Starting phenix.real_space_refine on Tue Aug 26 13:49:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itt_60878/08_2025/9itt_60878.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itt_60878/08_2025/9itt_60878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9itt_60878/08_2025/9itt_60878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itt_60878/08_2025/9itt_60878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9itt_60878/08_2025/9itt_60878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itt_60878/08_2025/9itt_60878.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 5 5.21 5 S 91 5.16 5 C 23707 2.51 5 N 6718 2.21 5 O 7200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37735 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3749 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 25, 'TRANS': 467} Chain: "B" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3793 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 26, 'TRANS': 471} Chain: "C" Number of atoms: 3769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3769 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 25, 'TRANS': 469} Chain: "D" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3593 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 438} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3593 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 438} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3608 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 440} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2215 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain: "R" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 997 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "S" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 538 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "Y" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1223 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain: "V" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1230 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "W" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 549 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "U" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 772 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 590 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 3, 'GLN:plan1': 12, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 292 Chain: "X" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 763 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 1, 'TRANS': 151} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 468 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 12, 'ASN:plan1': 4, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 289 Chain: "H" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 481 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "I" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 485 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "J" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 485 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 485 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 485 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "M" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 485 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "N" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 485 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "O" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 485 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "P" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 485 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "Q" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 485 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "Z" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1236 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 14, 'TRANS': 236} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 790 Unresolved non-hydrogen angles: 1033 Unresolved non-hydrogen dihedrals: 666 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 34, 'TYR:plan': 7, 'HIS:plan': 1, 'GLU:plan': 9, 'ASP:plan': 3, 'ASN:plan1': 12, 'GLN:plan1': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 404 Chain: "T" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1104 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'PTRANS': 10, 'TRANS': 213} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 709 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 599 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'ASN:plan1': 12, 'PHE:plan': 30, 'ASP:plan': 3, 'ARG:plan': 6, 'GLN:plan1': 4, 'GLU:plan': 7, 'TYR:plan': 6, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 369 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.40, per 1000 atoms: 0.20 Number of scatterers: 37735 At special positions: 0 Unit cell: (127.41, 140.43, 230.64, 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 91 16.00 P 14 15.00 Mg 5 11.99 O 7200 8.00 N 6718 7.00 C 23707 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: 3.44 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9524 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 34 sheets defined 59.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.820A pdb=" N THR A 88 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 89' Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.748A pdb=" N LEU A 110 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 223 through 226 removed outlier: 3.853A pdb=" N GLU A 226 " --> pdb=" O GLY A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 226' Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 278 through 292 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.622A pdb=" N GLY A 324 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 387 through 411 removed outlier: 5.347A pdb=" N LYS A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 436 Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.670A pdb=" N ARG A 487 " --> pdb=" O HIS A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 519 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.879A pdb=" N LEU B 110 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.671A pdb=" N GLN B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.886A pdb=" N GLU B 226 " --> pdb=" O GLY B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 246 through 259 removed outlier: 6.057A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 302 through 303 No H-bonds generated for 'chain 'B' and resid 302 through 303' Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 381 through 386 Processing helix chain 'B' and resid 387 through 407 removed outlier: 3.930A pdb=" N GLY B 395 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 removed outlier: 3.679A pdb=" N GLN B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 436 Processing helix chain 'B' and resid 444 through 457 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 482 Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.994A pdb=" N ARG B 487 " --> pdb=" O HIS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'C' and resid 85 through 89 removed outlier: 4.017A pdb=" N THR C 88 " --> pdb=" O ASP C 85 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 89 " --> pdb=" O ASP C 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 85 through 89' Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.635A pdb=" N LEU C 110 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 164 Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 208 through 222 Processing helix chain 'C' and resid 223 through 226 removed outlier: 3.814A pdb=" N GLU C 226 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 238 through 259 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 277 through 292 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.921A pdb=" N ARG C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 353 Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.656A pdb=" N ALA C 384 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 408 removed outlier: 3.898A pdb=" N GLY C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 removed outlier: 4.666A pdb=" N GLN C 412 " --> pdb=" O ALA C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 436 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'C' and resid 467 through 482 Processing helix chain 'C' and resid 483 through 493 removed outlier: 3.808A pdb=" N ARG C 487 " --> pdb=" O HIS C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 519 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.605A pdb=" N ARG D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 243 removed outlier: 4.548A pdb=" N GLY D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 268 Processing helix chain 'D' and resid 281 through 290 removed outlier: 3.613A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 324 Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.553A pdb=" N ARG D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 379 removed outlier: 3.588A pdb=" N VAL D 370 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D 371 " --> pdb=" O ALA D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 388 removed outlier: 3.669A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 411 removed outlier: 4.280A pdb=" N SER D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 119 through 123 Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 191 through 201 Processing helix chain 'E' and resid 222 through 243 removed outlier: 4.704A pdb=" N GLY E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.558A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 3.510A pdb=" N TYR E 364 " --> pdb=" O GLY E 360 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE E 383 " --> pdb=" O ASP E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 409 Processing helix chain 'E' and resid 429 through 442 removed outlier: 3.593A pdb=" N GLU E 435 " --> pdb=" O LYS E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.605A pdb=" N PHE E 453 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR E 454 " --> pdb=" O SER E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 119 through 123 Processing helix chain 'F' and resid 134 through 141 Processing helix chain 'F' and resid 158 through 171 Processing helix chain 'F' and resid 193 through 201 removed outlier: 3.654A pdb=" N MET F 197 " --> pdb=" O LEU F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'F' and resid 222 through 243 removed outlier: 3.589A pdb=" N ARG F 226 " --> pdb=" O PRO F 222 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY F 230 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR F 239 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE F 240 " --> pdb=" O MET F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 268 removed outlier: 3.833A pdb=" N PHE F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 315 through 323 removed outlier: 4.372A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 393 through 411 removed outlier: 4.043A pdb=" N SER F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 removed outlier: 3.516A pdb=" N GLY F 443 " --> pdb=" O ARG F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.779A pdb=" N TYR F 454 " --> pdb=" O SER F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.555A pdb=" N VAL F 462 " --> pdb=" O ASP F 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 60 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 67 through 71 removed outlier: 3.561A pdb=" N GLU G 71 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 4.716A pdb=" N ALA G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 148 through 151 Processing helix chain 'G' and resid 152 through 165 removed outlier: 4.339A pdb=" N SER G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 212 through 286 Proline residue: G 222 - end of helix Processing helix chain 'R' and resid 96 through 104 Processing helix chain 'R' and resid 107 through 127 Processing helix chain 'S' and resid 99 through 109 Processing helix chain 'S' and resid 110 through 112 No H-bonds generated for 'chain 'S' and resid 110 through 112' Processing helix chain 'S' and resid 142 through 154 removed outlier: 3.992A pdb=" N ARG S 146 " --> pdb=" O SER S 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 147 removed outlier: 5.997A pdb=" N ARG Y 31 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Proline residue: Y 32 - end of helix removed outlier: 3.898A pdb=" N GLU Y 39 " --> pdb=" O ASN Y 35 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG Y 40 " --> pdb=" O LEU Y 36 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP Y 50 " --> pdb=" O GLU Y 46 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA Y 51 " --> pdb=" O SER Y 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU Y 56 " --> pdb=" O GLU Y 52 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG Y 138 " --> pdb=" O LEU Y 134 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA Y 146 " --> pdb=" O ALA Y 142 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG Y 147 " --> pdb=" O GLU Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 150 through 160 removed outlier: 4.596A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU Y 160 " --> pdb=" O SER Y 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 29 Processing helix chain 'V' and resid 29 through 115 Processing helix chain 'V' and resid 115 through 120 removed outlier: 4.166A pdb=" N ARG V 119 " --> pdb=" O GLN V 115 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 138 removed outlier: 4.571A pdb=" N ARG V 138 " --> pdb=" O LEU V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 158 Processing helix chain 'W' and resid 98 through 109 Processing helix chain 'W' and resid 143 through 154 Processing helix chain 'U' and resid 7 through 122 removed outlier: 3.559A pdb=" N ILE U 12 " --> pdb=" O PRO U 8 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) Proline residue: U 32 - end of helix removed outlier: 3.951A pdb=" N ARG U 43 " --> pdb=" O GLU U 39 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL U 48 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA U 51 " --> pdb=" O SER U 47 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA U 70 " --> pdb=" O GLU U 66 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG U 71 " --> pdb=" O ALA U 67 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA U 72 " --> pdb=" O GLU U 68 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ARG U 73 " --> pdb=" O ILE U 69 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE U 79 " --> pdb=" O GLU U 75 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA U 81 " --> pdb=" O ALA U 77 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN U 82 " --> pdb=" O LYS U 78 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU U 101 " --> pdb=" O GLN U 97 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU U 103 " --> pdb=" O ARG U 99 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG U 104 " --> pdb=" O ARG U 100 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS U 106 " --> pdb=" O ALA U 102 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA U 111 " --> pdb=" O GLU U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 139 Processing helix chain 'X' and resid 9 through 148 removed outlier: 4.196A pdb=" N ALA X 13 " --> pdb=" O THR X 9 " (cutoff:3.500A) Proline residue: X 32 - end of helix removed outlier: 3.521A pdb=" N GLU X 46 " --> pdb=" O ARG X 42 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG X 62 " --> pdb=" O LEU X 58 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG X 63 " --> pdb=" O ALA X 59 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA X 77 " --> pdb=" O ARG X 73 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL X 80 " --> pdb=" O ALA X 76 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN X 145 " --> pdb=" O GLY X 141 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA X 146 " --> pdb=" O ALA X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 160 removed outlier: 3.824A pdb=" N SER X 156 " --> pdb=" O LEU X 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 38 removed outlier: 4.241A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix Processing helix chain 'H' and resid 41 through 70 removed outlier: 3.865A pdb=" N THR H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 17 Processing helix chain 'I' and resid 17 through 38 Processing helix chain 'I' and resid 41 through 71 removed outlier: 3.720A pdb=" N TYR I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 38 removed outlier: 3.885A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Proline residue: J 20 - end of helix Processing helix chain 'J' and resid 41 through 71 removed outlier: 3.596A pdb=" N TYR J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU J 59 " --> pdb=" O PHE J 55 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA J 60 " --> pdb=" O THR J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 16 Processing helix chain 'K' and resid 17 through 38 removed outlier: 3.984A pdb=" N VAL K 22 " --> pdb=" O ILE K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 71 removed outlier: 3.638A pdb=" N THR K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA K 60 " --> pdb=" O THR K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 38 removed outlier: 3.502A pdb=" N ALA L 17 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) Proline residue: L 20 - end of helix Processing helix chain 'L' and resid 41 through 71 removed outlier: 4.083A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR L 48 " --> pdb=" O ARG L 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 38 removed outlier: 3.636A pdb=" N ALA M 17 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE M 18 " --> pdb=" O GLY M 14 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 41 through 71 removed outlier: 3.782A pdb=" N GLY M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 15 Processing helix chain 'N' and resid 18 through 38 removed outlier: 5.590A pdb=" N ILE N 24 " --> pdb=" O PRO N 20 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY N 25 " --> pdb=" O GLY N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 71 removed outlier: 3.664A pdb=" N LEU N 59 " --> pdb=" O PHE N 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 38 removed outlier: 4.721A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Proline residue: O 20 - end of helix Processing helix chain 'O' and resid 42 through 71 removed outlier: 4.779A pdb=" N TYR O 48 " --> pdb=" O ARG O 44 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE O 70 " --> pdb=" O ILE O 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 15 Processing helix chain 'P' and resid 17 through 38 Processing helix chain 'P' and resid 41 through 71 removed outlier: 4.726A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 16 Processing helix chain 'Q' and resid 17 through 38 removed outlier: 3.639A pdb=" N VAL Q 22 " --> pdb=" O ILE Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 71 removed outlier: 3.512A pdb=" N TYR Q 48 " --> pdb=" O ARG Q 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 70 Processing helix chain 'Z' and resid 79 through 97 Processing helix chain 'Z' and resid 102 through 125 removed outlier: 3.714A pdb=" N ALA Z 106 " --> pdb=" O TYR Z 102 " (cutoff:3.500A) Proline residue: Z 108 - end of helix removed outlier: 3.602A pdb=" N LEU Z 125 " --> pdb=" O ASN Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 189 Processing helix chain 'Z' and resid 190 through 212 Processing helix chain 'Z' and resid 227 through 267 removed outlier: 3.704A pdb=" N ILE Z 233 " --> pdb=" O SER Z 229 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE Z 234 " --> pdb=" O PHE Z 230 " (cutoff:3.500A) Proline residue: Z 243 - end of helix removed outlier: 3.967A pdb=" N GLY Z 257 " --> pdb=" O ASN Z 253 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 304 removed outlier: 3.571A pdb=" N ALA Z 292 " --> pdb=" O ALA Z 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.678A pdb=" N VAL T 53 " --> pdb=" O THR T 49 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 100 Processing helix chain 'T' and resid 106 through 126 removed outlier: 3.538A pdb=" N LEU T 125 " --> pdb=" O ASN T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 189 Processing helix chain 'T' and resid 190 through 212 removed outlier: 3.562A pdb=" N THR T 194 " --> pdb=" O ASP T 190 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE T 195 " --> pdb=" O LEU T 191 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE T 197 " --> pdb=" O PHE T 193 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA T 212 " --> pdb=" O TRP T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 217 Processing helix chain 'T' and resid 228 through 268 Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 273 through 303 removed outlier: 3.602A pdb=" N VAL T 281 " --> pdb=" O TYR T 277 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE T 282 " --> pdb=" O GLY T 278 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 5.605A pdb=" N ARG A 100 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 52 " --> pdb=" O ALA A 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 5 through 11 current: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 31 removed outlier: 5.605A pdb=" N ARG A 100 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 52 " --> pdb=" O ALA A 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 67 through 74 current: chain 'F' and resid 29 through 33 removed outlier: 5.030A pdb=" N ASN F 29 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS F 55 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLN F 48 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL F 53 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL F 14 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE F 10 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG F 16 " --> pdb=" O GLN F 8 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 5 through 11 current: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 removed outlier: 4.728A pdb=" N LYS A 132 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.631A pdb=" N CYS A 200 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL A 231 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR A 202 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA A 233 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA A 204 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A 199 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL A 274 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 201 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP A 276 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL A 203 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR A 275 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL A 333 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP A 277 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU A 335 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A 173 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 4.513A pdb=" N ILE A 166 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.552A pdb=" N ALA B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU B 73 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 79 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 71 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU B 52 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ARG B 100 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASN B 28 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE S 131 " --> pdb=" O THR S 92 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL S 91 " --> pdb=" O HIS S 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.990A pdb=" N CYS B 200 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N VAL B 231 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR B 202 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA B 233 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA B 204 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 275 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.436A pdb=" N ARG E 16 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE E 10 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL E 14 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL E 57 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL E 45 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.841A pdb=" N ALA C 79 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 71 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 103 through 106 removed outlier: 4.713A pdb=" N LYS C 132 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.208A pdb=" N VAL C 199 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL C 274 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 201 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 333 through 335 Processing sheet with id=AB7, first strand: chain 'C' and resid 261 through 263 Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 49 removed outlier: 6.800A pdb=" N LYS D 55 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLN D 48 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL D 53 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL D 14 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE D 10 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG D 16 " --> pdb=" O GLN D 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AC1, first strand: chain 'D' and resid 79 through 81 Processing sheet with id=AC2, first strand: chain 'D' and resid 90 through 91 removed outlier: 6.428A pdb=" N PHE D 91 " --> pdb=" O PHE D 216 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN D 218 " --> pdb=" O PHE D 91 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 248 " --> pdb=" O PHE D 177 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N MET D 303 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU D 249 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR D 149 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL D 306 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 151 " --> pdb=" O VAL D 306 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 129 through 130 removed outlier: 4.540A pdb=" N PHE D 143 " --> pdb=" O PHE D 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 79 through 81 Processing sheet with id=AC5, first strand: chain 'E' and resid 90 through 91 removed outlier: 6.538A pdb=" N PHE E 91 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN E 218 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR E 149 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 202 through 203 Processing sheet with id=AC7, first strand: chain 'F' and resid 79 through 81 Processing sheet with id=AC8, first strand: chain 'F' and resid 90 through 91 removed outlier: 3.671A pdb=" N GLY F 182 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE F 177 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N PHE F 250 " --> pdb=" O PHE F 177 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL F 179 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP F 252 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA F 181 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N MET F 303 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU F 249 " --> pdb=" O MET F 303 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR F 149 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL F 306 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE F 151 " --> pdb=" O VAL F 306 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 129 through 130 removed outlier: 4.177A pdb=" N PHE F 143 " --> pdb=" O PHE F 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 138 through 140 removed outlier: 3.858A pdb=" N GLY G 138 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL G 79 " --> pdb=" O ASP G 117 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N TYR G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU G 81 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE G 121 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL G 83 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER G 78 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N TYR G 172 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA G 80 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE G 174 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU G 82 " --> pdb=" O ILE G 174 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N SER G 176 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N VAL G 84 " --> pdb=" O SER G 176 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N PHE G 178 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG G 185 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 13 through 15 removed outlier: 3.589A pdb=" N LEU R 15 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE R 3 " --> pdb=" O VAL R 19 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 13 through 15 removed outlier: 3.589A pdb=" N LEU R 15 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N HIS R 4 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE R 76 " --> pdb=" O HIS R 4 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU R 6 " --> pdb=" O ILE R 76 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 30 through 33 removed outlier: 3.870A pdb=" N ASP R 50 " --> pdb=" O SER R 23 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLU R 48 " --> pdb=" O PRO R 25 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL R 62 " --> pdb=" O GLY R 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 88 through 92 removed outlier: 6.652A pdb=" N ALA W 89 " --> pdb=" O THR W 119 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N HIS W 121 " --> pdb=" O ALA W 89 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL W 91 " --> pdb=" O HIS W 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'W' and resid 132 through 134 removed outlier: 3.552A pdb=" N ILE W 132 " --> pdb=" O LEU W 139 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 133 through 134 2448 hydrogen bonds defined for protein. 7134 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: 6.69 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10938 1.33 - 1.45: 5206 1.45 - 1.57: 21884 1.57 - 1.69: 21 1.69 - 1.81: 172 Bond restraints: 38221 Sorted by residual: bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C5 ADP D 501 " pdb=" C6 ADP D 501 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" N VAL D 157 " pdb=" CA VAL D 157 " ideal model delta sigma weight residual 1.452 1.494 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" N ILE R 87 " pdb=" CA ILE R 87 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.78e+00 bond pdb=" N VAL F 215 " pdb=" CA VAL F 215 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.66e+00 ... (remaining 38216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 51096 2.39 - 4.78: 794 4.78 - 7.16: 73 7.16 - 9.55: 8 9.55 - 11.94: 2 Bond angle restraints: 51973 Sorted by residual: angle pdb=" C GLN F 274 " pdb=" CA GLN F 274 " pdb=" CB GLN F 274 " ideal model delta sigma weight residual 116.63 111.64 4.99 1.16e+00 7.43e-01 1.85e+01 angle pdb=" C ALA S 99 " pdb=" CA ALA S 99 " pdb=" CB ALA S 99 " ideal model delta sigma weight residual 117.23 111.42 5.81 1.36e+00 5.41e-01 1.83e+01 angle pdb=" C ALA E 310 " pdb=" CA ALA E 310 " pdb=" CB ALA E 310 " ideal model delta sigma weight residual 116.54 111.65 4.89 1.15e+00 7.56e-01 1.81e+01 angle pdb=" C ALA U 146 " pdb=" CA ALA U 146 " pdb=" CB ALA U 146 " ideal model delta sigma weight residual 116.54 111.67 4.87 1.15e+00 7.56e-01 1.80e+01 angle pdb=" C ALA F 310 " pdb=" CA ALA F 310 " pdb=" CB ALA F 310 " ideal model delta sigma weight residual 117.23 111.79 5.44 1.36e+00 5.41e-01 1.60e+01 ... (remaining 51968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 22322 25.88 - 51.76: 764 51.76 - 77.64: 71 77.64 - 103.52: 15 103.52 - 129.40: 1 Dihedral angle restraints: 23173 sinusoidal: 8351 harmonic: 14822 Sorted by residual: dihedral pdb=" C2' ADP D 501 " pdb=" C1' ADP D 501 " pdb=" N9 ADP D 501 " pdb=" C4 ADP D 501 " ideal model delta sinusoidal sigma weight residual 91.55 -139.06 -129.40 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 -163.39 103.39 1 2.00e+01 2.50e-03 2.96e+01 dihedral pdb=" CA LEU R 34 " pdb=" C LEU R 34 " pdb=" N PRO R 35 " pdb=" CA PRO R 35 " ideal model delta harmonic sigma weight residual -180.00 -155.94 -24.06 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 23170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5076 0.058 - 0.116: 939 0.116 - 0.174: 169 0.174 - 0.232: 17 0.232 - 0.289: 8 Chirality restraints: 6209 Sorted by residual: chirality pdb=" C2' ATP A 602 " pdb=" C1' ATP A 602 " pdb=" C3' ATP A 602 " pdb=" O2' ATP A 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C2' ATP B 602 " pdb=" C1' ATP B 602 " pdb=" C3' ATP B 602 " pdb=" O2' ATP B 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2' ATP C 602 " pdb=" C1' ATP C 602 " pdb=" C3' ATP C 602 " pdb=" O2' ATP C 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 6206 not shown) Planarity restraints: 6880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS R 121 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C LYS R 121 " -0.059 2.00e-02 2.50e+03 pdb=" O LYS R 121 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU R 122 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG Y 31 " -0.055 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO Y 32 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO Y 32 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Y 32 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN Y 89 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C GLN Y 89 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN Y 89 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN Y 90 " -0.016 2.00e-02 2.50e+03 ... (remaining 6877 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 164 2.50 - 3.10: 29256 3.10 - 3.70: 59450 3.70 - 4.30: 84891 4.30 - 4.90: 142770 Nonbonded interactions: 316531 Sorted by model distance: nonbonded pdb=" OG1 THR D 160 " pdb="MG MG D 503 " model vdw 1.901 2.170 nonbonded pdb="MG MG B 601 " pdb=" O1G ATP B 602 " model vdw 1.901 2.170 nonbonded pdb=" OG1 THR B 183 " pdb="MG MG B 601 " model vdw 1.905 2.170 nonbonded pdb=" O2 PO4 D 502 " pdb="MG MG D 503 " model vdw 1.908 2.170 nonbonded pdb="MG MG A 601 " pdb=" O2B ATP A 602 " model vdw 1.910 2.170 ... (remaining 316526 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 519) selection = (chain 'B' and resid 27 through 519) selection = (chain 'C' and resid 27 through 519) } ncs_group { reference = (chain 'D' and resid 3 through 468) selection = chain 'E' selection = (chain 'F' and resid 3 through 468) } ncs_group { reference = chain 'H' selection = (chain 'I' and resid 3 through 70) selection = (chain 'J' and resid 3 through 70) selection = (chain 'K' and resid 3 through 70) selection = (chain 'L' and resid 3 through 70) selection = (chain 'M' and resid 3 through 70) selection = (chain 'N' and resid 3 through 70) selection = (chain 'O' and resid 3 through 70) selection = (chain 'P' and resid 3 through 70) selection = (chain 'Q' and resid 3 through 70) } ncs_group { reference = chain 'S' selection = (chain 'W' and resid 86 through 154) } ncs_group { reference = (chain 'T' and (resid 47 through 135 or resid 178 through 303)) selection = (chain 'Z' and resid 47 through 303) } ncs_group { reference = (chain 'U' and resid 8 through 158) selection = (chain 'V' and ((resid 8 through 140 and (name N or name CA or name C or name O \ or name CB )) or (resid 141 through 147 and (name N or name CA or name C or name \ O or name CB )) or resid 148 or (resid 149 through 158 and (name N or name CA o \ r name C or name O or name CB )))) selection = (chain 'X' and resid 8 through 158) selection = (chain 'Y' and ((resid 8 through 140 and (name N or name CA or name C or name O \ or name CB )) or (resid 141 through 147 and (name N or name CA or name C or name \ O or name CB )) or resid 148 or (resid 149 through 158 and (name N or name CA o \ r name C or name O or name CB )))) } 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.620 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 38221 Z= 0.253 Angle : 0.723 11.939 51973 Z= 0.428 Chirality : 0.048 0.289 6209 Planarity : 0.005 0.084 6880 Dihedral : 13.074 129.397 13649 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.26 % Allowed : 0.40 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.12), residues: 5161 helix: 1.40 (0.10), residues: 2826 sheet: -0.96 (0.23), residues: 508 loop : -1.08 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V 43 TYR 0.011 0.001 TYR D 427 PHE 0.028 0.001 PHE B 413 TRP 0.003 0.001 TRP C 471 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00448 (38221) covalent geometry : angle 0.72314 (51973) hydrogen bonds : bond 0.13662 ( 2439) hydrogen bonds : angle 5.65515 ( 7134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 665 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.9461 (tpt) cc_final: 0.9244 (tpt) REVERT: A 358 TYR cc_start: 0.8711 (t80) cc_final: 0.8232 (t80) REVERT: A 360 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8328 (mm-30) REVERT: A 426 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8427 (mm-30) REVERT: B 378 VAL cc_start: 0.9125 (p) cc_final: 0.8905 (m) REVERT: D 296 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8606 (mmtm) REVERT: D 397 LYS cc_start: 0.8210 (pttm) cc_final: 0.7829 (pmtt) REVERT: D 401 GLN cc_start: 0.8596 (mt0) cc_final: 0.8205 (mt0) REVERT: E 138 ASP cc_start: 0.7846 (t0) cc_final: 0.7520 (t0) REVERT: E 432 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7671 (mmpt) REVERT: G 169 ASP cc_start: 0.7914 (m-30) cc_final: 0.7700 (m-30) REVERT: R 7 ILE cc_start: 0.8181 (mm) cc_final: 0.7759 (tt) REVERT: R 41 MET cc_start: 0.6883 (mtt) cc_final: 0.6624 (mpt) REVERT: R 118 LYS cc_start: 0.8429 (tptp) cc_final: 0.7813 (tmtt) REVERT: S 143 LEU cc_start: 0.8042 (mt) cc_final: 0.7728 (mm) REVERT: V 52 GLU cc_start: 0.7435 (pm20) cc_final: 0.7213 (tm-30) REVERT: V 108 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8380 (tm-30) REVERT: W 101 GLN cc_start: 0.7424 (mt0) cc_final: 0.7137 (mm-40) REVERT: W 110 GLN cc_start: 0.8653 (mt0) cc_final: 0.8324 (pm20) REVERT: H 61 ILE cc_start: 0.6121 (mm) cc_final: 0.5918 (pp) REVERT: H 66 ILE cc_start: 0.1405 (mm) cc_final: 0.1183 (pt) REVERT: I 35 ILE cc_start: 0.5375 (mm) cc_final: 0.5171 (pt) REVERT: K 48 TYR cc_start: 0.5428 (m-80) cc_final: 0.5192 (m-10) REVERT: K 61 ILE cc_start: 0.7133 (mm) cc_final: 0.6736 (pp) REVERT: L 41 ILE cc_start: 0.5852 (tp) cc_final: 0.5557 (tp) REVERT: L 55 PHE cc_start: 0.7900 (m-80) cc_final: 0.7395 (m-80) REVERT: N 48 TYR cc_start: 0.3958 (m-10) cc_final: 0.3528 (m-10) REVERT: Q 35 ILE cc_start: 0.7106 (mm) cc_final: 0.6899 (tp) outliers start: 9 outliers final: 2 residues processed: 669 average time/residue: 0.6110 time to fit residues: 495.5512 Evaluate side-chains 388 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain F residue 382 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 483 HIS C 403 GLN D 164 GLN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 HIS S 110 GLN ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.145859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089740 restraints weight = 66131.893| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.18 r_work: 0.2995 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 38221 Z= 0.214 Angle : 0.632 7.841 51973 Z= 0.333 Chirality : 0.046 0.234 6209 Planarity : 0.005 0.076 6880 Dihedral : 6.813 132.040 5734 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.61 % Allowed : 9.45 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.12), residues: 5161 helix: 1.33 (0.10), residues: 2869 sheet: -1.06 (0.23), residues: 543 loop : -0.93 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 44 TYR 0.016 0.001 TYR G 209 PHE 0.037 0.002 PHE B 413 TRP 0.002 0.000 TRP B 471 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00504 (38221) covalent geometry : angle 0.63206 (51973) hydrogen bonds : bond 0.04612 ( 2439) hydrogen bonds : angle 4.55787 ( 7134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 391 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8447 (mm-30) REVERT: B 497 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8377 (mmm-85) REVERT: C 335 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8679 (tt0) REVERT: D 296 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8673 (mmtm) REVERT: E 138 ASP cc_start: 0.8141 (t0) cc_final: 0.7755 (t0) REVERT: E 139 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8641 (tp) REVERT: E 274 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: F 22 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8884 (m-30) REVERT: F 389 MET cc_start: 0.8848 (mmm) cc_final: 0.8583 (mmm) REVERT: G 47 ASP cc_start: 0.8260 (p0) cc_final: 0.7993 (p0) REVERT: G 51 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: R 7 ILE cc_start: 0.8357 (mm) cc_final: 0.7910 (tt) REVERT: R 41 MET cc_start: 0.6776 (mtt) cc_final: 0.6341 (mpt) REVERT: R 118 LYS cc_start: 0.8281 (tptp) cc_final: 0.7749 (tmtt) REVERT: S 102 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7800 (mttm) REVERT: Y 93 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: V 52 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: W 101 GLN cc_start: 0.7580 (mt0) cc_final: 0.7189 (tp40) REVERT: W 110 GLN cc_start: 0.8915 (mt0) cc_final: 0.8465 (pm20) REVERT: H 66 ILE cc_start: 0.1259 (mm) cc_final: 0.0941 (pt) REVERT: K 61 ILE cc_start: 0.6985 (mm) cc_final: 0.6544 (pp) REVERT: L 55 PHE cc_start: 0.7784 (m-80) cc_final: 0.7305 (m-80) REVERT: O 48 TYR cc_start: 0.5813 (m-80) cc_final: 0.5181 (m-80) outliers start: 92 outliers final: 37 residues processed: 448 average time/residue: 0.5641 time to fit residues: 314.3749 Evaluate side-chains 380 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 335 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 274 GLN Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain S residue 102 LYS Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 93 GLU Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 95 ILE Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 239 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 446 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 455 optimal weight: 20.0000 chunk 276 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN F 174 GLN ** Y 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.145932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.089401 restraints weight = 65790.954| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.95 r_work: 0.3006 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 38221 Z= 0.185 Angle : 0.599 12.463 51973 Z= 0.312 Chirality : 0.045 0.242 6209 Planarity : 0.005 0.077 6880 Dihedral : 6.684 129.285 5732 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.55 % Allowed : 12.74 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.12), residues: 5161 helix: 1.40 (0.09), residues: 2883 sheet: -0.99 (0.23), residues: 549 loop : -0.89 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 43 TYR 0.026 0.001 TYR D 364 PHE 0.037 0.001 PHE B 413 TRP 0.002 0.000 TRP C 471 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00431 (38221) covalent geometry : angle 0.59870 (51973) hydrogen bonds : bond 0.04233 ( 2439) hydrogen bonds : angle 4.36280 ( 7134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 359 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8730 (tp30) REVERT: B 196 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: B 497 ARG cc_start: 0.8710 (tpp-160) cc_final: 0.8441 (mmm-85) REVERT: C 335 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8919 (tt0) REVERT: D 126 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7903 (tt0) REVERT: D 198 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.7752 (mtpp) REVERT: E 138 ASP cc_start: 0.8320 (t0) cc_final: 0.8051 (t0) REVERT: E 274 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: E 397 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7681 (mtmp) REVERT: G 47 ASP cc_start: 0.8301 (p0) cc_final: 0.8053 (p0) REVERT: G 51 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: G 207 TYR cc_start: 0.8006 (m-80) cc_final: 0.7778 (m-10) REVERT: R 7 ILE cc_start: 0.8428 (mm) cc_final: 0.8030 (tt) REVERT: R 67 MET cc_start: 0.9107 (ttt) cc_final: 0.8770 (tmm) REVERT: R 118 LYS cc_start: 0.8272 (tptp) cc_final: 0.7780 (tmtt) REVERT: S 102 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7484 (mttm) REVERT: S 103 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8470 (tp30) REVERT: Y 93 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: W 101 GLN cc_start: 0.7568 (mt0) cc_final: 0.7116 (tp40) REVERT: W 110 GLN cc_start: 0.8839 (mt0) cc_final: 0.8402 (pm20) REVERT: W 139 LEU cc_start: 0.8487 (tp) cc_final: 0.8242 (tt) REVERT: K 33 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.6132 (mp10) REVERT: K 61 ILE cc_start: 0.6981 (mm) cc_final: 0.6557 (pp) REVERT: K 70 ILE cc_start: 0.0548 (OUTLIER) cc_final: 0.0313 (pt) REVERT: L 55 PHE cc_start: 0.7815 (m-80) cc_final: 0.7322 (m-80) REVERT: N 38 ASN cc_start: 0.6609 (t0) cc_final: 0.6214 (t0) REVERT: O 48 TYR cc_start: 0.5977 (m-80) cc_final: 0.5613 (m-10) REVERT: P 49 MET cc_start: 0.2644 (OUTLIER) cc_final: 0.2282 (ptt) outliers start: 90 outliers final: 28 residues processed: 419 average time/residue: 0.5718 time to fit residues: 296.5390 Evaluate side-chains 364 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 326 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain E residue 274 GLN Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain Y residue 93 GLU Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 143 LEU Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 380 optimal weight: 30.0000 chunk 379 optimal weight: 50.0000 chunk 164 optimal weight: 0.5980 chunk 456 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 475 optimal weight: 30.0000 chunk 384 optimal weight: 50.0000 chunk 233 optimal weight: 6.9990 chunk 343 optimal weight: 30.0000 chunk 502 optimal weight: 8.9990 chunk 488 optimal weight: 50.0000 overall best weight: 6.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 HIS C 309 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN S 117 HIS Y 35 ASN V 84 GLN ** V 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.139571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.082772 restraints weight = 66900.702| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.16 r_work: 0.2863 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.103 38221 Z= 0.525 Angle : 0.827 13.397 51973 Z= 0.433 Chirality : 0.055 0.349 6209 Planarity : 0.006 0.076 6880 Dihedral : 7.297 135.059 5730 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.89 % Allowed : 14.62 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.02 (0.12), residues: 5161 helix: 0.96 (0.09), residues: 2912 sheet: -1.31 (0.22), residues: 597 loop : -1.16 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 188 TYR 0.028 0.002 TYR D 364 PHE 0.043 0.002 PHE B 413 TRP 0.003 0.001 TRP C 471 HIS 0.010 0.002 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.01248 (38221) covalent geometry : angle 0.82738 (51973) hydrogen bonds : bond 0.05056 ( 2439) hydrogen bonds : angle 4.63565 ( 7134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 331 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLN cc_start: 0.9424 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: B 298 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8214 (mtp180) REVERT: B 476 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8301 (mm) REVERT: C 335 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8809 (tt0) REVERT: D 177 PHE cc_start: 0.8314 (m-80) cc_final: 0.8102 (m-10) REVERT: D 198 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.7968 (mtpp) REVERT: D 296 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8571 (mmtm) REVERT: E 138 ASP cc_start: 0.8546 (t0) cc_final: 0.8265 (t0) REVERT: E 274 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: F 197 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7777 (mpm) REVERT: G 31 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8431 (mttp) REVERT: G 47 ASP cc_start: 0.8166 (p0) cc_final: 0.7952 (p0) REVERT: G 51 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: R 7 ILE cc_start: 0.8312 (mm) cc_final: 0.7947 (tt) REVERT: R 118 LYS cc_start: 0.8446 (tptp) cc_final: 0.7823 (tmtt) REVERT: S 103 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8465 (tp30) REVERT: Y 93 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: V 52 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: W 101 GLN cc_start: 0.7436 (mt0) cc_final: 0.6931 (tp40) REVERT: W 110 GLN cc_start: 0.8920 (mt0) cc_final: 0.8449 (pm20) REVERT: W 113 TYR cc_start: 0.8120 (t80) cc_final: 0.7699 (t80) REVERT: W 139 LEU cc_start: 0.8424 (tp) cc_final: 0.8188 (tt) REVERT: K 61 ILE cc_start: 0.6677 (mm) cc_final: 0.6280 (pp) REVERT: L 55 PHE cc_start: 0.7795 (m-80) cc_final: 0.7293 (m-80) REVERT: N 38 ASN cc_start: 0.6670 (t0) cc_final: 0.6172 (t0) REVERT: O 48 TYR cc_start: 0.6134 (m-80) cc_final: 0.5793 (m-10) REVERT: P 49 MET cc_start: 0.2539 (OUTLIER) cc_final: 0.2233 (ptt) outliers start: 137 outliers final: 61 residues processed: 421 average time/residue: 0.5696 time to fit residues: 296.4846 Evaluate side-chains 378 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 305 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 274 GLN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain S residue 131 ILE Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 93 GLU Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 143 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 53 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 293 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 166 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 326 optimal weight: 9.9990 chunk 369 optimal weight: 50.0000 chunk 295 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 ASN ** V 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.144467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.088243 restraints weight = 65490.835| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.10 r_work: 0.2975 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38221 Z= 0.147 Angle : 0.604 12.897 51973 Z= 0.315 Chirality : 0.044 0.229 6209 Planarity : 0.005 0.074 6880 Dihedral : 6.769 129.310 5730 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.61 % Allowed : 16.92 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.12), residues: 5161 helix: 1.27 (0.10), residues: 2896 sheet: -1.31 (0.22), residues: 563 loop : -0.92 (0.16), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 178 TYR 0.032 0.001 TYR D 364 PHE 0.039 0.001 PHE B 413 TRP 0.006 0.001 TRP C 471 HIS 0.004 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00331 (38221) covalent geometry : angle 0.60401 (51973) hydrogen bonds : bond 0.04053 ( 2439) hydrogen bonds : angle 4.35662 ( 7134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 353 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8570 (tp30) REVERT: B 196 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: B 497 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8336 (mmm-85) REVERT: C 257 MET cc_start: 0.9496 (OUTLIER) cc_final: 0.9267 (ttm) REVERT: C 335 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8762 (tt0) REVERT: C 506 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8308 (tp30) REVERT: D 40 ARG cc_start: 0.8538 (ppt170) cc_final: 0.7049 (ppt170) REVERT: D 126 GLN cc_start: 0.8412 (tp-100) cc_final: 0.7882 (tt0) REVERT: D 177 PHE cc_start: 0.8238 (m-80) cc_final: 0.8030 (m-10) REVERT: D 197 MET cc_start: 0.8140 (tpt) cc_final: 0.7736 (tpt) REVERT: D 198 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.7691 (mtpp) REVERT: D 296 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8590 (mmtm) REVERT: E 22 ASP cc_start: 0.7718 (p0) cc_final: 0.7194 (p0) REVERT: E 23 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7927 (pm20) REVERT: F 407 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8146 (mt-10) REVERT: G 51 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8331 (pm20) REVERT: G 172 TYR cc_start: 0.7782 (m-80) cc_final: 0.7549 (m-80) REVERT: G 207 TYR cc_start: 0.7730 (m-10) cc_final: 0.7306 (m-10) REVERT: R 7 ILE cc_start: 0.8356 (mm) cc_final: 0.8095 (tt) REVERT: R 67 MET cc_start: 0.9012 (ttt) cc_final: 0.8745 (tmm) REVERT: R 118 LYS cc_start: 0.8370 (tptp) cc_final: 0.7763 (tmtt) REVERT: S 96 GLU cc_start: 0.7727 (pp20) cc_final: 0.7507 (pp20) REVERT: S 102 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7902 (mttm) REVERT: S 103 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8457 (tp30) REVERT: Y 93 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6777 (pm20) REVERT: V 52 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: W 101 GLN cc_start: 0.7541 (mt0) cc_final: 0.6999 (tp40) REVERT: W 110 GLN cc_start: 0.8889 (mt0) cc_final: 0.8401 (pm20) REVERT: W 139 LEU cc_start: 0.8503 (tp) cc_final: 0.8299 (tt) REVERT: I 49 MET cc_start: 0.5437 (tpt) cc_final: 0.4179 (mtt) REVERT: K 61 ILE cc_start: 0.6614 (mm) cc_final: 0.6223 (pp) REVERT: L 55 PHE cc_start: 0.7828 (m-80) cc_final: 0.7319 (m-80) REVERT: N 38 ASN cc_start: 0.6706 (t0) cc_final: 0.6226 (t0) REVERT: O 48 TYR cc_start: 0.6108 (m-80) cc_final: 0.5734 (m-10) REVERT: Q 44 ARG cc_start: 0.6737 (ttp80) cc_final: 0.6313 (ppp80) outliers start: 92 outliers final: 36 residues processed: 423 average time/residue: 0.5694 time to fit residues: 298.2770 Evaluate side-chains 368 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 323 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 93 GLU Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 95 ILE Chi-restraints excluded: chain W residue 143 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain Q residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 51 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 485 optimal weight: 50.0000 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 498 optimal weight: 40.0000 chunk 500 optimal weight: 30.0000 chunk 368 optimal weight: 0.8980 chunk 239 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS D 51 ASN D 128 GLN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.143588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.087140 restraints weight = 65870.675| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.16 r_work: 0.2950 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 38221 Z= 0.196 Angle : 0.620 12.746 51973 Z= 0.322 Chirality : 0.045 0.226 6209 Planarity : 0.005 0.067 6880 Dihedral : 6.652 128.986 5730 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.26 % Allowed : 17.40 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.12), residues: 5161 helix: 1.36 (0.10), residues: 2885 sheet: -1.32 (0.22), residues: 562 loop : -0.90 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 76 TYR 0.030 0.001 TYR D 364 PHE 0.037 0.001 PHE B 413 TRP 0.004 0.001 TRP C 471 HIS 0.007 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00460 (38221) covalent geometry : angle 0.62035 (51973) hydrogen bonds : bond 0.04090 ( 2439) hydrogen bonds : angle 4.28854 ( 7134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 337 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 TYR cc_start: 0.8817 (t80) cc_final: 0.8610 (t80) REVERT: B 102 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8691 (tp) REVERT: B 196 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: C 308 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8773 (tp) REVERT: C 335 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8781 (tt0) REVERT: D 40 ARG cc_start: 0.8571 (ppt170) cc_final: 0.7095 (ppt170) REVERT: D 126 GLN cc_start: 0.8432 (tp-100) cc_final: 0.7813 (tt0) REVERT: D 177 PHE cc_start: 0.8282 (m-80) cc_final: 0.8028 (m-10) REVERT: D 197 MET cc_start: 0.8183 (tpt) cc_final: 0.7845 (tpt) REVERT: D 198 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.7746 (mtpp) REVERT: D 296 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8544 (mmtm) REVERT: E 165 GLU cc_start: 0.7870 (tp30) cc_final: 0.7647 (tp30) REVERT: E 274 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: G 47 ASP cc_start: 0.8287 (p0) cc_final: 0.8045 (p0) REVERT: G 51 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: R 7 ILE cc_start: 0.8287 (mm) cc_final: 0.8001 (tt) REVERT: S 96 GLU cc_start: 0.7736 (pp20) cc_final: 0.7504 (pp20) REVERT: S 102 LYS cc_start: 0.8093 (mtmm) cc_final: 0.7840 (mttm) REVERT: Y 93 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6782 (pm20) REVERT: V 52 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: W 101 GLN cc_start: 0.7544 (mt0) cc_final: 0.6999 (tp40) REVERT: K 61 ILE cc_start: 0.6569 (mm) cc_final: 0.6169 (pp) REVERT: L 55 PHE cc_start: 0.7811 (m-80) cc_final: 0.7293 (m-80) REVERT: N 38 ASN cc_start: 0.6692 (t0) cc_final: 0.6190 (t0) REVERT: O 48 TYR cc_start: 0.6125 (m-80) cc_final: 0.5738 (m-10) outliers start: 115 outliers final: 55 residues processed: 421 average time/residue: 0.5572 time to fit residues: 291.8261 Evaluate side-chains 383 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 319 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 274 GLN Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain S residue 131 ILE Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 93 GLU Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 95 ILE Chi-restraints excluded: chain W residue 143 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 30 optimal weight: 3.9990 chunk 354 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 246 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 304 optimal weight: 6.9990 chunk 450 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 379 optimal weight: 0.6980 chunk 227 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS D 51 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN F 128 GLN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.145552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.089110 restraints weight = 65658.664| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.06 r_work: 0.2998 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 38221 Z= 0.140 Angle : 0.600 11.719 51973 Z= 0.309 Chirality : 0.044 0.207 6209 Planarity : 0.005 0.061 6880 Dihedral : 6.461 126.260 5730 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.90 % Allowed : 18.37 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.12), residues: 5161 helix: 1.48 (0.10), residues: 2878 sheet: -1.18 (0.22), residues: 572 loop : -0.80 (0.16), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 76 TYR 0.035 0.001 TYR D 364 PHE 0.039 0.001 PHE B 413 TRP 0.005 0.001 TRP C 471 HIS 0.007 0.001 HIS R 37 Details of bonding type rmsd covalent geometry : bond 0.00321 (38221) covalent geometry : angle 0.59995 (51973) hydrogen bonds : bond 0.03819 ( 2439) hydrogen bonds : angle 4.18785 ( 7134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 351 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8549 (tp30) REVERT: A 358 TYR cc_start: 0.8805 (t80) cc_final: 0.8603 (t80) REVERT: A 497 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8405 (mmm-85) REVERT: B 102 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8613 (tp) REVERT: B 196 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: B 276 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.6488 (t0) REVERT: B 497 ARG cc_start: 0.8641 (tpp-160) cc_final: 0.8381 (mmm-85) REVERT: C 257 MET cc_start: 0.9459 (OUTLIER) cc_final: 0.9235 (ttm) REVERT: C 335 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8748 (tt0) REVERT: C 390 MET cc_start: 0.9194 (mmt) cc_final: 0.8882 (mmt) REVERT: D 40 ARG cc_start: 0.8548 (ppt170) cc_final: 0.7077 (ppt170) REVERT: D 126 GLN cc_start: 0.8420 (tp-100) cc_final: 0.7851 (tt0) REVERT: D 177 PHE cc_start: 0.8257 (m-80) cc_final: 0.7994 (m-10) REVERT: D 195 HIS cc_start: 0.8130 (m90) cc_final: 0.7788 (m90) REVERT: D 197 MET cc_start: 0.8139 (tpt) cc_final: 0.7782 (tpt) REVERT: D 198 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.7654 (mtpp) REVERT: D 296 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8536 (mmtm) REVERT: E 274 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: F 389 MET cc_start: 0.8902 (mmm) cc_final: 0.8677 (mmm) REVERT: F 407 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8162 (mt-10) REVERT: G 47 ASP cc_start: 0.8264 (p0) cc_final: 0.8029 (p0) REVERT: G 51 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: G 207 TYR cc_start: 0.7782 (m-10) cc_final: 0.7572 (m-10) REVERT: R 7 ILE cc_start: 0.8289 (mm) cc_final: 0.8056 (tt) REVERT: R 126 LEU cc_start: 0.8425 (mt) cc_final: 0.8155 (mt) REVERT: S 96 GLU cc_start: 0.7659 (pp20) cc_final: 0.7409 (pp20) REVERT: S 102 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7871 (mttm) REVERT: Y 93 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: V 52 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: W 101 GLN cc_start: 0.7570 (mt0) cc_final: 0.7060 (tp40) REVERT: W 110 GLN cc_start: 0.8899 (mt0) cc_final: 0.8406 (pm20) REVERT: I 49 MET cc_start: 0.5209 (tpt) cc_final: 0.4008 (mtt) REVERT: K 61 ILE cc_start: 0.6553 (mm) cc_final: 0.6161 (pp) REVERT: K 70 ILE cc_start: 0.1299 (OUTLIER) cc_final: 0.0934 (pt) REVERT: L 55 PHE cc_start: 0.7819 (m-80) cc_final: 0.7301 (m-80) REVERT: N 38 ASN cc_start: 0.6746 (t0) cc_final: 0.6235 (t0) REVERT: O 48 TYR cc_start: 0.6113 (m-80) cc_final: 0.5747 (m-10) outliers start: 102 outliers final: 40 residues processed: 427 average time/residue: 0.5505 time to fit residues: 294.3259 Evaluate side-chains 384 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 332 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 274 GLN Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 93 GLU Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 143 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain Q residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 459 optimal weight: 0.0010 chunk 49 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 404 optimal weight: 30.0000 chunk 335 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 377 optimal weight: 50.0000 chunk 235 optimal weight: 3.9990 chunk 305 optimal weight: 10.0000 chunk 375 optimal weight: 8.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 149 HIS H 33 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.144844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088265 restraints weight = 65661.989| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.07 r_work: 0.2980 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38221 Z= 0.170 Angle : 0.611 11.858 51973 Z= 0.315 Chirality : 0.044 0.207 6209 Planarity : 0.005 0.060 6880 Dihedral : 6.432 126.480 5730 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.44 % Allowed : 19.10 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.12), residues: 5161 helix: 1.48 (0.10), residues: 2896 sheet: -1.17 (0.22), residues: 580 loop : -0.79 (0.16), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 104 TYR 0.032 0.001 TYR G 45 PHE 0.036 0.001 PHE B 413 TRP 0.003 0.001 TRP C 471 HIS 0.006 0.001 HIS R 37 Details of bonding type rmsd covalent geometry : bond 0.00397 (38221) covalent geometry : angle 0.61057 (51973) hydrogen bonds : bond 0.03864 ( 2439) hydrogen bonds : angle 4.16250 ( 7134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 341 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8544 (tp30) REVERT: A 358 TYR cc_start: 0.8807 (t80) cc_final: 0.8565 (t80) REVERT: B 102 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8643 (tp) REVERT: B 196 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: C 257 MET cc_start: 0.9471 (OUTLIER) cc_final: 0.9203 (ttm) REVERT: C 335 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8733 (tt0) REVERT: D 40 ARG cc_start: 0.8575 (ppt170) cc_final: 0.7094 (ppt170) REVERT: D 126 GLN cc_start: 0.8420 (tp-100) cc_final: 0.7830 (tt0) REVERT: D 177 PHE cc_start: 0.8198 (m-80) cc_final: 0.7981 (m-10) REVERT: D 197 MET cc_start: 0.8102 (tpt) cc_final: 0.7773 (tpt) REVERT: D 198 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.7662 (mtpp) REVERT: D 296 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8538 (mmtm) REVERT: E 274 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: F 40 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8376 (ptp-110) REVERT: F 407 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8233 (mt-10) REVERT: G 47 ASP cc_start: 0.8253 (p0) cc_final: 0.8025 (p0) REVERT: G 51 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: G 207 TYR cc_start: 0.7768 (m-10) cc_final: 0.7511 (m-10) REVERT: R 7 ILE cc_start: 0.8401 (mm) cc_final: 0.8129 (tt) REVERT: R 123 MET cc_start: 0.8824 (mtp) cc_final: 0.8589 (mtt) REVERT: R 126 LEU cc_start: 0.8490 (mt) cc_final: 0.8270 (mt) REVERT: S 96 GLU cc_start: 0.7737 (pp20) cc_final: 0.7486 (pp20) REVERT: S 102 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7866 (mttm) REVERT: Y 93 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6749 (pm20) REVERT: V 52 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: W 101 GLN cc_start: 0.7526 (mt0) cc_final: 0.6997 (tp40) REVERT: I 49 MET cc_start: 0.5435 (tpt) cc_final: 0.4166 (mtt) REVERT: K 61 ILE cc_start: 0.6455 (mm) cc_final: 0.6053 (pp) REVERT: K 70 ILE cc_start: 0.1365 (OUTLIER) cc_final: 0.1006 (pt) REVERT: L 55 PHE cc_start: 0.7828 (m-80) cc_final: 0.7332 (m-80) REVERT: N 38 ASN cc_start: 0.6689 (t0) cc_final: 0.6180 (t0) REVERT: O 48 TYR cc_start: 0.6008 (m-80) cc_final: 0.5702 (m-10) REVERT: P 49 MET cc_start: 0.2383 (OUTLIER) cc_final: 0.2029 (ptt) outliers start: 86 outliers final: 40 residues processed: 404 average time/residue: 0.5588 time to fit residues: 281.3348 Evaluate side-chains 379 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 326 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 274 GLN Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 131 ILE Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 93 GLU Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 143 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 269 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 417 optimal weight: 9.9990 chunk 463 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 363 optimal weight: 0.9980 chunk 461 optimal weight: 50.0000 chunk 78 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN D 51 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.144154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.087751 restraints weight = 66087.890| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.10 r_work: 0.2961 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 38221 Z= 0.195 Angle : 0.632 12.627 51973 Z= 0.325 Chirality : 0.045 0.388 6209 Planarity : 0.005 0.060 6880 Dihedral : 6.468 126.687 5730 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.13 % Allowed : 19.56 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.12), residues: 5161 helix: 1.48 (0.10), residues: 2896 sheet: -1.25 (0.22), residues: 571 loop : -0.80 (0.16), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG S 104 TYR 0.036 0.001 TYR D 364 PHE 0.035 0.001 PHE B 413 TRP 0.003 0.001 TRP C 471 HIS 0.008 0.001 HIS R 37 Details of bonding type rmsd covalent geometry : bond 0.00460 (38221) covalent geometry : angle 0.63189 (51973) hydrogen bonds : bond 0.03918 ( 2439) hydrogen bonds : angle 4.18974 ( 7134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 342 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 TYR cc_start: 0.8829 (t80) cc_final: 0.8564 (t80) REVERT: A 497 ARG cc_start: 0.8568 (tpp80) cc_final: 0.8327 (mmm-85) REVERT: B 102 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8653 (tp) REVERT: B 196 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: B 497 ARG cc_start: 0.8633 (tpp-160) cc_final: 0.8359 (mmm-85) REVERT: C 257 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.9204 (ttm) REVERT: C 335 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8750 (tt0) REVERT: D 40 ARG cc_start: 0.8583 (ppt170) cc_final: 0.7154 (ppt170) REVERT: D 126 GLN cc_start: 0.8427 (tp-100) cc_final: 0.7808 (tt0) REVERT: D 177 PHE cc_start: 0.8238 (m-80) cc_final: 0.8025 (m-10) REVERT: D 197 MET cc_start: 0.8084 (tpt) cc_final: 0.7766 (tpt) REVERT: D 198 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.7638 (mtpp) REVERT: D 296 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8538 (mmtm) REVERT: E 274 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: E 397 LYS cc_start: 0.7884 (ttmt) cc_final: 0.7413 (mtmp) REVERT: F 40 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8266 (ptp-110) REVERT: F 389 MET cc_start: 0.8977 (mmm) cc_final: 0.8725 (tpp) REVERT: F 407 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8238 (mt-10) REVERT: G 47 ASP cc_start: 0.8311 (p0) cc_final: 0.8092 (p0) REVERT: G 51 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: G 207 TYR cc_start: 0.7740 (m-10) cc_final: 0.7528 (m-10) REVERT: R 7 ILE cc_start: 0.8369 (mm) cc_final: 0.8109 (tt) REVERT: R 21 MET cc_start: 0.7861 (mmm) cc_final: 0.6108 (tpt) REVERT: S 102 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7871 (mttm) REVERT: Y 93 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6650 (pm20) REVERT: V 52 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: W 101 GLN cc_start: 0.7539 (mt0) cc_final: 0.6984 (tp40) REVERT: H 66 ILE cc_start: 0.1447 (mm) cc_final: 0.1132 (pt) REVERT: I 49 MET cc_start: 0.5500 (tpt) cc_final: 0.4273 (mtt) REVERT: K 61 ILE cc_start: 0.6241 (mm) cc_final: 0.5843 (pp) REVERT: L 55 PHE cc_start: 0.7803 (m-80) cc_final: 0.7330 (m-80) REVERT: N 38 ASN cc_start: 0.6617 (t0) cc_final: 0.6112 (t0) REVERT: N 66 ILE cc_start: 0.5229 (OUTLIER) cc_final: 0.4958 (tt) REVERT: O 33 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7315 (mp10) REVERT: O 48 TYR cc_start: 0.5985 (m-80) cc_final: 0.5699 (m-10) REVERT: P 49 MET cc_start: 0.2247 (OUTLIER) cc_final: 0.1900 (ptt) outliers start: 75 outliers final: 48 residues processed: 398 average time/residue: 0.5150 time to fit residues: 257.8996 Evaluate side-chains 384 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 324 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 274 GLN Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 93 GLU Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 143 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 454 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 340 optimal weight: 6.9990 chunk 363 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 351 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 GLN H 33 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.143277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087139 restraints weight = 65960.452| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.02 r_work: 0.2955 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 38221 Z= 0.233 Angle : 0.661 13.111 51973 Z= 0.342 Chirality : 0.047 0.512 6209 Planarity : 0.005 0.060 6880 Dihedral : 6.550 127.521 5730 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.27 % Allowed : 19.73 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.12), residues: 5161 helix: 1.41 (0.10), residues: 2908 sheet: -1.28 (0.22), residues: 573 loop : -0.81 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 76 TYR 0.035 0.001 TYR G 45 PHE 0.045 0.001 PHE Q 55 TRP 0.002 0.000 TRP B 471 HIS 0.009 0.001 HIS R 37 Details of bonding type rmsd covalent geometry : bond 0.00554 (38221) covalent geometry : angle 0.66073 (51973) hydrogen bonds : bond 0.04048 ( 2439) hydrogen bonds : angle 4.24430 ( 7134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10322 Ramachandran restraints generated. 5161 Oldfield, 0 Emsley, 5161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 337 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 TYR cc_start: 0.9008 (t80) cc_final: 0.8767 (t80) REVERT: B 102 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8693 (tp) REVERT: B 196 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: B 497 ARG cc_start: 0.8700 (tpp-160) cc_final: 0.8421 (mmm-85) REVERT: C 335 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8947 (tt0) REVERT: D 40 ARG cc_start: 0.8718 (ppt170) cc_final: 0.7316 (ppt170) REVERT: D 126 GLN cc_start: 0.8481 (tp-100) cc_final: 0.7790 (tt0) REVERT: D 195 HIS cc_start: 0.8393 (m90) cc_final: 0.8048 (m170) REVERT: D 197 MET cc_start: 0.8347 (tpt) cc_final: 0.8019 (tpt) REVERT: D 198 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.7793 (mtpp) REVERT: D 296 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8562 (mmtm) REVERT: E 274 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: E 426 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6582 (mttm) REVERT: F 389 MET cc_start: 0.9010 (mmm) cc_final: 0.8774 (tpp) REVERT: F 407 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8445 (mt-10) REVERT: G 47 ASP cc_start: 0.8315 (p0) cc_final: 0.8043 (p0) REVERT: G 51 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: R 7 ILE cc_start: 0.8477 (mm) cc_final: 0.8174 (tt) REVERT: S 102 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7730 (mttm) REVERT: S 103 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8372 (tp30) REVERT: Y 93 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6639 (pm20) REVERT: V 52 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: H 18 ILE cc_start: 0.5670 (mm) cc_final: 0.5426 (mm) REVERT: I 49 MET cc_start: 0.5245 (tpt) cc_final: 0.4126 (mtt) REVERT: K 61 ILE cc_start: 0.6223 (mm) cc_final: 0.5813 (pp) REVERT: L 55 PHE cc_start: 0.7785 (m-80) cc_final: 0.7314 (m-80) REVERT: N 38 ASN cc_start: 0.6596 (t0) cc_final: 0.6078 (t0) REVERT: N 66 ILE cc_start: 0.5228 (OUTLIER) cc_final: 0.4956 (tt) REVERT: O 48 TYR cc_start: 0.6071 (m-80) cc_final: 0.5773 (m-10) REVERT: P 49 MET cc_start: 0.2284 (OUTLIER) cc_final: 0.1991 (ptt) REVERT: Q 44 ARG cc_start: 0.5233 (ppp80) cc_final: 0.4780 (tmm-80) outliers start: 80 outliers final: 47 residues processed: 395 average time/residue: 0.5379 time to fit residues: 265.5674 Evaluate side-chains 390 residues out of total 4159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 332 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 274 GLN Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 93 GLU Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain V residue 52 GLU Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 143 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 86 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 191 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 496 optimal weight: 50.0000 chunk 415 optimal weight: 6.9990 chunk 274 optimal weight: 0.3980 chunk 172 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 ASN D 51 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN F 195 HIS W 101 GLN H 33 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.146215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.090671 restraints weight = 65586.097| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.12 r_work: 0.3017 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 38221 Z= 0.136 Angle : 0.629 12.625 51973 Z= 0.323 Chirality : 0.045 0.485 6209 Planarity : 0.005 0.061 6880 Dihedral : 6.363 123.944 5730 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.79 % Allowed : 20.30 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.12), residues: 5161 helix: 1.52 (0.10), residues: 2899 sheet: -1.17 (0.23), residues: 557 loop : -0.75 (0.16), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 76 TYR 0.036 0.001 TYR D 364 PHE 0.036 0.001 PHE B 413 TRP 0.006 0.001 TRP B 471 HIS 0.008 0.001 HIS R 37 Details of bonding type rmsd covalent geometry : bond 0.00309 (38221) covalent geometry : angle 0.62902 (51973) hydrogen bonds : bond 0.03742 ( 2439) hydrogen bonds : angle 4.14567 ( 7134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13776.28 seconds wall clock time: 234 minutes 18.99 seconds (14058.99 seconds total)