588A pdb=" N LYS C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 457 through 476 removed outlier: 4.314A pdb=" N THR C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.622A pdb=" N MET E 129 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 164 through 179 Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 228 through 249 removed outlier: 4.887A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.517A pdb=" N PHE E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 284 removed outlier: 3.651A pdb=" N GLY E 283 " --> pdb=" O SER E 280 " (cutoff:3.500A) 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: 4.136A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.772A pdb=" N SER E 418 " --> pdb=" O GLN E 414 " (cutoff:3.500A) 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 449 Processing helix chain 'E' and resid 456 through 460 removed outlier: 3.662A pdb=" N PHE E 460 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 475 removed outlier: 3.603A pdb=" N ALA E 469 " --> pdb=" O PRO E 465 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 475 " --> pdb=" O ALA E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.649A pdb=" N MET F 129 " --> pdb=" O PHE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 176 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 4.914A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 removed outlier: 4.146A pdb=" N PHE F 264 " --> pdb=" O ASN F 260 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 273 " --> pdb=" O SER F 269 " (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 345 Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 367 through 395 removed outlier: 4.818A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 399 removed outlier: 3.572A pdb=" N LEU F 399 " --> pdb=" O MET F 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 396 through 399' Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.694A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 428 removed outlier: 3.751A pdb=" N GLU F 425 " --> pdb=" O GLN F 422 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL F 426 " --> pdb=" O VAL F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 450 Processing helix chain 'F' and resid 456 through 460 removed outlier: 3.527A pdb=" N PHE F 460 " --> pdb=" O GLU F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 477 removed outlier: 3.523A pdb=" N ALA F 469 " --> pdb=" O PRO F 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 164 through 180 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 228 through 249 removed outlier: 4.964A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 removed outlier: 4.220A pdb=" N PHE D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.633A 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 Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 367 through 395 removed outlier: 4.121A 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: 3.683A 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 465 through 480 Processing helix chain 'G' and resid 3 through 32 removed outlier: 3.517A pdb=" N ALA G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 49 removed outlier: 3.803A pdb=" N ALA G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 99 removed outlier: 3.555A pdb=" N SER G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 117 removed outlier: 3.592A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 199 through 221 removed outlier: 3.521A pdb=" N ILE G 212 " --> pdb=" O ASN G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 271 removed outlier: 3.724A pdb=" N MET G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 30 removed outlier: 3.618A pdb=" N GLN O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 47 Processing helix chain 'O' and resid 48 through 57 removed outlier: 3.532A pdb=" N ASN O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'O' and resid 79 through 93 Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'O' and resid 97 through 113 Processing helix chain 'O' and resid 127 through 139 Processing helix chain 'O' and resid 156 through 159 Processing helix chain 'O' and resid 174 through 188 removed outlier: 3.841A pdb=" N LYS O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 121 removed outlier: 4.016A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix removed outlier: 3.831A pdb=" N SER K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 183 removed outlier: 3.573A pdb=" N ASP K 126 " --> pdb=" O HIS K 122 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN K 183 " --> pdb=" O LYS K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 206 removed outlier: 3.512A pdb=" N LEU K 201 " --> pdb=" O CYS K 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.492A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.934A 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 Processing helix chain 'M' and resid 53 through 58 Processing helix chain 'M' and resid 64 through 75 removed outlier: 3.684A pdb=" N ASP M 68 " --> pdb=" O GLY M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 123 Processing helix chain 'M' and resid 126 through 130 removed outlier: 3.504A pdb=" N GLN M 129 " --> pdb=" O PRO M 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET M 130 " --> pdb=" O PHE M 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 126 through 130' Processing helix chain 'M' and resid 131 through 139 Processing helix chain '3' and resid 2 through 15 removed outlier: 3.888A pdb=" N PHE 3 8 " --> pdb=" O THR 3 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 3 9 " --> pdb=" O ALA 3 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 3 15 " --> pdb=" O ALA 3 11 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 39 removed outlier: 3.623A pdb=" N GLY 3 26 " --> pdb=" O GLY 3 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE 3 33 " --> pdb=" O PHE 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 73 removed outlier: 3.644A pdb=" N MET 3 60 " --> pdb=" O LEU 3 56 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS 3 64 " --> pdb=" O MET 3 60 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 15 removed outlier: 3.887A pdb=" N PHE 4 8 " --> pdb=" O THR 4 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 4 9 " --> pdb=" O ALA 4 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 4 15 " --> pdb=" O ALA 4 11 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 39 removed outlier: 3.623A pdb=" N GLY 4 26 " --> pdb=" O GLY 4 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE 4 33 " --> pdb=" O PHE 4 29 " (cutoff:3.500A) Processing helix chain '4' and resid 42 through 73 removed outlier: 3.645A pdb=" N MET 4 60 " --> pdb=" O LEU 4 56 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS 4 64 " --> pdb=" O MET 4 60 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 15 removed outlier: 3.887A pdb=" N PHE 5 8 " --> pdb=" O THR 5 4 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE 5 9 " --> pdb=" O ALA 5 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 5 15 " --> pdb=" O ALA 5 11 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 39 removed outlier: 3.624A pdb=" N GLY 5 26 " --> pdb=" O GLY 5 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE 5 33 " --> pdb=" O PHE 5 29 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 73 removed outlier: 3.645A pdb=" N MET 5 60 " --> pdb=" O LEU 5 56 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS 5 64 " --> pdb=" O MET 5 60 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 15 removed outlier: 3.887A pdb=" N PHE 6 8 " --> pdb=" O THR 6 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 6 9 " --> pdb=" O ALA 6 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 6 15 " --> pdb=" O ALA 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 39 removed outlier: 3.623A pdb=" N GLY 6 26 " --> pdb=" O GLY 6 22 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 6 33 " --> pdb=" O PHE 6 29 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 73 removed outlier: 3.644A pdb=" N MET 6 60 " --> pdb=" O LEU 6 56 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS 6 64 " --> pdb=" O MET 6 60 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 15 removed outlier: 3.887A pdb=" N PHE 7 8 " --> pdb=" O THR 7 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 7 9 " --> pdb=" O ALA 7 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 7 15 " --> pdb=" O ALA 7 11 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 39 removed outlier: 3.623A pdb=" N GLY 7 26 " --> pdb=" O GLY 7 22 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 7 33 " --> pdb=" O PHE 7 29 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 73 removed outlier: 3.645A pdb=" N MET 7 60 " --> pdb=" O LEU 7 56 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS 7 64 " --> pdb=" O MET 7 60 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 15 removed outlier: 3.887A pdb=" N PHE 8 8 " --> pdb=" O THR 8 4 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE 8 9 " --> pdb=" O ALA 8 5 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR 8 15 " --> pdb=" O ALA 8 11 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 39 removed outlier: 3.623A pdb=" N GLY 8 26 " --> pdb=" O GLY 8 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE 8 33 " --> pdb=" O PHE 8 29 " (cutoff:3.500A) Processing helix chain '8' and resid 42 through 73 removed outlier: 3.645A pdb=" N MET 8 60 " --> pdb=" O LEU 8 56 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS 8 64 " --> pdb=" O MET 8 60 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 15 removed outlier: 3.887A pdb=" N PHE 1 8 " --> pdb=" O THR 1 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 1 9 " --> pdb=" O ALA 1 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 1 15 " --> pdb=" O ALA 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 39 removed outlier: 3.623A pdb=" N GLY 1 26 " --> pdb=" O GLY 1 22 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 1 33 " --> pdb=" O PHE 1 29 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 73 removed outlier: 3.644A pdb=" N MET 1 60 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS 1 64 " --> pdb=" O MET 1 60 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 15 removed outlier: 3.888A pdb=" N PHE 2 8 " --> pdb=" O THR 2 4 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE 2 9 " --> pdb=" O ALA 2 5 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR 2 15 " --> pdb=" O ALA 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 39 removed outlier: 3.624A pdb=" N GLY 2 26 " --> pdb=" O GLY 2 22 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 2 33 " --> pdb=" O PHE 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 73 removed outlier: 3.645A pdb=" N MET 2 60 " --> pdb=" O LEU 2 56 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS 2 64 " --> pdb=" O MET 2 60 " (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 122 removed outlier: 3.725A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 9 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 38 removed outlier: 4.272A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 removed outlier: 4.603A pdb=" N SER N 8 " --> pdb=" O LEU N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.716A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 68 through 87 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 3.966A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 127 Processing helix chain 'N' and resid 139 through 183 removed outlier: 4.114A pdb=" N ILE N 143 " --> pdb=" O PRO N 139 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE N 147 " --> pdb=" O ILE N 143 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.715A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR N 183 " --> pdb=" O LEU N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 225 Processing helix chain 'P' and resid 4 through 9 Processing helix chain 'P' and resid 9 through 18 removed outlier: 3.829A pdb=" N MET P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) Proline residue: P 15 - end of helix Processing helix chain 'P' and resid 21 through 41 removed outlier: 3.563A pdb=" N ALA P 41 " --> pdb=" O LYS P 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1 through 5 Processing helix chain 'Q' and resid 8 through 21 removed outlier: 3.507A pdb=" N MET Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR Q 14 " --> pdb=" O PRO Q 10 " (cutoff:3.500A) Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 29 Processing helix chain 'R' and resid 27 through 32 Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.480A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) removed outlier: 3.775A 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 'S' and resid 27 through 37 removed outlier: 4.297A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 68 through 94 Processing helix chain 'T' and resid 8 through 45 Proline residue: T 35 - end of helix removed outlier: 4.065A pdb=" N ALA T 45 " --> pdb=" O ARG T 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 19 through 43 removed outlier: 3.783A pdb=" N GLY J 23 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU J 26 " --> pdb=" O PHE J 22 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 35 removed outlier: 6.605A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 41 current: chain 'A' and resid 60 through 66 removed outlier: 5.661A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 75 current: chain 'B' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 60 through 66 removed outlier: 5.723A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 75 current: chain 'C' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 43 current: chain 'C' and resid 60 through 66 removed outlier: 5.648A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 75 current: chain 'E' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 23 through 28 current: chain 'E' and resid 49 through 57 removed outlier: 6.725A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 60 through 65 current: chain 'F' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 23 through 28 current: chain 'F' and resid 49 through 57 removed outlier: 6.645A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 60 through 65 current: chain 'D' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 23 through 28 current: chain 'D' and resid 49 through 57 removed outlier: 6.685A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 60 through 65 current: chain 'O' and resid 147 through 154 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 147 through 154 current: chain 'O' and resid 169 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.040A 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: 6.318A pdb=" N VAL A 108 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR A 200 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 267 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 202 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASP A 269 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 204 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.483A pdb=" N ILE A 167 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.153A 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 109 removed outlier: 6.634A pdb=" N VAL B 108 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR B 200 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE B 267 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 202 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASP B 269 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 204 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 264 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU B 324 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 266 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL B 326 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR B 268 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLU B 328 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.330A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.332A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.257A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.131A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLN E 224 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER E 184 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL E 221 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE E 186 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLY E 223 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY E 188 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL E 254 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL E 310 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU E 256 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA E 312 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE E 258 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.288A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.214A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.250A pdb=" N LYS F 154 " --> pdb=" O ALA F 334 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR F 336 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY F 156 " --> pdb=" O THR F 336 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.156A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.155A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.295A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL D 185 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP D 259 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA D 187 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL D 254 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL D 310 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU D 256 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA D 312 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE D 258 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR D 314 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU D 157 " --> pdb=" O ILE D 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.143A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.231A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS I 44 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AC2, first strand: chain 'H' and resid 17 through 18 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 47 current: chain 'H' and resid 72 through 77 Processing sheet with id=AC3, first strand: chain 'H' and resid 20 through 21 removed outlier: 6.291A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) 2171 hydrogen bonds defined for protein. 6294 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: 7.87 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6450 1.32 - 1.44: 9470 1.44 - 1.56: 22878 1.56 - 1.68: 21 1.68 - 1.81: 299 Bond restraints: 39118 Sorted by residual: 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 1.27e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.22e+02 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.285 0.089 1.00e-02 1.00e+04 7.85e+01 bond pdb=" C4 ATP A 601 " pdb=" N9 ATP A 601 " ideal model delta sigma weight residual 1.374 1.286 0.088 1.00e-02 1.00e+04 7.75e+01 ... (remaining 39113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 52627 3.35 - 6.70: 259 6.70 - 10.05: 26 10.05 - 13.41: 11 13.41 - 16.76: 4 Bond angle restraints: 52927 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.11 16.76 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 123.23 16.64 1.00e+00 1.00e+00 2.77e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 124.79 15.08 1.00e+00 1.00e+00 2.27e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 122.90 13.93 1.00e+00 1.00e+00 1.94e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 125.53 11.30 1.00e+00 1.00e+00 1.28e+02 ... (remaining 52922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.06: 22732 28.06 - 56.12: 850 56.12 - 84.19: 109 84.19 - 112.25: 17 112.25 - 140.31: 3 Dihedral angle restraints: 23711 sinusoidal: 9380 harmonic: 14331 Sorted by residual: 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 80.31 -140.31 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 74.99 -134.99 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 -176.35 116.35 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 23708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 5077 0.056 - 0.112: 942 0.112 - 0.169: 133 0.169 - 0.225: 5 0.225 - 0.281: 2 Chirality restraints: 6159 Sorted by residual: chirality pdb=" CB ILE S 98 " pdb=" CA ILE S 98 " pdb=" CG1 ILE S 98 " pdb=" CG2 ILE S 98 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 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 -2.45 -0.23 2.00e-01 2.50e+01 1.29e+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 -2.46 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 6156 not shown) Planarity restraints: 6753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 4 38 " 0.721 9.50e-02 1.11e+02 3.23e-01 6.36e+01 pdb=" NE ARG 4 38 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG 4 38 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG 4 38 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 4 38 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 16 " -0.712 9.50e-02 1.11e+02 3.19e-01 6.21e+01 pdb=" NE ARG J 16 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG J 16 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 16 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG J 16 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 53 " 0.007 2.00e-02 2.50e+03 1.75e-02 7.69e+00 pdb=" CG TRP M 53 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP M 53 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP M 53 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP M 53 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP M 53 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP M 53 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 53 " -0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 53 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP M 53 " 0.026 2.00e-02 2.50e+03 ... (remaining 6750 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 226 2.52 - 3.11: 30029 3.11 - 3.71: 59537 3.71 - 4.30: 90855 4.30 - 4.90: 147216 Nonbonded interactions: 327863 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 1.921 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 2.009 2.170 nonbonded pdb=" O1B ATP B 601 " pdb="MG MG B 602 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR F 166 " pdb="MG MG F 502 " model vdw 2.037 2.170 nonbonded pdb=" O1B ATP A 601 " pdb="MG MG A 602 " model vdw 2.087 2.170 ... (remaining 327858 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' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } 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' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.760 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: 0.900 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 34.600 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 39118 Z= 0.348 Angle : 0.715 16.757 52927 Z= 0.447 Chirality : 0.044 0.281 6159 Planarity : 0.007 0.323 6753 Dihedral : 14.856 140.310 14541 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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 are not related in a simple way. whole: -3.00 (0.10), residues: 4962 helix: -2.10 (0.08), residues: 2713 sheet: -1.49 (0.20), residues: 560 loop : -1.58 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 108 TYR 0.023 0.001 TYR G 193 PHE 0.025 0.001 PHE J 34 TRP 0.027 0.002 TRP M 53 HIS 0.005 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00635 (39118) covalent geometry : angle 0.71452 (52927) hydrogen bonds : bond 0.20144 ( 2171) hydrogen bonds : angle 7.84901 ( 6294) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 777 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LYS cc_start: 0.8241 (tppt) cc_final: 0.7870 (tptt) REVERT: B 498 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7723 (tptt) REVERT: C 124 LYS cc_start: 0.7898 (mmtm) cc_final: 0.7684 (mttm) REVERT: C 471 HIS cc_start: 0.6327 (t70) cc_final: 0.5995 (t-170) REVERT: D 475 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7666 (tmtt) REVERT: 4 38 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6849 (ttm170) REVERT: N 66 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7836 (mtt180) REVERT: R 32 ARG cc_start: 0.5789 (mmp-170) cc_final: 0.5450 (mmm160) outliers start: 2 outliers final: 4 residues processed: 779 average time/residue: 0.8126 time to fit residues: 747.2157 Evaluate side-chains 586 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 581 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain R residue 77 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 470 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS A 385 GLN A 396 GLN A 405 GLN A 477 GLN A 503 ASN B 48 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN E 210 ASN E 370 HIS E 458 GLN F 27 GLN F 180 HIS F 197 ASN F 296 GLN F 331 HIS F 458 GLN D 180 HIS D 266 GLN G 120 HIS G 150 ASN G 163 ASN O 57 ASN O 84 ASN O 92 ASN O 97 ASN K 86 ASN K 92 GLN K 102 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 HIS K 180 HIS K 183 GLN M 159 ASN 6 45 GLN 2 45 GLN H 85 ASN H 111 ASN I 34 ASN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 127 HIS N 172 HIS N 225 ASN Q 5 ASN Q 25 GLN Q 46 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115522 restraints weight = 55085.054| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.09 r_work: 0.3316 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39118 Z= 0.140 Angle : 0.599 11.097 52927 Z= 0.307 Chirality : 0.043 0.164 6159 Planarity : 0.005 0.147 6753 Dihedral : 7.312 145.148 5530 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.87 % Favored : 98.07 % Rotamer: Outliers : 1.93 % Allowed : 13.44 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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 are not related in a simple way. whole: -0.65 (0.11), residues: 4962 helix: 0.14 (0.10), residues: 2669 sheet: -0.98 (0.21), residues: 561 loop : -0.93 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 128 TYR 0.020 0.001 TYR M 85 PHE 0.025 0.001 PHE L 43 TRP 0.024 0.002 TRP M 12 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00298 (39118) covalent geometry : angle 0.59928 (52927) hydrogen bonds : bond 0.05225 ( 2171) hydrogen bonds : angle 4.86227 ( 6294) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 636 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.8793 (p0) cc_final: 0.8540 (p0) REVERT: A 498 LYS cc_start: 0.7556 (tppt) cc_final: 0.7315 (tptt) REVERT: B 67 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: B 475 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.6837 (mp10) REVERT: B 476 HIS cc_start: 0.8098 (m-70) cc_final: 0.7850 (m170) REVERT: B 498 LYS cc_start: 0.7470 (ttmt) cc_final: 0.6841 (tptt) REVERT: C 124 LYS cc_start: 0.7453 (mmtm) cc_final: 0.7128 (mttm) REVERT: C 224 ASP cc_start: 0.8170 (t0) cc_final: 0.7381 (t0) REVERT: C 471 HIS cc_start: 0.5546 (t70) cc_final: 0.4752 (t-170) REVERT: F 210 ASN cc_start: 0.8597 (t0) cc_final: 0.8125 (t0) REVERT: F 388 GLN cc_start: 0.6923 (mm-40) cc_final: 0.6697 (mm-40) REVERT: F 402 GLU cc_start: 0.6543 (mm-30) cc_final: 0.6230 (tp30) REVERT: D 205 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: D 475 LYS cc_start: 0.7113 (ttmt) cc_final: 0.6607 (tmtt) REVERT: G 35 GLU cc_start: 0.8317 (tt0) cc_final: 0.8091 (tt0) REVERT: G 53 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: G 110 ASP cc_start: 0.8603 (t70) cc_final: 0.8266 (m-30) REVERT: G 113 ARG cc_start: 0.8541 (tmm-80) cc_final: 0.7964 (ttp80) REVERT: K 174 ILE cc_start: 0.7754 (tp) cc_final: 0.7510 (tt) REVERT: M 55 TYR cc_start: 0.7656 (t80) cc_final: 0.7388 (t80) REVERT: M 59 ASN cc_start: 0.7085 (m-40) cc_final: 0.6730 (m110) REVERT: M 115 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7554 (mp0) REVERT: 5 66 MET cc_start: 0.6391 (tpt) cc_final: 0.6031 (tpt) REVERT: 7 44 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7369 (mm-40) REVERT: 7 47 PHE cc_start: 0.8616 (t80) cc_final: 0.8366 (t80) REVERT: 7 75 MET cc_start: 0.7139 (mpp) cc_final: 0.6843 (mpm) REVERT: 8 58 GLU cc_start: 0.8529 (tt0) cc_final: 0.8166 (mm-30) REVERT: N 140 MET cc_start: 0.6257 (ptm) cc_final: 0.5476 (tpt) REVERT: N 181 MET cc_start: 0.8336 (tpp) cc_final: 0.8113 (tpp) REVERT: N 223 HIS cc_start: 0.8346 (t70) cc_final: 0.7972 (t-170) REVERT: R 32 ARG cc_start: 0.6111 (mmp-170) cc_final: 0.5553 (mmm160) REVERT: R 81 TYR cc_start: 0.7162 (t80) cc_final: 0.6838 (t80) REVERT: S 84 MET cc_start: 0.8652 (mmp) cc_final: 0.7713 (mmp) outliers start: 78 outliers final: 20 residues processed: 675 average time/residue: 0.7788 time to fit residues: 626.5019 Evaluate side-chains 601 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 576 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain 7 residue 44 GLN Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain S residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 90 optimal weight: 6.9990 chunk 434 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 487 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 249 optimal weight: 2.9990 chunk 440 optimal weight: 0.7980 chunk 187 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS C 78 ASN F 27 GLN F 224 GLN F 430 HIS F 458 GLN G 150 ASN O 34 GLN O 57 ASN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN L 69 GLN I 34 ASN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN P 22 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.145474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109221 restraints weight = 54966.509| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.09 r_work: 0.3239 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 39118 Z= 0.260 Angle : 0.659 12.942 52927 Z= 0.337 Chirality : 0.047 0.243 6159 Planarity : 0.004 0.043 6753 Dihedral : 7.312 157.378 5518 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.44 % Favored : 97.52 % Rotamer: Outliers : 2.79 % Allowed : 15.54 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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 are not related in a simple way. whole: -0.11 (0.12), residues: 4962 helix: 0.64 (0.10), residues: 2663 sheet: -0.80 (0.21), residues: 576 loop : -0.78 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 128 TYR 0.023 0.002 TYR G 44 PHE 0.032 0.002 PHE H 45 TRP 0.022 0.002 TRP M 12 HIS 0.007 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00622 (39118) covalent geometry : angle 0.65929 (52927) hydrogen bonds : bond 0.05572 ( 2171) hydrogen bonds : angle 4.74391 ( 6294) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 593 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.8745 (p0) cc_final: 0.8375 (p0) REVERT: A 498 LYS cc_start: 0.7441 (tppt) cc_final: 0.7218 (tptt) REVERT: B 52 MET cc_start: 0.8714 (tpp) cc_final: 0.8469 (tpp) REVERT: B 67 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: B 466 ASN cc_start: 0.7686 (m-40) cc_final: 0.7457 (m110) REVERT: B 498 LYS cc_start: 0.7408 (ttmt) cc_final: 0.6723 (tptt) REVERT: C 124 LYS cc_start: 0.7464 (mmtm) cc_final: 0.7129 (mttm) REVERT: C 224 ASP cc_start: 0.8236 (t0) cc_final: 0.7469 (t0) REVERT: C 471 HIS cc_start: 0.5488 (t70) cc_final: 0.4855 (t-170) REVERT: E 29 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6542 (p0) REVERT: E 128 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: E 205 GLU cc_start: 0.8298 (tt0) cc_final: 0.7878 (tt0) REVERT: E 224 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7322 (mm-40) REVERT: F 217 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7868 (mptm) REVERT: F 344 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7654 (mt-10) REVERT: F 388 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6742 (mm-40) REVERT: F 402 GLU cc_start: 0.6565 (mm-30) cc_final: 0.6244 (tp30) REVERT: F 422 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8108 (tm-30) REVERT: D 205 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: D 355 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8380 (t0) REVERT: D 362 ASP cc_start: 0.8137 (t0) cc_final: 0.7825 (t0) REVERT: D 475 LYS cc_start: 0.7106 (ttmt) cc_final: 0.6603 (tmtt) REVERT: G 36 ARG cc_start: 0.8181 (ptp-170) cc_final: 0.7894 (ptt-90) REVERT: G 53 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: G 110 ASP cc_start: 0.8618 (t70) cc_final: 0.8310 (m-30) REVERT: G 113 ARG cc_start: 0.8512 (tmm-80) cc_final: 0.8000 (ttp80) REVERT: K 104 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7175 (pp) REVERT: K 141 ARG cc_start: 0.7531 (mmm-85) cc_final: 0.7311 (mtm-85) REVERT: K 146 ARG cc_start: 0.8274 (mmp80) cc_final: 0.7864 (mtp85) REVERT: L 48 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8440 (mmm160) REVERT: L 68 GLN cc_start: 0.8014 (pm20) cc_final: 0.7588 (pm20) REVERT: M 115 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7781 (mp0) REVERT: 3 72 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8421 (tt) REVERT: 4 60 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7507 (mmt) REVERT: 4 66 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7147 (mpp) REVERT: 4 75 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.5958 (mpm) REVERT: 7 44 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: 7 75 MET cc_start: 0.7297 (mpp) cc_final: 0.7002 (mpp) REVERT: 8 58 GLU cc_start: 0.8593 (tt0) cc_final: 0.8100 (mm-30) REVERT: N 140 MET cc_start: 0.6303 (ptm) cc_final: 0.5664 (tpt) REVERT: N 223 HIS cc_start: 0.8551 (t70) cc_final: 0.8015 (t-170) REVERT: Q 6 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8700 (m) REVERT: R 32 ARG cc_start: 0.6127 (mmp-170) cc_final: 0.5905 (mmm160) REVERT: R 81 TYR cc_start: 0.7183 (t80) cc_final: 0.6834 (t80) REVERT: S 84 MET cc_start: 0.8581 (mmp) cc_final: 0.7701 (mmp) outliers start: 113 outliers final: 38 residues processed: 659 average time/residue: 0.7495 time to fit residues: 590.1688 Evaluate side-chains 610 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 557 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 72 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 60 MET Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 4 THR Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain 7 residue 44 GLN Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain 1 residue 67 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 47 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 28 optimal weight: 0.0870 chunk 430 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 447 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 487 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 260 ASN F 27 GLN F 458 GLN G 150 ASN O 57 ASN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN P 22 GLN Q 25 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.150423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115684 restraints weight = 54537.833| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.01 r_work: 0.3339 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 39118 Z= 0.114 Angle : 0.560 13.520 52927 Z= 0.283 Chirality : 0.042 0.186 6159 Planarity : 0.004 0.045 6753 Dihedral : 6.689 165.995 5518 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.98 % Rotamer: Outliers : 2.25 % Allowed : 17.22 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 0.60 (0.12), residues: 4962 helix: 1.28 (0.10), residues: 2659 sheet: -0.50 (0.22), residues: 553 loop : -0.56 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 141 TYR 0.020 0.001 TYR M 56 PHE 0.022 0.001 PHE R 79 TRP 0.019 0.001 TRP M 12 HIS 0.006 0.001 HIS K 103 Details of bonding type rmsd covalent geometry : bond 0.00242 (39118) covalent geometry : angle 0.55959 (52927) hydrogen bonds : bond 0.04301 ( 2171) hydrogen bonds : angle 4.39735 ( 6294) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 622 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.8782 (tpp) cc_final: 0.8483 (tpp) REVERT: B 67 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: B 466 ASN cc_start: 0.7757 (m-40) cc_final: 0.7508 (m110) REVERT: B 498 LYS cc_start: 0.7447 (ttmt) cc_final: 0.6847 (tptt) REVERT: C 124 LYS cc_start: 0.7478 (mmtm) cc_final: 0.7148 (mttm) REVERT: C 224 ASP cc_start: 0.8247 (t0) cc_final: 0.7527 (t0) REVERT: C 436 MET cc_start: 0.7770 (mtp) cc_final: 0.7399 (ptm) REVERT: C 471 HIS cc_start: 0.5510 (t70) cc_final: 0.4850 (t-170) REVERT: E 29 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6636 (p0) REVERT: E 205 GLU cc_start: 0.8246 (tt0) cc_final: 0.7840 (tt0) REVERT: F 174 ASN cc_start: 0.8056 (t0) cc_final: 0.7449 (t0) REVERT: F 210 ASN cc_start: 0.8563 (t0) cc_final: 0.8076 (t0) REVERT: F 344 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7715 (mt-10) REVERT: F 388 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6590 (mm-40) REVERT: F 402 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6242 (tp30) REVERT: F 408 SER cc_start: 0.7791 (t) cc_final: 0.7500 (p) REVERT: D 170 MET cc_start: 0.7943 (mmt) cc_final: 0.7627 (mmt) REVERT: D 205 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7230 (tp30) REVERT: D 402 GLU cc_start: 0.7057 (mp0) cc_final: 0.6803 (tm-30) REVERT: D 475 LYS cc_start: 0.7082 (ttmt) cc_final: 0.6563 (tmtt) REVERT: G 36 ARG cc_start: 0.8113 (ptp-170) cc_final: 0.7863 (ptt-90) REVERT: G 53 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: G 110 ASP cc_start: 0.8528 (t70) cc_final: 0.8177 (m-30) REVERT: G 113 ARG cc_start: 0.8517 (tmm-80) cc_final: 0.8012 (ttp80) REVERT: G 147 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: G 241 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: O 103 SER cc_start: 0.6459 (t) cc_final: 0.6113 (p) REVERT: K 84 LYS cc_start: 0.8332 (ttmm) cc_final: 0.7819 (tptt) REVERT: K 164 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8342 (tpp) REVERT: K 167 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8495 (tmm-80) REVERT: L 51 LYS cc_start: 0.8067 (mmpt) cc_final: 0.7811 (mmpt) REVERT: M 115 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7692 (mp0) REVERT: 3 60 MET cc_start: 0.7646 (mmm) cc_final: 0.7241 (mpp) REVERT: 3 72 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8356 (tt) REVERT: 4 32 LEU cc_start: 0.8362 (tp) cc_final: 0.8139 (tp) REVERT: 4 66 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7619 (mtt) REVERT: 4 75 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.5890 (mpm) REVERT: 5 66 MET cc_start: 0.6104 (tpt) cc_final: 0.5783 (tmm) REVERT: 7 47 PHE cc_start: 0.8630 (t80) cc_final: 0.8297 (t80) REVERT: 1 75 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6293 (mtt) REVERT: 2 58 GLU cc_start: 0.7840 (tp30) cc_final: 0.7593 (tp30) REVERT: N 140 MET cc_start: 0.6218 (ptm) cc_final: 0.5698 (tpt) REVERT: N 169 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8897 (tt) REVERT: N 181 MET cc_start: 0.7922 (tpp) cc_final: 0.7687 (tpp) REVERT: R 81 TYR cc_start: 0.7173 (t80) cc_final: 0.6839 (t80) REVERT: S 84 MET cc_start: 0.8575 (mmp) cc_final: 0.7732 (mmp) REVERT: J 40 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6010 (mp0) outliers start: 91 outliers final: 22 residues processed: 671 average time/residue: 0.7247 time to fit residues: 583.5094 Evaluate side-chains 597 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 562 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 72 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 29 PHE Chi-restraints excluded: chain J residue 40 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 104 optimal weight: 7.9990 chunk 274 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 394 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 381 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 418 optimal weight: 0.5980 chunk 384 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN G 150 ASN O 57 ASN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN Q 25 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.149217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114477 restraints weight = 54644.374| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.08 r_work: 0.3303 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39118 Z= 0.142 Angle : 0.568 13.857 52927 Z= 0.288 Chirality : 0.043 0.165 6159 Planarity : 0.004 0.052 6753 Dihedral : 6.637 177.835 5518 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.04 % Favored : 97.94 % Rotamer: Outliers : 2.32 % Allowed : 18.48 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 0.82 (0.12), residues: 4962 helix: 1.42 (0.10), residues: 2678 sheet: -0.43 (0.22), residues: 556 loop : -0.40 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 32 TYR 0.021 0.001 TYR M 56 PHE 0.024 0.001 PHE 3 69 TRP 0.019 0.001 TRP M 12 HIS 0.005 0.001 HIS N 223 Details of bonding type rmsd covalent geometry : bond 0.00323 (39118) covalent geometry : angle 0.56820 (52927) hydrogen bonds : bond 0.04408 ( 2171) hydrogen bonds : angle 4.34161 ( 6294) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 586 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.8750 (tpp) cc_final: 0.8427 (tpp) REVERT: B 67 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: B 454 ASP cc_start: 0.7820 (m-30) cc_final: 0.7589 (m-30) REVERT: B 466 ASN cc_start: 0.7767 (m-40) cc_final: 0.7517 (m110) REVERT: B 498 LYS cc_start: 0.7402 (ttmt) cc_final: 0.6782 (tptt) REVERT: C 124 LYS cc_start: 0.7459 (mmtm) cc_final: 0.7137 (mttm) REVERT: C 224 ASP cc_start: 0.8232 (t0) cc_final: 0.7527 (t0) REVERT: C 436 MET cc_start: 0.7772 (mtp) cc_final: 0.7418 (ptm) REVERT: C 471 HIS cc_start: 0.5473 (t70) cc_final: 0.4810 (t-170) REVERT: E 29 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6582 (p0) REVERT: E 205 GLU cc_start: 0.8274 (tt0) cc_final: 0.7868 (tt0) REVERT: F 174 ASN cc_start: 0.8033 (t0) cc_final: 0.7439 (t0) REVERT: F 344 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7664 (mt-10) REVERT: F 388 GLN cc_start: 0.6953 (mm-40) cc_final: 0.6534 (mm-40) REVERT: F 402 GLU cc_start: 0.6551 (mm-30) cc_final: 0.6230 (tp30) REVERT: F 422 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8012 (tm-30) REVERT: D 475 LYS cc_start: 0.7025 (ttmt) cc_final: 0.6509 (tmtt) REVERT: G 74 ASP cc_start: 0.8462 (m-30) cc_final: 0.8092 (m-30) REVERT: O 15 GLU cc_start: 0.6515 (mp0) cc_final: 0.6168 (mp0) REVERT: O 103 SER cc_start: 0.6391 (t) cc_final: 0.6048 (p) REVERT: K 84 LYS cc_start: 0.8320 (ttmm) cc_final: 0.7750 (tptt) REVERT: K 104 ILE cc_start: 0.7537 (pp) cc_final: 0.7196 (pp) REVERT: K 146 ARG cc_start: 0.8231 (mmp80) cc_final: 0.7631 (mtp180) REVERT: K 164 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8628 (tpp) REVERT: K 167 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8543 (tmm-80) REVERT: K 178 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6958 (pp20) REVERT: L 68 GLN cc_start: 0.7616 (pm20) cc_final: 0.7269 (pm20) REVERT: L 69 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8272 (mp10) REVERT: 3 60 MET cc_start: 0.7549 (mmm) cc_final: 0.7205 (mpp) REVERT: 3 72 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8352 (tt) REVERT: 4 60 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7442 (mmt) REVERT: 4 66 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7630 (mtt) REVERT: 4 75 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6029 (mpm) REVERT: 5 60 MET cc_start: 0.8590 (mmp) cc_final: 0.8332 (mpp) REVERT: 5 66 MET cc_start: 0.6068 (tpt) cc_final: 0.5731 (tmm) REVERT: 1 75 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6412 (mtt) REVERT: N 169 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8941 (tt) REVERT: N 181 MET cc_start: 0.7939 (tpp) cc_final: 0.7438 (tpp) REVERT: Q 29 LEU cc_start: 0.8851 (mt) cc_final: 0.8646 (mp) REVERT: Q 44 MET cc_start: 0.5453 (mmt) cc_final: 0.4922 (mpp) REVERT: R 81 TYR cc_start: 0.7080 (t80) cc_final: 0.6763 (t80) REVERT: S 84 MET cc_start: 0.8608 (mmp) cc_final: 0.7760 (mmp) REVERT: J 40 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6003 (mp0) outliers start: 94 outliers final: 32 residues processed: 640 average time/residue: 0.7100 time to fit residues: 548.1343 Evaluate side-chains 595 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 552 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain O residue 57 ASN Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 72 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 60 MET Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 38 ARG Chi-restraints excluded: chain 2 residue 66 MET Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain J residue 40 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 289 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 315 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS A 405 GLN A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN E 224 GLN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN G 150 ASN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107874 restraints weight = 54985.627| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.06 r_work: 0.3224 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 39118 Z= 0.326 Angle : 0.705 14.055 52927 Z= 0.360 Chirality : 0.050 0.216 6159 Planarity : 0.005 0.044 6753 Dihedral : 7.263 163.051 5518 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.90 % Favored : 97.08 % Rotamer: Outliers : 2.82 % Allowed : 18.48 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 0.35 (0.12), residues: 4962 helix: 0.96 (0.10), residues: 2678 sheet: -0.66 (0.21), residues: 593 loop : -0.46 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 39 TYR 0.022 0.002 TYR G 44 PHE 0.035 0.002 PHE H 45 TRP 0.025 0.002 TRP M 12 HIS 0.008 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00785 (39118) covalent geometry : angle 0.70499 (52927) hydrogen bonds : bond 0.05584 ( 2171) hydrogen bonds : angle 4.65482 ( 6294) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 566 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: B 67 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: B 399 GLU cc_start: 0.7871 (tp30) cc_final: 0.7605 (mp0) REVERT: B 415 GLN cc_start: 0.6677 (mt0) cc_final: 0.6191 (mt0) REVERT: B 466 ASN cc_start: 0.7689 (m-40) cc_final: 0.7425 (m110) REVERT: B 475 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: B 498 LYS cc_start: 0.7439 (ttmt) cc_final: 0.6767 (tptt) REVERT: C 124 LYS cc_start: 0.7465 (mmtm) cc_final: 0.7154 (mttm) REVERT: C 224 ASP cc_start: 0.8261 (t0) cc_final: 0.7511 (t0) REVERT: C 471 HIS cc_start: 0.5469 (t70) cc_final: 0.4838 (t-170) REVERT: C 496 LYS cc_start: 0.6099 (tttm) cc_final: 0.5659 (tppt) REVERT: E 29 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6621 (p0) REVERT: E 128 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7000 (mm-30) REVERT: E 205 GLU cc_start: 0.8248 (tt0) cc_final: 0.7848 (tt0) REVERT: F 205 GLU cc_start: 0.7708 (tp30) cc_final: 0.7240 (mp0) REVERT: F 344 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7661 (mt-10) REVERT: F 388 GLN cc_start: 0.7100 (mm-40) cc_final: 0.6673 (mm-40) REVERT: F 402 GLU cc_start: 0.6563 (mm-30) cc_final: 0.6216 (tp30) REVERT: F 422 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8060 (tm-30) REVERT: D 362 ASP cc_start: 0.8051 (t0) cc_final: 0.7688 (t0) REVERT: D 475 LYS cc_start: 0.7034 (ttmt) cc_final: 0.6541 (tmtt) REVERT: G 74 ASP cc_start: 0.8533 (m-30) cc_final: 0.8178 (m-30) REVERT: O 15 GLU cc_start: 0.6616 (mp0) cc_final: 0.6210 (mp0) REVERT: K 146 ARG cc_start: 0.8295 (mmp80) cc_final: 0.7804 (mtm180) REVERT: K 164 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8503 (tpp) REVERT: K 167 ARG cc_start: 0.8897 (ttp80) cc_final: 0.8566 (tmm-80) REVERT: L 51 LYS cc_start: 0.8147 (mmpt) cc_final: 0.7893 (mmpt) REVERT: L 68 GLN cc_start: 0.7660 (pm20) cc_final: 0.7238 (pm20) REVERT: L 69 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8211 (mp10) REVERT: M 40 ARG cc_start: 0.8807 (mmm-85) cc_final: 0.8548 (mtp180) REVERT: M 151 TYR cc_start: 0.8314 (m-80) cc_final: 0.8057 (m-80) REVERT: 3 72 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8408 (tt) REVERT: 4 60 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7518 (mmt) REVERT: 4 75 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6246 (mpm) REVERT: 5 66 MET cc_start: 0.6509 (tpt) cc_final: 0.6041 (tmm) REVERT: 7 75 MET cc_start: 0.7232 (mpp) cc_final: 0.6805 (mpp) REVERT: 1 75 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7060 (mtt) REVERT: N 101 ASN cc_start: 0.8906 (m-40) cc_final: 0.8515 (m110) REVERT: N 140 MET cc_start: 0.6358 (ptm) cc_final: 0.5726 (tpt) REVERT: N 169 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9017 (tt) REVERT: N 181 MET cc_start: 0.8023 (tpp) cc_final: 0.7720 (tpp) REVERT: P 26 ILE cc_start: 0.8778 (mp) cc_final: 0.8566 (mp) REVERT: Q 42 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7767 (ppp) REVERT: Q 44 MET cc_start: 0.5640 (mmt) cc_final: 0.5050 (mpp) REVERT: R 81 TYR cc_start: 0.7253 (t80) cc_final: 0.6946 (t80) REVERT: S 83 LEU cc_start: 0.8632 (mp) cc_final: 0.8405 (mt) REVERT: S 84 MET cc_start: 0.8656 (mmp) cc_final: 0.7769 (mmp) outliers start: 114 outliers final: 47 residues processed: 629 average time/residue: 0.7246 time to fit residues: 548.8191 Evaluate side-chains 598 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 539 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 150 LEU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 72 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 60 MET Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 51 TRP Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain T residue 8 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 55 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 292 optimal weight: 0.0370 chunk 483 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 373 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 415 optimal weight: 3.9990 chunk 363 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS A 405 GLN A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN E 260 ASN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN G 150 ASN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112462 restraints weight = 54293.718| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.08 r_work: 0.3287 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39118 Z= 0.138 Angle : 0.589 13.466 52927 Z= 0.299 Chirality : 0.043 0.287 6159 Planarity : 0.004 0.046 6753 Dihedral : 6.564 139.789 5518 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.04 % Favored : 97.94 % Rotamer: Outliers : 2.42 % Allowed : 19.62 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 0.78 (0.12), residues: 4962 helix: 1.35 (0.10), residues: 2681 sheet: -0.41 (0.22), residues: 544 loop : -0.37 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 48 TYR 0.022 0.001 TYR B 446 PHE 0.026 0.001 PHE 3 69 TRP 0.021 0.001 TRP M 12 HIS 0.004 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00314 (39118) covalent geometry : angle 0.58949 (52927) hydrogen bonds : bond 0.04452 ( 2171) hydrogen bonds : angle 4.40981 ( 6294) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 598 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.8673 (tpp) cc_final: 0.8414 (tpp) REVERT: B 67 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: B 399 GLU cc_start: 0.7805 (tp30) cc_final: 0.7561 (mp0) REVERT: B 466 ASN cc_start: 0.7707 (m-40) cc_final: 0.7448 (m110) REVERT: B 498 LYS cc_start: 0.7399 (ttmt) cc_final: 0.6724 (tptt) REVERT: C 124 LYS cc_start: 0.7442 (mmtm) cc_final: 0.7113 (mttm) REVERT: C 224 ASP cc_start: 0.8191 (t0) cc_final: 0.7497 (t0) REVERT: C 426 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6459 (mp0) REVERT: C 471 HIS cc_start: 0.5489 (t70) cc_final: 0.4842 (t-170) REVERT: E 29 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6605 (p0) REVERT: E 205 GLU cc_start: 0.8222 (tt0) cc_final: 0.7796 (tt0) REVERT: F 174 ASN cc_start: 0.7992 (t0) cc_final: 0.7362 (t0) REVERT: F 205 GLU cc_start: 0.7657 (tp30) cc_final: 0.7188 (mp0) REVERT: F 210 ASN cc_start: 0.8442 (t0) cc_final: 0.8034 (t0) REVERT: F 344 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7626 (mt-10) REVERT: F 388 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6548 (mm-40) REVERT: F 402 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6189 (tp30) REVERT: F 422 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8017 (tm-30) REVERT: D 170 MET cc_start: 0.7839 (mmt) cc_final: 0.7565 (mmt) REVERT: D 362 ASP cc_start: 0.7995 (t0) cc_final: 0.7589 (t0) REVERT: D 475 LYS cc_start: 0.6984 (ttmt) cc_final: 0.6492 (tmtt) REVERT: G 53 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: G 74 ASP cc_start: 0.8420 (m-30) cc_final: 0.8148 (m-30) REVERT: G 147 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: O 15 GLU cc_start: 0.6521 (mp0) cc_final: 0.6050 (mp0) REVERT: O 103 SER cc_start: 0.6492 (t) cc_final: 0.6135 (p) REVERT: O 163 ILE cc_start: 0.8279 (mt) cc_final: 0.7965 (mm) REVERT: K 84 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7717 (tptt) REVERT: K 164 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8484 (tpp) REVERT: K 167 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8601 (tmm-80) REVERT: K 178 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6932 (pp20) REVERT: L 68 GLN cc_start: 0.7719 (pm20) cc_final: 0.7337 (pm20) REVERT: L 69 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8412 (mp10) REVERT: L 82 PHE cc_start: 0.6688 (m-10) cc_final: 0.6202 (m-10) REVERT: M 40 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.8137 (mtp180) REVERT: 3 72 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8369 (tt) REVERT: 4 75 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6273 (mpm) REVERT: 5 66 MET cc_start: 0.6252 (tpt) cc_final: 0.5898 (tmm) REVERT: 7 75 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6670 (mpm) REVERT: 1 75 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.6928 (mtt) REVERT: I 37 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7643 (tptt) REVERT: N 22 LEU cc_start: 0.7689 (tt) cc_final: 0.7155 (mt) REVERT: N 101 ASN cc_start: 0.8818 (m-40) cc_final: 0.8477 (m-40) REVERT: N 140 MET cc_start: 0.6331 (ptm) cc_final: 0.5733 (tpt) REVERT: N 169 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8940 (tt) REVERT: N 181 MET cc_start: 0.7844 (tpp) cc_final: 0.7575 (tpp) REVERT: P 26 ILE cc_start: 0.8644 (mp) cc_final: 0.8433 (mp) REVERT: Q 44 MET cc_start: 0.5823 (mmt) cc_final: 0.5490 (mpp) REVERT: R 81 TYR cc_start: 0.7189 (t80) cc_final: 0.6805 (t80) REVERT: S 84 MET cc_start: 0.8621 (mmp) cc_final: 0.8273 (mmp) REVERT: J 40 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5933 (mp0) outliers start: 98 outliers final: 38 residues processed: 656 average time/residue: 0.6959 time to fit residues: 552.2809 Evaluate side-chains 617 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 565 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 72 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 75 MET Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 66 MET Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 51 TRP Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain J residue 40 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 179 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 273 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 262 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 300 optimal weight: 0.7980 chunk 450 optimal weight: 7.9990 chunk 69 optimal weight: 0.3980 chunk 197 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN G 150 ASN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN N 127 HIS P 22 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.111665 restraints weight = 54302.013| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.07 r_work: 0.3276 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 39118 Z= 0.163 Angle : 0.615 13.347 52927 Z= 0.310 Chirality : 0.044 0.265 6159 Planarity : 0.004 0.053 6753 Dihedral : 6.405 119.759 5518 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.32 % Favored : 97.66 % Rotamer: Outliers : 2.17 % Allowed : 20.26 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 0.83 (0.12), residues: 4962 helix: 1.39 (0.10), residues: 2688 sheet: -0.54 (0.21), residues: 592 loop : -0.27 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 146 TYR 0.029 0.001 TYR M 56 PHE 0.028 0.001 PHE 3 69 TRP 0.028 0.001 TRP M 12 HIS 0.005 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00381 (39118) covalent geometry : angle 0.61506 (52927) hydrogen bonds : bond 0.04553 ( 2171) hydrogen bonds : angle 4.39815 ( 6294) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 578 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.8671 (tpp) cc_final: 0.8373 (tpp) REVERT: B 67 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: B 399 GLU cc_start: 0.7825 (tp30) cc_final: 0.7564 (mp0) REVERT: B 466 ASN cc_start: 0.7761 (m-40) cc_final: 0.7529 (m110) REVERT: B 498 LYS cc_start: 0.7442 (ttmt) cc_final: 0.6754 (tptt) REVERT: C 124 LYS cc_start: 0.7441 (mmtm) cc_final: 0.7114 (mttm) REVERT: C 224 ASP cc_start: 0.8183 (t0) cc_final: 0.7509 (t0) REVERT: C 471 HIS cc_start: 0.5478 (t70) cc_final: 0.4834 (t-170) REVERT: E 29 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6585 (p0) REVERT: E 205 GLU cc_start: 0.8240 (tt0) cc_final: 0.7838 (tt0) REVERT: E 458 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7488 (mp-120) REVERT: F 174 ASN cc_start: 0.7989 (t0) cc_final: 0.7371 (t0) REVERT: F 205 GLU cc_start: 0.7659 (tp30) cc_final: 0.7184 (mp0) REVERT: F 210 ASN cc_start: 0.8437 (t0) cc_final: 0.8049 (t0) REVERT: F 344 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7620 (mt-10) REVERT: F 388 GLN cc_start: 0.7003 (mm-40) cc_final: 0.6529 (mm-40) REVERT: F 402 GLU cc_start: 0.6563 (mm-30) cc_final: 0.6199 (tp30) REVERT: F 422 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8022 (tm-30) REVERT: D 170 MET cc_start: 0.7824 (mmt) cc_final: 0.7548 (mmt) REVERT: D 205 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: D 362 ASP cc_start: 0.7963 (t0) cc_final: 0.7547 (t0) REVERT: D 385 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6904 (mttt) REVERT: D 475 LYS cc_start: 0.6963 (ttmt) cc_final: 0.6478 (tmtt) REVERT: G 53 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: G 74 ASP cc_start: 0.8433 (m-30) cc_final: 0.8143 (m-30) REVERT: G 147 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: O 15 GLU cc_start: 0.6691 (mp0) cc_final: 0.6218 (mp0) REVERT: O 103 SER cc_start: 0.6482 (t) cc_final: 0.6162 (p) REVERT: O 163 ILE cc_start: 0.8241 (mt) cc_final: 0.7947 (mm) REVERT: K 84 LYS cc_start: 0.8373 (ttmm) cc_final: 0.7752 (tptt) REVERT: K 167 ARG cc_start: 0.8899 (ttp80) cc_final: 0.8624 (tmm-80) REVERT: L 68 GLN cc_start: 0.7746 (pm20) cc_final: 0.7415 (pm20) REVERT: L 94 LYS cc_start: 0.8769 (tptp) cc_final: 0.8385 (mmmm) REVERT: M 40 ARG cc_start: 0.8824 (mmm-85) cc_final: 0.8236 (mtp180) REVERT: 3 66 MET cc_start: 0.8216 (mmm) cc_final: 0.7929 (mmt) REVERT: 3 72 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8363 (tt) REVERT: 4 75 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6311 (mpm) REVERT: 7 75 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6667 (mpm) REVERT: I 37 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7660 (tptt) REVERT: N 22 LEU cc_start: 0.7677 (tt) cc_final: 0.7140 (mt) REVERT: N 101 ASN cc_start: 0.8787 (m-40) cc_final: 0.8475 (m-40) REVERT: N 140 MET cc_start: 0.6389 (ptm) cc_final: 0.5680 (tpp) REVERT: N 169 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8947 (tt) REVERT: N 181 MET cc_start: 0.7893 (tpp) cc_final: 0.7637 (tpp) REVERT: P 22 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7951 (mm110) REVERT: P 26 ILE cc_start: 0.8646 (mp) cc_final: 0.8412 (mp) REVERT: Q 1 MET cc_start: 0.6806 (tpt) cc_final: 0.6562 (tpt) REVERT: Q 6 THR cc_start: 0.9000 (p) cc_final: 0.8612 (t) REVERT: Q 42 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7713 (ppp) REVERT: Q 44 MET cc_start: 0.5790 (mmt) cc_final: 0.5488 (mpp) REVERT: R 81 TYR cc_start: 0.7232 (t80) cc_final: 0.6869 (t80) REVERT: S 84 MET cc_start: 0.8648 (mmp) cc_final: 0.8211 (mpp) REVERT: J 40 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.5891 (mp0) outliers start: 88 outliers final: 46 residues processed: 630 average time/residue: 0.7190 time to fit residues: 545.4149 Evaluate side-chains 628 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 568 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 72 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 75 MET Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 38 ARG Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 51 TRP Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain J residue 40 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 329 optimal weight: 8.9990 chunk 391 optimal weight: 1.9990 chunk 397 optimal weight: 0.0670 chunk 163 optimal weight: 0.9990 chunk 449 optimal weight: 4.9990 chunk 293 optimal weight: 0.9990 chunk 457 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 373 optimal weight: 2.9990 chunk 325 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN G 150 ASN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 172 HIS L 69 GLN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 127 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113661 restraints weight = 54303.895| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.10 r_work: 0.3310 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39118 Z= 0.124 Angle : 0.605 16.564 52927 Z= 0.302 Chirality : 0.043 0.223 6159 Planarity : 0.004 0.056 6753 Dihedral : 6.100 110.974 5518 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.78 % Allowed : 21.25 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 1.06 (0.12), residues: 4962 helix: 1.57 (0.10), residues: 2676 sheet: -0.25 (0.22), residues: 556 loop : -0.24 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 48 TYR 0.023 0.001 TYR B 446 PHE 0.028 0.001 PHE 3 69 TRP 0.023 0.001 TRP M 12 HIS 0.005 0.001 HIS E 454 Details of bonding type rmsd covalent geometry : bond 0.00276 (39118) covalent geometry : angle 0.60460 (52927) hydrogen bonds : bond 0.04156 ( 2171) hydrogen bonds : angle 4.30536 ( 6294) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 599 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 PHE cc_start: 0.7355 (m-80) cc_final: 0.7078 (m-80) REVERT: A 463 LYS cc_start: 0.7571 (ttmm) cc_final: 0.7321 (pttp) REVERT: B 52 MET cc_start: 0.8705 (tpp) cc_final: 0.8375 (tpp) REVERT: B 67 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: B 399 GLU cc_start: 0.7781 (tp30) cc_final: 0.7531 (mp0) REVERT: B 466 ASN cc_start: 0.7723 (m-40) cc_final: 0.7497 (m110) REVERT: B 498 LYS cc_start: 0.7387 (ttmt) cc_final: 0.6686 (tptt) REVERT: C 124 LYS cc_start: 0.7439 (mmtm) cc_final: 0.7117 (mttm) REVERT: C 224 ASP cc_start: 0.8184 (t0) cc_final: 0.7520 (t0) REVERT: C 426 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6374 (mp0) REVERT: C 471 HIS cc_start: 0.5475 (t70) cc_final: 0.4814 (t-170) REVERT: E 29 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6637 (p0) REVERT: E 205 GLU cc_start: 0.8243 (tt0) cc_final: 0.7844 (tt0) REVERT: F 174 ASN cc_start: 0.7939 (t0) cc_final: 0.7351 (t0) REVERT: F 205 GLU cc_start: 0.7618 (tp30) cc_final: 0.7149 (mp0) REVERT: F 210 ASN cc_start: 0.8475 (t0) cc_final: 0.8065 (t0) REVERT: F 344 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7576 (mt-10) REVERT: F 388 GLN cc_start: 0.6884 (mm-40) cc_final: 0.6479 (mm-40) REVERT: F 402 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6211 (tp30) REVERT: F 408 SER cc_start: 0.7701 (t) cc_final: 0.7408 (p) REVERT: F 422 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8000 (tm-30) REVERT: D 170 MET cc_start: 0.7799 (mmt) cc_final: 0.7543 (mmt) REVERT: D 205 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7109 (tp30) REVERT: D 475 LYS cc_start: 0.6918 (ttmt) cc_final: 0.6440 (tmtt) REVERT: G 53 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: G 74 ASP cc_start: 0.8422 (m-30) cc_final: 0.8197 (m-30) REVERT: G 113 ARG cc_start: 0.8519 (tmm-80) cc_final: 0.8117 (ttp80) REVERT: G 147 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: O 15 GLU cc_start: 0.6641 (mp0) cc_final: 0.6159 (mp0) REVERT: O 163 ILE cc_start: 0.8255 (mt) cc_final: 0.7970 (mm) REVERT: K 84 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7718 (tptt) REVERT: K 141 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7530 (mtm-85) REVERT: K 178 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6947 (pp20) REVERT: L 69 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: L 82 PHE cc_start: 0.6766 (m-10) cc_final: 0.6259 (m-10) REVERT: L 94 LYS cc_start: 0.8758 (tptp) cc_final: 0.8442 (mmmm) REVERT: M 40 ARG cc_start: 0.8850 (mmm-85) cc_final: 0.8240 (mtp180) REVERT: 3 66 MET cc_start: 0.8216 (mmm) cc_final: 0.7936 (mmt) REVERT: 3 72 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8359 (tt) REVERT: 4 66 MET cc_start: 0.7697 (mtp) cc_final: 0.7469 (mtt) REVERT: 4 75 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6228 (mpm) REVERT: 7 75 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6699 (mpm) REVERT: 1 75 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.6952 (mtt) REVERT: I 37 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7640 (tptt) REVERT: N 22 LEU cc_start: 0.7626 (tt) cc_final: 0.7129 (mt) REVERT: N 140 MET cc_start: 0.6387 (ptm) cc_final: 0.5763 (tpt) REVERT: N 169 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8915 (tt) REVERT: N 181 MET cc_start: 0.7717 (tpp) cc_final: 0.7312 (tpp) REVERT: P 26 ILE cc_start: 0.8607 (mp) cc_final: 0.8349 (mp) REVERT: Q 1 MET cc_start: 0.6751 (tpt) cc_final: 0.6476 (tpt) REVERT: Q 42 MET cc_start: 0.8038 (ppp) cc_final: 0.7668 (ppp) REVERT: R 81 TYR cc_start: 0.7182 (t80) cc_final: 0.6791 (t80) REVERT: R 88 ARG cc_start: 0.8309 (mmt90) cc_final: 0.8010 (mpt-90) REVERT: S 84 MET cc_start: 0.8703 (mmp) cc_final: 0.8489 (mmp) REVERT: J 40 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6062 (mp0) outliers start: 72 outliers final: 36 residues processed: 640 average time/residue: 0.7052 time to fit residues: 545.7786 Evaluate side-chains 623 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 573 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 72 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 75 MET Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 38 ARG Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain Q residue 51 TRP Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain J residue 40 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 337 optimal weight: 0.8980 chunk 378 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 379 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 268 optimal weight: 0.8980 chunk 401 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN E 224 GLN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN G 150 ASN L 69 GLN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 127 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.149434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114441 restraints weight = 53935.672| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.05 r_work: 0.3322 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39118 Z= 0.125 Angle : 0.619 14.219 52927 Z= 0.308 Chirality : 0.043 0.246 6159 Planarity : 0.004 0.060 6753 Dihedral : 5.999 105.536 5518 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.56 % Allowed : 21.87 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % 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 are not related in a simple way. whole: 1.13 (0.12), residues: 4962 helix: 1.61 (0.10), residues: 2680 sheet: -0.22 (0.22), residues: 557 loop : -0.18 (0.16), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 48 TYR 0.023 0.001 TYR B 446 PHE 0.034 0.001 PHE C 468 TRP 0.022 0.001 TRP M 12 HIS 0.005 0.001 HIS K 103 Details of bonding type rmsd covalent geometry : bond 0.00280 (39118) covalent geometry : angle 0.61903 (52927) hydrogen bonds : bond 0.04134 ( 2171) hydrogen bonds : angle 4.28218 ( 6294) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9924 Ramachandran restraints generated. 4962 Oldfield, 0 Emsley, 4962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 585 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 PHE cc_start: 0.7401 (m-80) cc_final: 0.7201 (m-80) REVERT: A 463 LYS cc_start: 0.7528 (ttmm) cc_final: 0.7276 (pttp) REVERT: B 52 MET cc_start: 0.8712 (tpp) cc_final: 0.8388 (tpp) REVERT: B 67 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: B 399 GLU cc_start: 0.7797 (tp30) cc_final: 0.7542 (mp0) REVERT: B 466 ASN cc_start: 0.7710 (m-40) cc_final: 0.7482 (m110) REVERT: B 498 LYS cc_start: 0.7377 (ttmt) cc_final: 0.6661 (tptt) REVERT: C 124 LYS cc_start: 0.7450 (mmtm) cc_final: 0.7129 (mttm) REVERT: C 224 ASP cc_start: 0.8175 (t0) cc_final: 0.7511 (t0) REVERT: C 471 HIS cc_start: 0.5484 (t70) cc_final: 0.4842 (t-170) REVERT: E 29 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6649 (p0) REVERT: E 205 GLU cc_start: 0.8267 (tt0) cc_final: 0.7874 (tt0) REVERT: F 174 ASN cc_start: 0.7935 (t0) cc_final: 0.7378 (t0) REVERT: F 205 GLU cc_start: 0.7565 (tp30) cc_final: 0.7118 (mp0) REVERT: F 210 ASN cc_start: 0.8456 (t0) cc_final: 0.8084 (t0) REVERT: F 344 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7560 (mt-10) REVERT: F 388 GLN cc_start: 0.6884 (mm-40) cc_final: 0.6468 (mm-40) REVERT: F 402 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6210 (tp30) REVERT: F 408 SER cc_start: 0.7642 (t) cc_final: 0.7353 (p) REVERT: F 422 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7983 (tm-30) REVERT: D 170 MET cc_start: 0.7760 (mmt) cc_final: 0.7527 (mmt) REVERT: D 205 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: D 475 LYS cc_start: 0.6911 (ttmt) cc_final: 0.6432 (tmtt) REVERT: G 53 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: G 74 ASP cc_start: 0.8416 (m-30) cc_final: 0.8128 (m-30) REVERT: G 113 ARG cc_start: 0.8506 (tmm-80) cc_final: 0.8200 (ttp80) REVERT: G 147 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: O 15 GLU cc_start: 0.6676 (mp0) cc_final: 0.6229 (mp0) REVERT: O 163 ILE cc_start: 0.8271 (mt) cc_final: 0.8017 (mm) REVERT: K 84 LYS cc_start: 0.8288 (ttmm) cc_final: 0.7611 (tptt) REVERT: K 178 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6914 (pp20) REVERT: L 51 LYS cc_start: 0.8099 (mmpt) cc_final: 0.7831 (mmtp) REVERT: L 81 MET cc_start: 0.8443 (tmt) cc_final: 0.8204 (tpp) REVERT: L 94 LYS cc_start: 0.8753 (tptp) cc_final: 0.8426 (mmmm) REVERT: L 96 GLU cc_start: 0.2045 (pp20) cc_final: 0.1718 (pp20) REVERT: M 40 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8252 (mtp180) REVERT: 3 66 MET cc_start: 0.8230 (mmm) cc_final: 0.7956 (mmt) REVERT: 3 72 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8365 (tt) REVERT: 4 75 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6285 (mpm) REVERT: 7 75 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6677 (mpm) REVERT: H 109 LYS cc_start: 0.8486 (mttp) cc_final: 0.8023 (mptt) REVERT: I 37 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7630 (tptt) REVERT: N 22 LEU cc_start: 0.7635 (tt) cc_final: 0.7146 (mt) REVERT: N 55 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8886 (mtpp) REVERT: N 140 MET cc_start: 0.6428 (ptm) cc_final: 0.5817 (tpt) REVERT: N 169 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8883 (tt) REVERT: N 181 MET cc_start: 0.7697 (tpp) cc_final: 0.7288 (tpp) REVERT: P 26 ILE cc_start: 0.8579 (mp) cc_final: 0.8316 (mp) REVERT: Q 1 MET cc_start: 0.6671 (tpt) cc_final: 0.6454 (tpt) REVERT: Q 6 THR cc_start: 0.8949 (p) cc_final: 0.8406 (t) REVERT: R 67 MET cc_start: 0.8679 (ttm) cc_final: 0.8453 (mtp) REVERT: R 81 TYR cc_start: 0.7168 (t80) cc_final: 0.6951 (t80) REVERT: J 40 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6092 (mp0) outliers start: 63 outliers final: 35 residues processed: 620 average time/residue: 0.7203 time to fit residues: 538.3506 Evaluate side-chains 616 residues out of total 4065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 569 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain 3 residue 72 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 75 MET Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 38 ARG Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 51 TRP Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain J residue 40 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 391 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 474 optimal weight: 0.7980 chunk 471 optimal weight: 2.9990 chunk 407 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 287 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 477 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN G 150 ASN ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 127 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113290 restraints weight = 54084.490| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.09 r_work: 0.3305 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39118 Z= 0.141 Angle : 0.633 19.153 52927 Z= 0.314 Chirality : 0.044 0.251 6159 Planarity : 0.004 0.059 6753 Dihedral : 5.997 106.144 5518 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.63 % Allowed : 22.14 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.12 (0.12), residues: 4962 helix: 1.60 (0.10), residues: 2680 sheet: -0.20 (0.22), residues: 558 loop : -0.17 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 373 TYR 0.024 0.001 TYR M 56 PHE 0.031 0.001 PHE 3 69 TRP 0.034 0.002 TRP M 12 HIS 0.006 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00326 (39118) covalent geometry : angle 0.63273 (52927) hydrogen bonds : bond 0.04211 ( 2171) hydrogen bonds : angle 4.29973 ( 6294) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18252.65 seconds wall clock time: 309 minutes 51.79 seconds (18591.79 seconds total)