Starting phenix.real_space_refine on Tue Aug 26 15:18:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itk_60869/08_2025/9itk_60869.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itk_60869/08_2025/9itk_60869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itk_60869/08_2025/9itk_60869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itk_60869/08_2025/9itk_60869.map" model { file = "/net/cci-nas-00/data/ceres_data/9itk_60869/08_2025/9itk_60869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itk_60869/08_2025/9itk_60869.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 9 5.49 5 Mg 3 5.21 5 S 95 5.16 5 C 24368 2.51 5 N 6767 2.21 5 O 7274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.02s 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: 38516 Number of models: 1 Model: "" Number of chains: 29 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: "H" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "I" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "J" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "K" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "N" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "O" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "P" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Q" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} 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: "T" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1799 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "U" 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: "X" 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: "Y" 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: "Z" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1147 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 735 Unresolved non-hydrogen angles: 961 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 9, 'PHE:plan': 32, 'ASP:plan': 3, 'ASN:plan1': 12, 'ARG:plan': 6, 'GLN:plan1': 3, 'TYR:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 380 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.47, per 1000 atoms: 0.22 Number of scatterers: 38516 At special positions: 0 Unit cell: (134.85, 135.78, 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 95 16.00 P 9 15.00 Mg 3 11.99 O 7274 8.00 N 6767 7.00 C 24368 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: 2.76 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9544 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 38 sheets defined 58.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.511A 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: 3.758A 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 Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.641A pdb=" N THR A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 387 through 407 removed outlier: 5.211A pdb=" N LYS A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.878A pdb=" N GLN A 412 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 436 Processing helix chain 'A' and resid 444 through 456 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: 3.680A 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: 3.581A 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: 3.525A 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 238 through 244 Processing helix chain 'B' and resid 246 through 260 removed outlier: 5.879A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.501A pdb=" N HIS B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.910A pdb=" N ALA B 300 " --> pdb=" O GLY B 297 " (cutoff:3.500A) 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 315 removed outlier: 4.004A pdb=" N ARG B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) 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 removed outlier: 3.533A pdb=" N THR B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.767A pdb=" N ALA B 384 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 414 removed outlier: 3.765A pdb=" N GLY B 395 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LYS B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N PHE B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 435 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: 3.857A 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 107 through 111 removed outlier: 3.781A 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 238 through 259 Proline residue: C 246 - end of helix removed outlier: 3.518A pdb=" N ILE C 256 " --> pdb=" O MET C 252 " (cutoff:3.500A) 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: 3.896A 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: 3.859A pdb=" N ALA C 384 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.694A pdb=" N GLY C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 removed outlier: 3.568A pdb=" N ALA C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 4.777A 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: 3.755A pdb=" N ARG C 487 " --> pdb=" O HIS C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 519 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 158 through 174 Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'D' and resid 222 through 243 removed outlier: 4.756A pdb=" N GLY D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.564A pdb=" N PHE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.596A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 379 through 388 removed outlier: 4.283A pdb=" N ILE D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 5.588A pdb=" N SER D 393 " --> pdb=" O GLU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.958A pdb=" N LEU D 398 " --> pdb=" O ASP D 394 " (cutoff:3.500A) 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 134 through 140 Processing helix chain 'E' and resid 158 through 174 Processing helix chain 'E' and resid 191 through 201 Processing helix chain 'E' and resid 222 through 243 removed outlier: 4.909A pdb=" N GLY E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU E 243 " --> pdb=" O TYR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.651A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 332 through 338 removed outlier: 3.702A pdb=" N ARG E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 4.624A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE E 383 " --> pdb=" O ASP E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 410 Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 458 through 468 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 158 through 171 Processing helix chain 'F' and resid 193 through 201 Processing helix chain 'F' and resid 222 through 243 removed outlier: 4.733A pdb=" N GLY F 230 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR F 239 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE F 240 " --> pdb=" O MET F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 268 removed outlier: 3.691A 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: 4.314A 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 355 through 360 Processing helix chain 'F' and resid 360 through 380 removed outlier: 4.520A pdb=" N LEU F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR F 377 " --> pdb=" O VAL F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 388 through 392 removed outlier: 3.740A pdb=" N GLU F 391 " --> pdb=" O GLY F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 Processing helix chain 'F' and resid 414 through 418 removed outlier: 3.895A pdb=" N GLN F 418 " --> pdb=" O THR F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.727A pdb=" N TYR F 454 " --> pdb=" O SER F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.519A 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 removed outlier: 3.584A pdb=" N MET G 49 " --> pdb=" O TYR G 45 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU G 51 " --> pdb=" O ASP G 47 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG G 59 " --> pdb=" O ASN G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 removed outlier: 3.520A pdb=" N LEU G 70 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 112 removed outlier: 3.812A pdb=" N THR G 107 " --> pdb=" O GLY G 103 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU G 108 " --> pdb=" O ARG G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 148 through 165 removed outlier: 4.006A pdb=" N ILE G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 286 Proline residue: G 222 - end of helix removed outlier: 3.598A pdb=" N ALA G 282 " --> pdb=" O VAL G 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 38 removed outlier: 3.909A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix removed outlier: 3.675A pdb=" N GLY H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 70 removed outlier: 3.965A pdb=" N THR H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE H 55 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU H 57 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 17 removed outlier: 3.667A pdb=" N VAL I 7 " --> pdb=" O GLY I 3 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL I 13 " --> pdb=" O THR I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 38 removed outlier: 4.240A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG I 37 " --> pdb=" O GLN I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 72 removed outlier: 3.823A pdb=" N THR I 47 " --> pdb=" O ASN I 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU I 59 " --> pdb=" O PHE I 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 38 removed outlier: 3.608A pdb=" N VAL J 7 " --> pdb=" O GLY J 3 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Proline residue: J 20 - end of helix removed outlier: 3.552A pdb=" N GLY J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 73 removed outlier: 3.955A pdb=" N THR J 47 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY J 52 " --> pdb=" O TYR J 48 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU J 59 " --> pdb=" O PHE J 55 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 17 removed outlier: 3.870A pdb=" N VAL K 13 " --> pdb=" O THR K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 38 removed outlier: 3.786A pdb=" N VAL K 22 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 72 removed outlier: 4.021A pdb=" N THR K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE K 55 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA K 60 " --> pdb=" O THR K 56 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY K 63 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 17 removed outlier: 3.682A pdb=" N VAL L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 38 removed outlier: 3.517A pdb=" N VAL L 22 " --> pdb=" O ILE L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 73 removed outlier: 3.801A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 15 removed outlier: 3.723A pdb=" N VAL M 7 " --> pdb=" O GLY M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 38 removed outlier: 3.800A pdb=" N VAL M 22 " --> pdb=" O ILE M 18 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE M 27 " --> pdb=" O GLY M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 72 removed outlier: 4.235A pdb=" N THR M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU M 59 " --> pdb=" O PHE M 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 removed outlier: 3.964A pdb=" N THR N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 38 removed outlier: 3.731A pdb=" N GLY N 25 " --> pdb=" O GLY N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 72 removed outlier: 3.831A pdb=" N TYR N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE N 51 " --> pdb=" O THR N 47 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU N 59 " --> pdb=" O PHE N 55 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA N 60 " --> pdb=" O THR N 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE N 66 " --> pdb=" O PHE N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 16 removed outlier: 4.092A pdb=" N ALA O 10 " --> pdb=" O LEU O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 38 removed outlier: 3.599A pdb=" N VAL O 22 " --> pdb=" O ILE O 18 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY O 25 " --> pdb=" O GLY O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 73 removed outlier: 3.739A pdb=" N THR O 47 " --> pdb=" O ASN O 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR O 48 " --> pdb=" O ARG O 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 removed outlier: 3.632A pdb=" N VAL P 13 " --> pdb=" O THR P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 38 removed outlier: 3.631A pdb=" N GLY P 25 " --> pdb=" O GLY P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 72 removed outlier: 4.861A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU P 59 " --> pdb=" O PHE P 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 3.758A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE Q 18 " --> pdb=" O GLY Q 14 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Proline residue: Q 20 - end of helix removed outlier: 3.753A pdb=" N GLY Q 25 " --> pdb=" O GLY Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 72 removed outlier: 3.604A pdb=" N VAL Q 45 " --> pdb=" O ILE Q 41 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA Q 60 " --> pdb=" O THR Q 56 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 102 Processing helix chain 'R' and resid 109 through 128 removed outlier: 3.595A pdb=" N LEU R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG R 127 " --> pdb=" O MET R 123 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 111 removed outlier: 3.698A pdb=" N LEU S 109 " --> pdb=" O ILE S 105 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN S 111 " --> pdb=" O ARG S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 154 Processing helix chain 'T' and resid 50 through 72 removed outlier: 3.686A pdb=" N VAL T 54 " --> pdb=" O ASN T 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP T 59 " --> pdb=" O ALA T 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA T 68 " --> pdb=" O ALA T 64 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 99 Processing helix chain 'T' and resid 102 through 124 Proline residue: T 108 - end of helix Processing helix chain 'T' and resid 186 through 189 Processing helix chain 'T' and resid 190 through 214 removed outlier: 3.503A pdb=" N ILE T 205 " --> pdb=" O SER T 201 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU T 206 " --> pdb=" O PHE T 202 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP T 208 " --> pdb=" O PHE T 204 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 267 removed outlier: 3.642A pdb=" N PHE T 236 " --> pdb=" O GLY T 232 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU T 240 " --> pdb=" O PHE T 236 " (cutoff:3.500A) Proline residue: T 243 - end of helix removed outlier: 3.509A pdb=" N GLY T 257 " --> pdb=" O ASN T 253 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET T 264 " --> pdb=" O LEU T 260 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA T 265 " --> pdb=" O LEU T 261 " (cutoff:3.500A) Processing helix chain 'T' and resid 272 through 304 removed outlier: 4.602A pdb=" N PHE T 276 " --> pdb=" O LEU T 272 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY T 278 " --> pdb=" O LEU T 274 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 27 removed outlier: 3.744A pdb=" N ASN U 17 " --> pdb=" O ALA U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 140 removed outlier: 3.776A pdb=" N ARG U 138 " --> pdb=" O LEU U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 151 through 158 Processing helix chain 'V' and resid 7 through 29 Processing helix chain 'V' and resid 29 through 115 removed outlier: 3.535A pdb=" N ARG V 55 " --> pdb=" O ALA V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 115 through 120 Processing helix chain 'V' and resid 126 through 138 Processing helix chain 'V' and resid 148 through 158 Processing helix chain 'W' and resid 98 through 109 removed outlier: 3.881A pdb=" N LEU W 109 " --> pdb=" O ILE W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 143 through 154 removed outlier: 3.549A pdb=" N ILE W 150 " --> pdb=" O ARG W 146 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN W 151 " --> pdb=" O LEU W 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 121 removed outlier: 3.554A pdb=" N PHE X 11 " --> pdb=" O ASN X 7 " (cutoff:3.500A) Proline residue: X 32 - end of helix Processing helix chain 'X' and resid 126 through 136 Processing helix chain 'Y' and resid 9 through 148 Proline residue: Y 32 - end of helix Processing helix chain 'Y' and resid 149 through 151 No H-bonds generated for 'chain 'Y' and resid 149 through 151' Processing helix chain 'Y' and resid 152 through 160 removed outlier: 3.543A pdb=" N ALA Y 159 " --> pdb=" O GLU Y 155 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 70 removed outlier: 3.785A pdb=" N ILE Z 56 " --> pdb=" O PHE Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 99 removed outlier: 3.582A pdb=" N ILE Z 87 " --> pdb=" O VAL Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 125 removed outlier: 3.705A pdb=" N LEU Z 109 " --> pdb=" O THR Z 105 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU Z 115 " --> pdb=" O ALA Z 111 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU Z 125 " --> pdb=" O ASN Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 211 removed outlier: 3.882A pdb=" N THR Z 194 " --> pdb=" O ASP Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 232 through 267 Proline residue: Z 243 - end of helix Processing helix chain 'Z' and resid 274 through 279 Processing helix chain 'Z' and resid 279 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 5.681A pdb=" N ARG A 100 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.956A 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: 5.681A pdb=" N ARG A 100 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.956A 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 68 through 73 current: chain 'F' and resid 30 through 33 removed outlier: 6.749A pdb=" N LYS F 55 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN F 48 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL F 53 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL F 14 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE F 10 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 6.793A 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: 3.520A pdb=" N VAL A 106 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.373A 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: 3.513A pdb=" N ASP A 276 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 205 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A 333 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 277 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLU A 335 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 173 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A 359 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 175 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 4.477A 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: 3.704A pdb=" N ALA B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 77 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 81 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA B 70 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU B 52 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B 53 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 98 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASN B 28 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N GLY B 99 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 13.538A pdb=" N GLN B 26 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA S 89 " --> pdb=" O THR S 119 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N HIS S 121 " --> pdb=" O ALA S 89 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL S 91 " --> pdb=" O HIS S 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 106 removed outlier: 4.449A pdb=" N LYS B 132 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.900A pdb=" N CYS B 200 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL B 231 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR B 202 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA B 233 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 204 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 333 through 335 removed outlier: 8.282A pdb=" N ILE B 334 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 174 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AB3, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AB4, first strand: chain 'C' and resid 77 through 82 removed outlier: 6.739A pdb=" N SER C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU C 73 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA C 79 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU C 52 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 53 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ARG C 100 " --> pdb=" O ILE C 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 103 through 106 removed outlier: 4.470A pdb=" N LYS C 132 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AB7, first strand: chain 'C' and resid 333 through 336 Processing sheet with id=AB8, first strand: chain 'C' and resid 261 through 263 Processing sheet with id=AB9, first strand: chain 'D' and resid 44 through 49 removed outlier: 5.586A pdb=" N VAL D 45 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL D 57 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL D 14 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE D 10 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG D 16 " --> pdb=" O GLN D 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AC2, first strand: chain 'D' and resid 79 through 81 Processing sheet with id=AC3, first strand: chain 'D' and resid 90 through 91 removed outlier: 6.477A pdb=" N PHE D 91 " --> pdb=" O PHE D 216 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.666A pdb=" N PHE D 130 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE D 143 " --> pdb=" O PHE D 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 304 through 305 removed outlier: 5.745A pdb=" N THR D 149 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA D 150 " --> pdb=" O ILE D 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 202 through 203 Processing sheet with id=AC7, first strand: chain 'E' and resid 31 through 34 removed outlier: 5.873A pdb=" N VAL E 45 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL E 57 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL E 14 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE E 10 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG E 16 " --> pdb=" O GLN E 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 79 through 81 Processing sheet with id=AC9, first strand: chain 'E' and resid 90 through 91 removed outlier: 6.345A pdb=" N PHE E 91 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN E 218 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE E 177 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET E 303 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU E 249 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR E 149 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS E 148 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ILE E 329 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA E 150 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 129 through 130 removed outlier: 3.520A pdb=" N PHE E 130 " --> pdb=" O PHE E 143 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE E 143 " --> pdb=" O PHE E 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 202 through 203 Processing sheet with id=AD3, first strand: chain 'F' and resid 79 through 81 Processing sheet with id=AD4, first strand: chain 'F' and resid 90 through 91 removed outlier: 6.940A pdb=" N ILE F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N MET F 303 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU F 249 " --> pdb=" O MET F 303 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR F 149 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL F 306 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE F 151 " --> pdb=" O VAL F 306 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 128 through 129 removed outlier: 3.796A pdb=" N GLN F 128 " --> pdb=" O ARG F 145 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 202 through 203 Processing sheet with id=AD7, first strand: chain 'G' and resid 138 through 140 removed outlier: 10.636A pdb=" N GLY G 138 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL G 118 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N ALA G 140 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR G 120 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL G 79 " --> pdb=" O ASP G 117 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N TYR G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU G 81 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE G 121 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL G 83 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER G 78 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N TYR G 172 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA G 80 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE G 174 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU G 82 " --> pdb=" O ILE G 174 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N SER G 176 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N VAL G 84 " --> pdb=" O SER G 176 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 208 through 209 removed outlier: 5.984A pdb=" N THR G 208 " --> pdb=" O MET R 41 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE R 43 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY R 65 " --> pdb=" O LEU R 44 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE R 51 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU R 48 " --> pdb=" O PRO R 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP R 50 " --> pdb=" O SER R 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 18 through 19 removed outlier: 6.026A pdb=" N HIS R 4 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE R 76 " --> pdb=" O HIS R 4 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU R 6 " --> pdb=" O ILE R 76 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL R 62 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL R 81 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLY R 64 " --> pdb=" O ASP R 79 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 88 through 89 Processing sheet with id=AE2, first strand: chain 'W' and resid 92 through 93 2430 hydrogen bonds defined for protein. 7056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.96 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12449 1.34 - 1.45: 4421 1.45 - 1.57: 21998 1.57 - 1.69: 15 1.69 - 1.81: 180 Bond restraints: 39063 Sorted by residual: bond pdb=" N VAL T 181 " pdb=" CA VAL T 181 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.50e-03 1.78e+04 2.24e+01 bond pdb=" N VAL E 308 " pdb=" CA VAL E 308 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.92e+01 bond pdb=" N VAL G 194 " pdb=" CA VAL G 194 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.15e-02 7.56e+03 1.19e+01 bond pdb=" N GLY F 153 " pdb=" CA GLY F 153 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.02e-02 9.61e+03 9.83e+00 bond pdb=" N THR C 501 " pdb=" CA THR C 501 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.62e+00 ... (remaining 39058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 51450 1.52 - 3.03: 1312 3.03 - 4.55: 222 4.55 - 6.06: 73 6.06 - 7.58: 14 Bond angle restraints: 53071 Sorted by residual: angle pdb=" N ILE O 41 " pdb=" CA ILE O 41 " pdb=" C ILE O 41 " ideal model delta sigma weight residual 111.77 105.77 6.00 1.04e+00 9.25e-01 3.33e+01 angle pdb=" N ILE H 41 " pdb=" CA ILE H 41 " pdb=" C ILE H 41 " ideal model delta sigma weight residual 112.29 107.17 5.12 9.40e-01 1.13e+00 2.96e+01 angle pdb=" N ILE Q 41 " pdb=" CA ILE Q 41 " pdb=" C ILE Q 41 " ideal model delta sigma weight residual 111.91 107.38 4.53 8.90e-01 1.26e+00 2.59e+01 angle pdb=" N ILE I 41 " pdb=" CA ILE I 41 " pdb=" C ILE I 41 " ideal model delta sigma weight residual 111.91 107.76 4.15 8.90e-01 1.26e+00 2.18e+01 angle pdb=" N PHE T 40 " pdb=" CA PHE T 40 " pdb=" C PHE T 40 " ideal model delta sigma weight residual 113.38 108.14 5.24 1.17e+00 7.31e-01 2.01e+01 ... (remaining 53066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 21539 17.99 - 35.98: 1694 35.98 - 53.97: 313 53.97 - 71.96: 55 71.96 - 89.95: 29 Dihedral angle restraints: 23630 sinusoidal: 8762 harmonic: 14868 Sorted by residual: dihedral pdb=" CA TYR B 247 " pdb=" C TYR B 247 " pdb=" N ALA B 248 " pdb=" CA ALA B 248 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ARG F 372 " pdb=" C ARG F 372 " pdb=" N VAL F 373 " pdb=" CA VAL F 373 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ASP S 140 " pdb=" C ASP S 140 " pdb=" N ASN S 141 " pdb=" CA ASN S 141 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 23627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4772 0.048 - 0.096: 1180 0.096 - 0.144: 316 0.144 - 0.192: 27 0.192 - 0.240: 3 Chirality restraints: 6298 Sorted by residual: chirality pdb=" CB ILE C 53 " pdb=" CA ILE C 53 " pdb=" CG1 ILE C 53 " pdb=" CG2 ILE C 53 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU B 308 " pdb=" CB LEU B 308 " pdb=" CD1 LEU B 308 " pdb=" CD2 LEU B 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE G 274 " pdb=" N ILE G 274 " pdb=" C ILE G 274 " pdb=" CB ILE G 274 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.46e-01 ... (remaining 6295 not shown) Planarity restraints: 6999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 355 " 0.070 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO D 356 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 356 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 356 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 374 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C LEU F 374 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU F 374 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN F 375 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY M 19 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO M 20 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO M 20 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO M 20 " 0.036 5.00e-02 4.00e+02 ... (remaining 6996 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 243 2.53 - 3.12: 31219 3.12 - 3.72: 62657 3.72 - 4.31: 85257 4.31 - 4.90: 143669 Nonbonded interactions: 323045 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O2B ATP B 602 " model vdw 1.938 2.170 nonbonded pdb="MG MG A 601 " pdb=" O3G ATP A 602 " model vdw 1.953 2.170 nonbonded pdb=" OG1 THR B 183 " pdb="MG MG B 601 " model vdw 1.962 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ATP C 602 " model vdw 1.981 2.170 nonbonded pdb=" OG1 THR A 183 " pdb="MG MG A 601 " model vdw 1.996 2.170 ... (remaining 323040 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' selection = (chain 'B' and (resid 27 through 519 or resid 601 through 602)) selection = (chain 'C' and (resid 27 through 519 or resid 601 through 602)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 3 through 468) } ncs_group { reference = chain 'H' selection = (chain 'I' and resid 2 through 72) selection = (chain 'J' and resid 2 through 72) selection = (chain 'K' and resid 2 through 72) selection = (chain 'L' and resid 2 through 72) selection = chain 'M' selection = (chain 'N' and resid 2 through 72) selection = (chain 'O' and resid 2 through 72) selection = (chain 'P' and resid 2 through 72) selection = (chain 'Q' and resid 2 through 72) } ncs_group { reference = chain 'S' selection = (chain 'W' and resid 86 through 154) } ncs_group { reference = (chain 'T' and ((resid 31 through 41 and (name N or name CA or name C or name O \ or name CB )) or resid 42 or (resid 43 through 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 or (resid 46 through 78 and (name N or na \ me CA or name C or name O or name CB )) or resid 79 or (resid 80 through 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 or (resid 121 \ through 123 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 24 or (resid 125 through 127 and (name N or name CA or name C or name O or name \ CB )) or resid 128 or (resid 129 and (name N or name CA or name C or name O or n \ ame CB )) or resid 130 or (resid 131 through 132 and (name N or name CA or name \ C or name O or name CB )) or resid 133 or (resid 134 through 135 and (name N or \ name CA or name C or name O or name CB )) or resid 177 or (resid 178 through 208 \ and (name N or name CA or name C or name O or name CB )) or resid 209 or (resid \ 210 through 213 and (name N or name CA or name C or name O or name CB )) or res \ id 214 or (resid 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 or (resid 217 through 225 and (name N or name CA or name C or name O \ or name CB )) or resid 226 or (resid 227 through 231 and (name N or name CA or n \ ame C or name O or name CB )) or resid 232 or (resid 233 through 251 and (name N \ or name CA or name C or name O or name CB )) or resid 252 or (resid 253 through \ 256 and (name N or name CA or name C or name O or name CB )) or resid 257 or (r \ esid 258 through 277 and (name N or name CA or name C or name O or name CB )) or \ resid 278 or (resid 279 through 283 and (name N or name CA or name C or name O \ or name CB )) or resid 284 or (resid 285 through 304 and (name N or name CA or n \ ame C or name O or name CB )))) selection = chain 'Z' } ncs_group { reference = (chain 'U' 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 '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 158) } 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: 3.890 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 32.180 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 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:5.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 0.090 39063 Z= 0.226 Angle : 0.596 7.580 53071 Z= 0.346 Chirality : 0.045 0.240 6298 Planarity : 0.004 0.103 6999 Dihedral : 13.751 89.946 14086 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.24 % Allowed : 0.51 % Favored : 99.25 % 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: 5181 helix: 1.31 (0.10), residues: 2731 sheet: -0.42 (0.24), residues: 499 loop : -0.93 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 497 TYR 0.027 0.001 TYR E 454 PHE 0.022 0.001 PHE L 62 TRP 0.018 0.002 TRP A 471 HIS 0.003 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00432 (39063) covalent geometry : angle 0.59624 (53071) hydrogen bonds : bond 0.20742 ( 2424) hydrogen bonds : angle 6.93717 ( 7056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 955 time to evaluate : 1.454 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: A 390 MET cc_start: 0.8321 (mmm) cc_final: 0.8099 (tpt) REVERT: A 391 ARG cc_start: 0.7472 (ptm160) cc_final: 0.7064 (ptp90) REVERT: B 151 THR cc_start: 0.8734 (m) cc_final: 0.8492 (t) REVERT: B 403 GLN cc_start: 0.8428 (tt0) cc_final: 0.8125 (tp40) REVERT: B 407 LEU cc_start: 0.7952 (mt) cc_final: 0.7367 (mp) REVERT: C 145 THR cc_start: 0.8298 (m) cc_final: 0.8082 (p) REVERT: C 179 GLN cc_start: 0.8433 (mt0) cc_final: 0.8199 (mt0) REVERT: D 193 LEU cc_start: 0.6949 (mp) cc_final: 0.6694 (mt) REVERT: E 94 LEU cc_start: 0.8460 (mt) cc_final: 0.8180 (mm) REVERT: E 173 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7233 (mt-10) REVERT: E 187 SER cc_start: 0.8701 (m) cc_final: 0.8256 (t) REVERT: E 357 ASN cc_start: 0.8290 (m-40) cc_final: 0.8049 (m-40) REVERT: G 6 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7250 (tm-30) REVERT: G 149 LEU cc_start: 0.8174 (tt) cc_final: 0.7918 (tt) REVERT: G 168 TYR cc_start: 0.7971 (m-80) cc_final: 0.7715 (m-80) REVERT: G 215 GLU cc_start: 0.8031 (tp30) cc_final: 0.7772 (tp30) REVERT: I 29 SER cc_start: 0.7777 (t) cc_final: 0.7538 (p) REVERT: I 41 ILE cc_start: 0.7461 (tp) cc_final: 0.7151 (mp) REVERT: N 6 LEU cc_start: 0.7746 (mt) cc_final: 0.7534 (mt) REVERT: N 48 TYR cc_start: 0.8261 (m-10) cc_final: 0.7898 (m-80) REVERT: N 61 ILE cc_start: 0.7348 (mp) cc_final: 0.7112 (OUTLIER) REVERT: O 43 ASN cc_start: 0.8139 (t0) cc_final: 0.7859 (t0) REVERT: O 48 TYR cc_start: 0.7476 (m-80) cc_final: 0.7272 (m-80) REVERT: Q 6 LEU cc_start: 0.6645 (mp) cc_final: 0.6195 (mt) REVERT: R 17 ASP cc_start: 0.7531 (p0) cc_final: 0.7175 (p0) REVERT: R 18 ASP cc_start: 0.7478 (m-30) cc_final: 0.6811 (m-30) REVERT: R 50 ASP cc_start: 0.7284 (m-30) cc_final: 0.5791 (m-30) REVERT: R 60 PHE cc_start: 0.6099 (m-80) cc_final: 0.5703 (m-80) REVERT: R 105 GLU cc_start: 0.2641 (OUTLIER) cc_final: 0.1847 (pm20) REVERT: R 112 MET cc_start: 0.7684 (mtm) cc_final: 0.7358 (mtp) REVERT: R 118 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7562 (mmmm) REVERT: S 93 SER cc_start: 0.6933 (m) cc_final: 0.6504 (t) REVERT: T 89 GLU cc_start: 0.8333 (pt0) cc_final: 0.8102 (pt0) REVERT: T 96 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8611 (ptm160) REVERT: T 99 ASN cc_start: 0.7775 (t0) cc_final: 0.7540 (t160) REVERT: T 102 TYR cc_start: 0.8518 (m-80) cc_final: 0.8080 (m-80) REVERT: T 208 TRP cc_start: 0.6692 (m100) cc_final: 0.6076 (m100) REVERT: U 34 MET cc_start: 0.7676 (mmt) cc_final: 0.7142 (mtm) REVERT: U 131 LEU cc_start: 0.8434 (tp) cc_final: 0.8183 (mp) REVERT: V 20 LEU cc_start: 0.8326 (tt) cc_final: 0.7975 (mt) REVERT: V 122 SER cc_start: 0.8044 (m) cc_final: 0.7750 (t) REVERT: W 117 HIS cc_start: 0.7334 (m90) cc_final: 0.7048 (m-70) outliers start: 9 outliers final: 5 residues processed: 962 average time/residue: 0.5300 time to fit residues: 638.4652 Evaluate side-chains 498 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 493 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain R residue 105 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 0.7980 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 309 HIS B 483 HIS C 309 HIS ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 GLN G 218 ASN ** G 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN M 5 ASN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.143612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086973 restraints weight = 68695.503| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.80 r_work: 0.2936 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 39063 Z= 0.234 Angle : 0.703 10.016 53071 Z= 0.369 Chirality : 0.049 0.354 6298 Planarity : 0.005 0.056 6999 Dihedral : 6.216 89.594 5750 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.89 % Allowed : 14.76 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.46 (0.12), residues: 5181 helix: 1.28 (0.10), residues: 2790 sheet: -0.52 (0.23), residues: 563 loop : -0.87 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 59 TYR 0.025 0.002 TYR E 454 PHE 0.049 0.002 PHE O 55 TRP 0.014 0.002 TRP T 208 HIS 0.006 0.001 HIS T 31 Details of bonding type rmsd covalent geometry : bond 0.00539 (39063) covalent geometry : angle 0.70345 (53071) hydrogen bonds : bond 0.05093 ( 2424) hydrogen bonds : angle 4.78185 ( 7056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 536 time to evaluate : 1.414 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: A 270 ASP cc_start: 0.8314 (p0) cc_final: 0.7939 (p0) REVERT: A 390 MET cc_start: 0.8857 (mmm) cc_final: 0.8620 (tpt) REVERT: A 391 ARG cc_start: 0.8032 (ptm160) cc_final: 0.7453 (ptp-170) REVERT: A 431 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8500 (mm) REVERT: A 452 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9013 (mm) REVERT: A 476 LEU cc_start: 0.8702 (mt) cc_final: 0.8219 (mt) REVERT: A 480 ARG cc_start: 0.8778 (ttm110) cc_final: 0.8391 (ttm110) REVERT: B 47 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8081 (pp30) REVERT: B 276 ASP cc_start: 0.7084 (t70) cc_final: 0.6718 (t0) REVERT: B 352 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9129 (mp) REVERT: B 403 GLN cc_start: 0.8749 (tt0) cc_final: 0.8055 (tp40) REVERT: B 407 LEU cc_start: 0.7843 (mt) cc_final: 0.7148 (mp) REVERT: B 519 SER cc_start: 0.9321 (t) cc_final: 0.8991 (p) REVERT: C 74 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: C 116 ASN cc_start: 0.8776 (m-40) cc_final: 0.8549 (t0) REVERT: C 145 THR cc_start: 0.9068 (m) cc_final: 0.8669 (p) REVERT: C 221 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8716 (ttp80) REVERT: C 470 LYS cc_start: 0.9240 (ttpp) cc_final: 0.8984 (ttpp) REVERT: D 101 MET cc_start: 0.8714 (mpt) cc_final: 0.8414 (mpm) REVERT: D 193 LEU cc_start: 0.7923 (mp) cc_final: 0.7622 (mp) REVERT: D 404 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7650 (mtp-110) REVERT: D 411 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8562 (p) REVERT: D 455 MET cc_start: 0.8414 (tpt) cc_final: 0.8145 (mmm) REVERT: E 173 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8040 (mt-10) REVERT: E 214 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8987 (mtp) REVERT: E 312 ASP cc_start: 0.8344 (t0) cc_final: 0.8014 (t0) REVERT: E 450 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8362 (mt-10) REVERT: F 76 ARG cc_start: 0.8985 (ptp-110) cc_final: 0.8599 (ptm160) REVERT: F 390 GLU cc_start: 0.8155 (mp0) cc_final: 0.7755 (mm-30) REVERT: G 26 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8400 (mtm) REVERT: G 220 ILE cc_start: 0.7786 (tt) cc_final: 0.7489 (tt) REVERT: H 48 TYR cc_start: 0.6673 (m-10) cc_final: 0.6133 (m-80) REVERT: J 24 ILE cc_start: 0.8562 (mt) cc_final: 0.8329 (pp) REVERT: J 33 GLN cc_start: 0.7151 (mm110) cc_final: 0.6721 (mm110) REVERT: K 61 ILE cc_start: 0.7363 (mm) cc_final: 0.6800 (pp) REVERT: M 2 GLU cc_start: 0.2278 (tt0) cc_final: 0.1874 (tp30) REVERT: N 38 ASN cc_start: 0.6852 (t0) cc_final: 0.6599 (t0) REVERT: N 66 ILE cc_start: 0.4464 (OUTLIER) cc_final: 0.4263 (tp) REVERT: O 43 ASN cc_start: 0.7997 (t0) cc_final: 0.7761 (t0) REVERT: R 11 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: R 17 ASP cc_start: 0.7705 (p0) cc_final: 0.7333 (p0) REVERT: R 18 ASP cc_start: 0.7415 (m-30) cc_final: 0.6675 (m-30) REVERT: R 75 THR cc_start: 0.7922 (m) cc_final: 0.7429 (p) REVERT: R 105 GLU cc_start: 0.3325 (OUTLIER) cc_final: 0.2573 (pm20) REVERT: R 110 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6821 (mtp-110) REVERT: R 118 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7673 (mmmm) REVERT: S 101 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7832 (tp40) REVERT: S 107 ARG cc_start: 0.8884 (pmt-80) cc_final: 0.8587 (tpm170) REVERT: T 96 ARG cc_start: 0.9412 (ttp80) cc_final: 0.9093 (ptp90) REVERT: T 208 TRP cc_start: 0.7628 (m100) cc_final: 0.7094 (m100) REVERT: T 230 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7263 (p90) REVERT: T 291 PHE cc_start: 0.9401 (t80) cc_final: 0.9153 (m-80) REVERT: U 34 MET cc_start: 0.7851 (mmt) cc_final: 0.7249 (mtm) REVERT: U 120 MET cc_start: 0.9468 (mmm) cc_final: 0.8813 (tmm) REVERT: V 122 SER cc_start: 0.7839 (m) cc_final: 0.7457 (t) REVERT: W 96 GLU cc_start: 0.8354 (tp30) cc_final: 0.8057 (tp30) REVERT: W 139 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6802 (tp) outliers start: 145 outliers final: 36 residues processed: 626 average time/residue: 0.5444 time to fit residues: 426.2967 Evaluate side-chains 485 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 434 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain S residue 121 HIS Chi-restraints excluded: chain T residue 230 PHE Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 390 optimal weight: 9.9990 chunk 306 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 443 optimal weight: 6.9990 chunk 427 optimal weight: 5.9990 chunk 509 optimal weight: 50.0000 chunk 447 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 43 optimal weight: 0.0570 chunk 320 optimal weight: 20.0000 overall best weight: 2.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN D 51 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN E 29 ASN ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN F 220 ASN ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 GLN ** G 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 ASN T 99 ASN ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.140037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.082133 restraints weight = 68434.985| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.74 r_work: 0.2828 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 39063 Z= 0.308 Angle : 0.691 9.607 53071 Z= 0.363 Chirality : 0.049 0.272 6298 Planarity : 0.005 0.056 6999 Dihedral : 6.206 82.033 5745 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.07 % Allowed : 17.23 % Favored : 77.70 % 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: 0.50 (0.12), residues: 5181 helix: 1.35 (0.10), residues: 2809 sheet: -0.50 (0.23), residues: 569 loop : -0.97 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG W 104 TYR 0.019 0.002 TYR Q 48 PHE 0.024 0.002 PHE K 62 TRP 0.009 0.001 TRP T 208 HIS 0.005 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00729 (39063) covalent geometry : angle 0.69131 (53071) hydrogen bonds : bond 0.05057 ( 2424) hydrogen bonds : angle 4.62635 ( 7056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 437 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8068 (mmm-85) cc_final: 0.7857 (mmm-85) REVERT: A 64 GLU cc_start: 0.8660 (mp0) cc_final: 0.8314 (pt0) REVERT: A 315 ARG cc_start: 0.9451 (OUTLIER) cc_final: 0.8169 (mtm-85) REVERT: A 391 ARG cc_start: 0.8316 (ptm160) cc_final: 0.7787 (ttp-170) REVERT: A 470 LYS cc_start: 0.7420 (tmtt) cc_final: 0.7161 (tmtt) REVERT: B 47 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8291 (pp30) REVERT: B 276 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7099 (t0) REVERT: B 403 GLN cc_start: 0.8732 (tt0) cc_final: 0.8118 (tp40) REVERT: B 407 LEU cc_start: 0.8212 (mt) cc_final: 0.7658 (mp) REVERT: B 519 SER cc_start: 0.9210 (t) cc_final: 0.8819 (p) REVERT: C 85 ASP cc_start: 0.8413 (p0) cc_final: 0.8211 (p0) REVERT: C 102 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8892 (mt) REVERT: C 335 GLU cc_start: 0.9035 (tt0) cc_final: 0.8722 (tt0) REVERT: D 59 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8770 (mmt) REVERT: D 404 ARG cc_start: 0.8320 (ttm110) cc_final: 0.7662 (mtp-110) REVERT: D 411 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8712 (p) REVERT: E 197 MET cc_start: 0.8847 (mtt) cc_final: 0.8599 (mtp) REVERT: F 22 ASP cc_start: 0.8678 (p0) cc_final: 0.8168 (p0) REVERT: F 40 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8441 (ptp90) REVERT: F 128 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8546 (pt0) REVERT: F 185 GLU cc_start: 0.7948 (tp30) cc_final: 0.7707 (tp30) REVERT: F 271 MET cc_start: 0.9138 (mtp) cc_final: 0.8930 (mtt) REVERT: F 350 THR cc_start: 0.9036 (p) cc_final: 0.8810 (p) REVERT: F 389 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8203 (mmm) REVERT: F 390 GLU cc_start: 0.8578 (mp0) cc_final: 0.8253 (mm-30) REVERT: G 220 ILE cc_start: 0.7928 (tt) cc_final: 0.7662 (tt) REVERT: H 37 ARG cc_start: 0.8293 (mtp-110) cc_final: 0.8062 (mtp-110) REVERT: I 49 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5826 (tmm) REVERT: J 33 GLN cc_start: 0.7125 (mm110) cc_final: 0.6796 (mm110) REVERT: J 38 ASN cc_start: 0.7492 (p0) cc_final: 0.6878 (p0) REVERT: J 49 MET cc_start: 0.6600 (ttp) cc_final: 0.6227 (ptt) REVERT: K 57 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7186 (mt-10) REVERT: K 61 ILE cc_start: 0.7389 (mm) cc_final: 0.6955 (pp) REVERT: M 33 GLN cc_start: 0.7024 (mt0) cc_final: 0.6795 (mm110) REVERT: N 38 ASN cc_start: 0.7018 (t0) cc_final: 0.6670 (t0) REVERT: R 11 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: R 17 ASP cc_start: 0.7749 (p0) cc_final: 0.7498 (p0) REVERT: R 18 ASP cc_start: 0.7598 (m-30) cc_final: 0.6950 (m-30) REVERT: R 41 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7751 (mmm) REVERT: R 67 MET cc_start: 0.7516 (tpp) cc_final: 0.6843 (tpp) REVERT: R 75 THR cc_start: 0.8400 (m) cc_final: 0.7917 (p) REVERT: R 105 GLU cc_start: 0.3698 (OUTLIER) cc_final: 0.3459 (pm20) REVERT: R 110 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6911 (mtm110) REVERT: S 93 SER cc_start: 0.6807 (m) cc_final: 0.6385 (t) REVERT: T 89 GLU cc_start: 0.7840 (pt0) cc_final: 0.7620 (pt0) REVERT: T 92 TYR cc_start: 0.9033 (t80) cc_final: 0.8712 (m-80) REVERT: T 96 ARG cc_start: 0.9428 (ttp80) cc_final: 0.9201 (mpt180) REVERT: T 121 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7810 (m-40) REVERT: T 208 TRP cc_start: 0.7737 (m100) cc_final: 0.7174 (m100) REVERT: T 230 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7170 (p90) REVERT: T 291 PHE cc_start: 0.9383 (t80) cc_final: 0.9099 (m-80) REVERT: U 34 MET cc_start: 0.7825 (mmt) cc_final: 0.7227 (mtm) REVERT: U 120 MET cc_start: 0.9454 (mmm) cc_final: 0.8927 (tmm) REVERT: U 138 ARG cc_start: 0.6475 (tpt90) cc_final: 0.6009 (mmp80) REVERT: V 122 SER cc_start: 0.7915 (m) cc_final: 0.7556 (t) REVERT: W 133 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6775 (tpp80) REVERT: W 136 ASP cc_start: 0.8134 (t0) cc_final: 0.7857 (t70) REVERT: W 139 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6721 (tp) outliers start: 189 outliers final: 64 residues processed: 571 average time/residue: 0.5406 time to fit residues: 387.7062 Evaluate side-chains 484 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 402 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 121 HIS Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain T residue 121 ASN Chi-restraints excluded: chain T residue 230 PHE Chi-restraints excluded: chain T residue 240 LEU Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain W residue 133 ARG Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 233 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 465 optimal weight: 50.0000 chunk 130 optimal weight: 0.5980 chunk 489 optimal weight: 40.0000 chunk 94 optimal weight: 0.6980 chunk 420 optimal weight: 7.9990 chunk 254 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 207 GLN B 47 GLN C 309 HIS ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN E 29 ASN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN G 55 ASN G 184 GLN ** G 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.142442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.083483 restraints weight = 67909.505| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.59 r_work: 0.2893 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39063 Z= 0.142 Angle : 0.598 11.216 53071 Z= 0.309 Chirality : 0.045 0.292 6298 Planarity : 0.004 0.060 6999 Dihedral : 5.945 82.453 5745 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.70 % Allowed : 19.59 % Favored : 76.71 % 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: 0.70 (0.12), residues: 5181 helix: 1.53 (0.10), residues: 2805 sheet: -0.51 (0.23), residues: 551 loop : -0.85 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 480 TYR 0.026 0.001 TYR E 454 PHE 0.026 0.001 PHE K 62 TRP 0.008 0.001 TRP T 208 HIS 0.006 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00320 (39063) covalent geometry : angle 0.59834 (53071) hydrogen bonds : bond 0.04252 ( 2424) hydrogen bonds : angle 4.40155 ( 7056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 448 time to evaluate : 1.345 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: A 41 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7346 (mmp80) REVERT: A 64 GLU cc_start: 0.8592 (mp0) cc_final: 0.8285 (pt0) REVERT: A 342 SER cc_start: 0.9411 (m) cc_final: 0.8998 (p) REVERT: A 422 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7969 (mmtp) REVERT: B 47 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8108 (pp30) REVERT: B 403 GLN cc_start: 0.8704 (tt0) cc_final: 0.8116 (tp40) REVERT: B 407 LEU cc_start: 0.8129 (mt) cc_final: 0.7610 (mp) REVERT: B 519 SER cc_start: 0.9112 (t) cc_final: 0.8704 (p) REVERT: C 85 ASP cc_start: 0.8417 (p0) cc_final: 0.8194 (p0) REVERT: C 335 GLU cc_start: 0.9009 (tt0) cc_final: 0.8704 (tt0) REVERT: C 416 ASP cc_start: 0.8223 (t0) cc_final: 0.7640 (t0) REVERT: D 59 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8554 (mmt) REVERT: D 404 ARG cc_start: 0.8260 (ttm110) cc_final: 0.7605 (mtp-110) REVERT: D 411 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8653 (p) REVERT: D 414 PHE cc_start: 0.8202 (m-10) cc_final: 0.7845 (m-10) REVERT: E 197 MET cc_start: 0.8740 (mtt) cc_final: 0.8493 (mtp) REVERT: E 325 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8351 (mp) REVERT: F 22 ASP cc_start: 0.8413 (p0) cc_final: 0.8185 (p0) REVERT: F 128 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8474 (pt0) REVERT: F 185 GLU cc_start: 0.7737 (tp30) cc_final: 0.7507 (tp30) REVERT: F 271 MET cc_start: 0.9100 (mtp) cc_final: 0.8877 (mtt) REVERT: F 350 THR cc_start: 0.8909 (p) cc_final: 0.8685 (p) REVERT: F 389 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8049 (mmm) REVERT: F 390 GLU cc_start: 0.8515 (mp0) cc_final: 0.8204 (mm-30) REVERT: G 169 ASP cc_start: 0.8163 (m-30) cc_final: 0.7376 (p0) REVERT: G 220 ILE cc_start: 0.7929 (tt) cc_final: 0.7691 (tt) REVERT: I 49 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5901 (tmm) REVERT: I 56 THR cc_start: 0.6235 (OUTLIER) cc_final: 0.6000 (p) REVERT: J 24 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8057 (pp) REVERT: J 33 GLN cc_start: 0.7298 (mm110) cc_final: 0.6916 (mm110) REVERT: J 38 ASN cc_start: 0.7384 (p0) cc_final: 0.6710 (p0) REVERT: J 49 MET cc_start: 0.6863 (ttp) cc_final: 0.6639 (ptt) REVERT: K 57 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7038 (mp0) REVERT: K 61 ILE cc_start: 0.7450 (mm) cc_final: 0.6966 (pp) REVERT: M 33 GLN cc_start: 0.6986 (mt0) cc_final: 0.6747 (mm110) REVERT: N 38 ASN cc_start: 0.7051 (t0) cc_final: 0.6679 (t0) REVERT: R 11 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: R 17 ASP cc_start: 0.7698 (p0) cc_final: 0.7455 (p0) REVERT: R 18 ASP cc_start: 0.7282 (m-30) cc_final: 0.6597 (m-30) REVERT: R 67 MET cc_start: 0.7767 (tpp) cc_final: 0.7479 (mmm) REVERT: R 75 THR cc_start: 0.8449 (m) cc_final: 0.8238 (p) REVERT: R 105 GLU cc_start: 0.3870 (OUTLIER) cc_final: 0.3439 (pm20) REVERT: R 110 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6899 (mtm110) REVERT: R 118 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8158 (mmmm) REVERT: S 93 SER cc_start: 0.6767 (m) cc_final: 0.6334 (t) REVERT: T 96 ARG cc_start: 0.9435 (ttp80) cc_final: 0.9172 (ptp90) REVERT: T 208 TRP cc_start: 0.7680 (m100) cc_final: 0.7055 (m100) REVERT: T 230 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7131 (p90) REVERT: T 291 PHE cc_start: 0.9381 (t80) cc_final: 0.9113 (m-80) REVERT: U 34 MET cc_start: 0.7800 (mmt) cc_final: 0.7167 (ttm) REVERT: U 120 MET cc_start: 0.9455 (mmm) cc_final: 0.8948 (tmm) REVERT: U 138 ARG cc_start: 0.6502 (tpt90) cc_final: 0.6097 (mmp80) REVERT: V 122 SER cc_start: 0.7899 (m) cc_final: 0.7537 (t) REVERT: W 88 ASP cc_start: 0.8281 (p0) cc_final: 0.8059 (p0) REVERT: W 133 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6671 (tpp80) REVERT: W 136 ASP cc_start: 0.8176 (t0) cc_final: 0.7845 (t0) REVERT: W 139 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6732 (tp) outliers start: 138 outliers final: 45 residues processed: 541 average time/residue: 0.5326 time to fit residues: 362.3995 Evaluate side-chains 464 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 403 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain T residue 121 ASN Chi-restraints excluded: chain T residue 230 PHE Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 133 ARG Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 417 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 386 optimal weight: 7.9990 chunk 395 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 chunk 299 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN T 82 ASN T 121 ASN T 253 ASN ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.141040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.082978 restraints weight = 67825.672| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.85 r_work: 0.2858 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 39063 Z= 0.197 Angle : 0.617 12.563 53071 Z= 0.318 Chirality : 0.046 0.298 6298 Planarity : 0.005 0.094 6999 Dihedral : 5.909 82.370 5743 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.19 % Allowed : 20.18 % Favored : 75.64 % 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: 0.67 (0.12), residues: 5181 helix: 1.51 (0.10), residues: 2781 sheet: -0.59 (0.23), residues: 572 loop : -0.83 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 480 TYR 0.022 0.001 TYR H 48 PHE 0.017 0.001 PHE K 62 TRP 0.009 0.001 TRP T 208 HIS 0.006 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00464 (39063) covalent geometry : angle 0.61655 (53071) hydrogen bonds : bond 0.04245 ( 2424) hydrogen bonds : angle 4.33469 ( 7056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 436 time to evaluate : 1.265 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 41 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7676 (mmm-85) REVERT: A 64 GLU cc_start: 0.8606 (mp0) cc_final: 0.8338 (pt0) REVERT: A 342 SER cc_start: 0.9444 (m) cc_final: 0.9048 (p) REVERT: A 422 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8026 (mmtp) REVERT: B 47 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8349 (pp30) REVERT: B 403 GLN cc_start: 0.8743 (tt0) cc_final: 0.8126 (tp40) REVERT: B 407 LEU cc_start: 0.8232 (mt) cc_final: 0.7688 (mp) REVERT: B 519 SER cc_start: 0.9133 (t) cc_final: 0.8722 (p) REVERT: C 85 ASP cc_start: 0.8479 (p0) cc_final: 0.8211 (p0) REVERT: C 221 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8391 (ttp80) REVERT: C 335 GLU cc_start: 0.9083 (tt0) cc_final: 0.8824 (tt0) REVERT: C 476 LEU cc_start: 0.8726 (mt) cc_final: 0.8509 (mp) REVERT: D 59 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8620 (mmt) REVERT: D 404 ARG cc_start: 0.8360 (ttm110) cc_final: 0.7629 (mtp-110) REVERT: D 411 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8717 (p) REVERT: E 197 MET cc_start: 0.8849 (mtt) cc_final: 0.8609 (mtp) REVERT: E 325 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8512 (mp) REVERT: F 271 MET cc_start: 0.9154 (mtp) cc_final: 0.8919 (mtt) REVERT: F 389 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8259 (mmm) REVERT: F 390 GLU cc_start: 0.8580 (mp0) cc_final: 0.8282 (mm-30) REVERT: G 169 ASP cc_start: 0.8244 (m-30) cc_final: 0.7343 (p0) REVERT: I 56 THR cc_start: 0.6146 (OUTLIER) cc_final: 0.5945 (p) REVERT: J 24 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.8022 (pp) REVERT: J 33 GLN cc_start: 0.7440 (mm110) cc_final: 0.7163 (mm110) REVERT: J 38 ASN cc_start: 0.7356 (p0) cc_final: 0.7137 (p0) REVERT: K 43 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7400 (t0) REVERT: K 61 ILE cc_start: 0.7162 (mm) cc_final: 0.6712 (pp) REVERT: M 33 GLN cc_start: 0.7066 (mt0) cc_final: 0.6804 (mm110) REVERT: N 38 ASN cc_start: 0.7239 (t0) cc_final: 0.6859 (t0) REVERT: R 9 THR cc_start: 0.8932 (m) cc_final: 0.8717 (t) REVERT: R 11 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: R 17 ASP cc_start: 0.7735 (p0) cc_final: 0.7495 (p0) REVERT: R 18 ASP cc_start: 0.7196 (m-30) cc_final: 0.6526 (m-30) REVERT: R 21 MET cc_start: 0.8303 (tpt) cc_final: 0.8069 (tpt) REVERT: R 75 THR cc_start: 0.8544 (m) cc_final: 0.8272 (p) REVERT: R 91 ARG cc_start: 0.5737 (OUTLIER) cc_final: 0.5378 (ptt-90) REVERT: R 110 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7670 (mmm160) REVERT: S 93 SER cc_start: 0.6765 (m) cc_final: 0.6265 (t) REVERT: S 120 TYR cc_start: 0.7623 (m-10) cc_final: 0.7421 (m-10) REVERT: S 147 LEU cc_start: 0.8690 (mm) cc_final: 0.8489 (mm) REVERT: T 96 ARG cc_start: 0.9447 (ttp80) cc_final: 0.9178 (ptp90) REVERT: T 208 TRP cc_start: 0.7673 (m100) cc_final: 0.7059 (m100) REVERT: T 230 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.7019 (p90) REVERT: U 34 MET cc_start: 0.7794 (mmt) cc_final: 0.7152 (ttm) REVERT: U 120 MET cc_start: 0.9464 (mmt) cc_final: 0.8997 (tmm) REVERT: U 138 ARG cc_start: 0.6750 (tpt90) cc_final: 0.6310 (mmp80) REVERT: V 34 MET cc_start: 0.7391 (ttp) cc_final: 0.6929 (tmm) REVERT: V 122 SER cc_start: 0.7960 (m) cc_final: 0.7573 (t) REVERT: W 88 ASP cc_start: 0.8284 (p0) cc_final: 0.8067 (p0) REVERT: W 136 ASP cc_start: 0.8067 (t0) cc_final: 0.7631 (t0) REVERT: W 139 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6803 (tp) outliers start: 156 outliers final: 55 residues processed: 549 average time/residue: 0.5541 time to fit residues: 381.1304 Evaluate side-chains 466 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 396 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 43 ASN Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain O residue 50 PHE Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain T residue 121 ASN Chi-restraints excluded: chain T residue 230 PHE Chi-restraints excluded: chain T residue 287 GLN Chi-restraints excluded: chain U residue 69 ILE Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 174 optimal weight: 0.9990 chunk 352 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 207 optimal weight: 0.0980 chunk 317 optimal weight: 7.9990 chunk 370 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 497 optimal weight: 30.0000 chunk 417 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 47 GLN B 424 GLN ** C 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN E 29 ASN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 ASN O 43 ASN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 ASN T 97 ASN T 121 ASN ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.141580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.082464 restraints weight = 68191.139| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.57 r_work: 0.2875 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 39063 Z= 0.166 Angle : 0.617 17.411 53071 Z= 0.315 Chirality : 0.045 0.325 6298 Planarity : 0.004 0.076 6999 Dihedral : 5.755 83.621 5739 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.81 % Allowed : 21.41 % Favored : 74.78 % 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: 0.73 (0.12), residues: 5181 helix: 1.55 (0.10), residues: 2792 sheet: -0.56 (0.23), residues: 571 loop : -0.78 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 480 TYR 0.030 0.001 TYR E 454 PHE 0.016 0.001 PHE K 62 TRP 0.008 0.001 TRP T 208 HIS 0.006 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00386 (39063) covalent geometry : angle 0.61718 (53071) hydrogen bonds : bond 0.04107 ( 2424) hydrogen bonds : angle 4.27307 ( 7056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 440 time to evaluate : 1.284 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 41 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7408 (mmp80) REVERT: A 64 GLU cc_start: 0.8568 (mp0) cc_final: 0.8325 (pt0) REVERT: A 342 SER cc_start: 0.9424 (m) cc_final: 0.9040 (p) REVERT: A 422 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8045 (mmtp) REVERT: A 513 LYS cc_start: 0.9000 (mmpt) cc_final: 0.8797 (mtmt) REVERT: B 47 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8225 (pp30) REVERT: B 403 GLN cc_start: 0.8733 (tt0) cc_final: 0.8126 (tp40) REVERT: B 407 LEU cc_start: 0.8211 (mt) cc_final: 0.7686 (mp) REVERT: B 519 SER cc_start: 0.9076 (t) cc_final: 0.8687 (p) REVERT: C 41 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8171 (mmt180) REVERT: C 85 ASP cc_start: 0.8555 (p0) cc_final: 0.8287 (p0) REVERT: C 335 GLU cc_start: 0.9074 (tt0) cc_final: 0.8771 (tt0) REVERT: C 416 ASP cc_start: 0.8101 (t0) cc_final: 0.7558 (t0) REVERT: C 476 LEU cc_start: 0.8769 (mt) cc_final: 0.8566 (mp) REVERT: D 59 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8603 (mmt) REVERT: D 404 ARG cc_start: 0.8316 (ttm110) cc_final: 0.7626 (mtp-110) REVERT: D 411 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8649 (p) REVERT: E 197 MET cc_start: 0.8811 (mtt) cc_final: 0.8566 (mtp) REVERT: F 271 MET cc_start: 0.9163 (mtp) cc_final: 0.8888 (mtt) REVERT: F 389 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8227 (mmm) REVERT: F 390 GLU cc_start: 0.8576 (mp0) cc_final: 0.8261 (mm-30) REVERT: G 169 ASP cc_start: 0.8175 (m-30) cc_final: 0.7299 (p0) REVERT: J 33 GLN cc_start: 0.7515 (mm110) cc_final: 0.7159 (mm110) REVERT: J 37 ARG cc_start: 0.8378 (ttm110) cc_final: 0.7969 (ttm110) REVERT: J 38 ASN cc_start: 0.7288 (OUTLIER) cc_final: 0.6770 (p0) REVERT: J 49 MET cc_start: 0.6878 (ttp) cc_final: 0.6575 (tmm) REVERT: K 43 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7410 (t0) REVERT: K 61 ILE cc_start: 0.7021 (mm) cc_final: 0.6602 (pp) REVERT: M 33 GLN cc_start: 0.7006 (mt0) cc_final: 0.6761 (mm110) REVERT: N 38 ASN cc_start: 0.7246 (t0) cc_final: 0.6863 (t0) REVERT: R 9 THR cc_start: 0.8941 (m) cc_final: 0.8721 (t) REVERT: R 11 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: R 18 ASP cc_start: 0.7220 (m-30) cc_final: 0.6458 (m-30) REVERT: R 21 MET cc_start: 0.8338 (tpt) cc_final: 0.8074 (tpt) REVERT: R 41 MET cc_start: 0.7934 (mmm) cc_final: 0.7303 (tpp) REVERT: R 91 ARG cc_start: 0.5717 (OUTLIER) cc_final: 0.5363 (ptt-90) REVERT: R 110 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7037 (mtm110) REVERT: S 93 SER cc_start: 0.6781 (m) cc_final: 0.6284 (t) REVERT: S 104 ARG cc_start: 0.9408 (tpp80) cc_final: 0.8864 (tpt90) REVERT: S 108 GLU cc_start: 0.8617 (tp30) cc_final: 0.7507 (pt0) REVERT: S 147 LEU cc_start: 0.8603 (mm) cc_final: 0.8401 (mm) REVERT: S 151 GLN cc_start: 0.8774 (mm110) cc_final: 0.8573 (mm110) REVERT: T 96 ARG cc_start: 0.9466 (ttp80) cc_final: 0.9255 (ptm160) REVERT: T 121 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8190 (m110) REVERT: T 208 TRP cc_start: 0.7684 (m100) cc_final: 0.7050 (m100) REVERT: T 230 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6889 (p90) REVERT: U 34 MET cc_start: 0.7793 (mmt) cc_final: 0.7159 (ttm) REVERT: U 120 MET cc_start: 0.9456 (mmt) cc_final: 0.8999 (tmm) REVERT: U 138 ARG cc_start: 0.6747 (tpt90) cc_final: 0.6385 (mmp80) REVERT: V 122 SER cc_start: 0.7963 (m) cc_final: 0.7566 (t) REVERT: W 88 ASP cc_start: 0.8308 (p0) cc_final: 0.8101 (p0) REVERT: W 139 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6753 (tp) outliers start: 142 outliers final: 56 residues processed: 542 average time/residue: 0.5386 time to fit residues: 364.8506 Evaluate side-chains 465 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 395 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 43 ASN Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain T residue 121 ASN Chi-restraints excluded: chain T residue 230 PHE Chi-restraints excluded: chain U residue 69 ILE Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 167 optimal weight: 0.9990 chunk 296 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 228 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 399 optimal weight: 0.9980 chunk 460 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 425 optimal weight: 20.0000 chunk 466 optimal weight: 50.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 GLN O 43 ASN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 ASN T 121 ASN ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.141857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.082741 restraints weight = 67996.299| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.58 r_work: 0.2879 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 39063 Z= 0.158 Angle : 0.618 14.647 53071 Z= 0.317 Chirality : 0.045 0.327 6298 Planarity : 0.004 0.067 6999 Dihedral : 5.728 86.690 5739 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.49 % Allowed : 22.40 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.12), residues: 5181 helix: 1.55 (0.10), residues: 2794 sheet: -0.66 (0.22), residues: 579 loop : -0.76 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 37 TYR 0.020 0.001 TYR H 48 PHE 0.036 0.001 PHE J 62 TRP 0.008 0.001 TRP T 208 HIS 0.006 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00366 (39063) covalent geometry : angle 0.61765 (53071) hydrogen bonds : bond 0.04049 ( 2424) hydrogen bonds : angle 4.24012 ( 7056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 419 time to evaluate : 1.237 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 41 ARG cc_start: 0.7721 (mmm-85) cc_final: 0.7381 (mmp80) REVERT: A 64 GLU cc_start: 0.8576 (mp0) cc_final: 0.8280 (pt0) REVERT: A 270 ASP cc_start: 0.8460 (p0) cc_final: 0.8220 (p0) REVERT: A 342 SER cc_start: 0.9414 (m) cc_final: 0.9037 (p) REVERT: A 422 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8037 (mmtp) REVERT: B 47 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8235 (pp30) REVERT: B 403 GLN cc_start: 0.8737 (tt0) cc_final: 0.8133 (tp40) REVERT: B 407 LEU cc_start: 0.8237 (mt) cc_final: 0.7700 (mp) REVERT: B 476 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8589 (mm) REVERT: B 519 SER cc_start: 0.9067 (t) cc_final: 0.8678 (p) REVERT: C 85 ASP cc_start: 0.8553 (p0) cc_final: 0.8270 (p0) REVERT: C 102 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8785 (mt) REVERT: C 335 GLU cc_start: 0.9114 (tt0) cc_final: 0.8844 (tt0) REVERT: C 416 ASP cc_start: 0.8121 (t0) cc_final: 0.7860 (t0) REVERT: D 59 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8609 (mmt) REVERT: D 404 ARG cc_start: 0.8327 (ttm110) cc_final: 0.7659 (mtp-110) REVERT: D 411 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8636 (p) REVERT: E 37 ASN cc_start: 0.8293 (t0) cc_final: 0.7743 (m-40) REVERT: E 197 MET cc_start: 0.8782 (mtt) cc_final: 0.8537 (mtp) REVERT: E 382 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8205 (p0) REVERT: F 271 MET cc_start: 0.9163 (mtp) cc_final: 0.8880 (mtt) REVERT: F 389 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8238 (mmm) REVERT: F 390 GLU cc_start: 0.8539 (mp0) cc_final: 0.8199 (mm-30) REVERT: G 169 ASP cc_start: 0.8193 (m-30) cc_final: 0.7323 (p0) REVERT: J 33 GLN cc_start: 0.7510 (mm110) cc_final: 0.7163 (mm110) REVERT: J 37 ARG cc_start: 0.8416 (ttm110) cc_final: 0.7928 (ttm110) REVERT: J 38 ASN cc_start: 0.6923 (OUTLIER) cc_final: 0.6634 (p0) REVERT: J 49 MET cc_start: 0.6969 (ttp) cc_final: 0.6708 (tmm) REVERT: K 43 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7318 (t0) REVERT: K 50 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6797 (m-80) REVERT: K 61 ILE cc_start: 0.6897 (mm) cc_final: 0.6497 (pp) REVERT: N 38 ASN cc_start: 0.7244 (t0) cc_final: 0.6861 (t0) REVERT: R 9 THR cc_start: 0.8918 (m) cc_final: 0.8715 (t) REVERT: R 11 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: R 17 ASP cc_start: 0.7944 (p0) cc_final: 0.7734 (p0) REVERT: R 18 ASP cc_start: 0.7643 (m-30) cc_final: 0.7095 (m-30) REVERT: R 21 MET cc_start: 0.8256 (tpt) cc_final: 0.7988 (tpt) REVERT: R 41 MET cc_start: 0.7916 (mmm) cc_final: 0.7238 (tpp) REVERT: R 110 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7539 (mtp-110) REVERT: S 93 SER cc_start: 0.6725 (m) cc_final: 0.6212 (t) REVERT: S 104 ARG cc_start: 0.9412 (tpp80) cc_final: 0.8844 (tpt90) REVERT: S 108 GLU cc_start: 0.8629 (tp30) cc_final: 0.7444 (pt0) REVERT: T 96 ARG cc_start: 0.9447 (ttp80) cc_final: 0.9164 (ptp90) REVERT: T 121 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8190 (m110) REVERT: T 208 TRP cc_start: 0.7668 (m100) cc_final: 0.7032 (m100) REVERT: T 230 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6904 (p90) REVERT: U 34 MET cc_start: 0.7795 (mmt) cc_final: 0.7166 (ttm) REVERT: U 120 MET cc_start: 0.9450 (mmt) cc_final: 0.9005 (tmm) REVERT: U 138 ARG cc_start: 0.6785 (tpt90) cc_final: 0.6425 (mmp80) REVERT: V 122 SER cc_start: 0.7960 (m) cc_final: 0.7562 (t) REVERT: W 97 LEU cc_start: 0.6714 (tp) cc_final: 0.6339 (tp) REVERT: W 104 ARG cc_start: 0.7751 (ttm110) cc_final: 0.7442 (ptp-110) outliers start: 130 outliers final: 58 residues processed: 511 average time/residue: 0.5663 time to fit residues: 361.9987 Evaluate side-chains 458 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 385 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 43 ASN Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 72 PHE Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain T residue 121 ASN Chi-restraints excluded: chain T residue 230 PHE Chi-restraints excluded: chain U residue 69 ILE Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 329 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 chunk 481 optimal weight: 9.9990 chunk 490 optimal weight: 30.0000 chunk 327 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 510 optimal weight: 40.0000 chunk 417 optimal weight: 30.0000 chunk 409 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 214 GLN C 309 HIS D 8 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 ASN L 5 ASN O 43 ASN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 4 HIS T 82 ASN ** T 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.135984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.077363 restraints weight = 67326.596| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.45 r_work: 0.2752 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.084 39063 Z= 0.433 Angle : 0.794 14.539 53071 Z= 0.413 Chirality : 0.053 0.339 6298 Planarity : 0.006 0.099 6999 Dihedral : 6.286 89.876 5739 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.00 % Allowed : 22.30 % Favored : 73.71 % 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: 0.37 (0.12), residues: 5181 helix: 1.24 (0.10), residues: 2794 sheet: -0.62 (0.22), residues: 583 loop : -0.97 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG W 146 TYR 0.034 0.002 TYR E 454 PHE 0.039 0.002 PHE J 62 TRP 0.012 0.002 TRP T 122 HIS 0.006 0.002 HIS D 324 Details of bonding type rmsd covalent geometry : bond 0.01033 (39063) covalent geometry : angle 0.79406 (53071) hydrogen bonds : bond 0.04810 ( 2424) hydrogen bonds : angle 4.53378 ( 7056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 390 time to evaluate : 1.165 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 64 GLU cc_start: 0.8578 (mp0) cc_final: 0.8246 (pt0) REVERT: A 315 ARG cc_start: 0.9428 (OUTLIER) cc_final: 0.8242 (mtm-85) REVERT: A 422 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8059 (mmpt) REVERT: B 47 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8495 (pp30) REVERT: B 139 ILE cc_start: 0.8585 (tp) cc_final: 0.8139 (pp) REVERT: B 403 GLN cc_start: 0.8716 (tt0) cc_final: 0.8067 (tp40) REVERT: B 407 LEU cc_start: 0.8160 (mt) cc_final: 0.7729 (mp) REVERT: B 519 SER cc_start: 0.9014 (t) cc_final: 0.8607 (p) REVERT: C 85 ASP cc_start: 0.8539 (p0) cc_final: 0.8290 (p0) REVERT: C 335 GLU cc_start: 0.9233 (tt0) cc_final: 0.8985 (tt0) REVERT: D 59 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8744 (mmt) REVERT: D 303 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.8145 (tpp) REVERT: D 404 ARG cc_start: 0.8350 (ttm110) cc_final: 0.7599 (mtp-110) REVERT: D 411 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8706 (p) REVERT: E 37 ASN cc_start: 0.8525 (t0) cc_final: 0.7901 (m-40) REVERT: E 197 MET cc_start: 0.8777 (mtt) cc_final: 0.8576 (mtp) REVERT: E 382 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8274 (p0) REVERT: F 389 MET cc_start: 0.8880 (mmm) cc_final: 0.8443 (mmm) REVERT: F 390 GLU cc_start: 0.8723 (mp0) cc_final: 0.8463 (mm-30) REVERT: G 214 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7251 (pp20) REVERT: H 37 ARG cc_start: 0.7885 (mtp-110) cc_final: 0.7485 (mtt-85) REVERT: J 37 ARG cc_start: 0.8472 (ttm110) cc_final: 0.7964 (ttm110) REVERT: J 38 ASN cc_start: 0.7262 (OUTLIER) cc_final: 0.6880 (p0) REVERT: K 35 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7431 (tp) REVERT: M 44 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6281 (mtp85) REVERT: N 38 ASN cc_start: 0.7329 (t0) cc_final: 0.6920 (t0) REVERT: R 11 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: R 18 ASP cc_start: 0.7341 (m-30) cc_final: 0.6965 (m-30) REVERT: R 21 MET cc_start: 0.8306 (tpt) cc_final: 0.7875 (tpt) REVERT: R 41 MET cc_start: 0.7920 (mmm) cc_final: 0.7295 (tpt) REVERT: R 91 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5454 (ptt-90) REVERT: S 93 SER cc_start: 0.6694 (m) cc_final: 0.6225 (t) REVERT: S 108 GLU cc_start: 0.8605 (tp30) cc_final: 0.7982 (pt0) REVERT: T 208 TRP cc_start: 0.7857 (m100) cc_final: 0.7175 (m100) REVERT: T 230 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6686 (p90) REVERT: U 34 MET cc_start: 0.7804 (mmt) cc_final: 0.7176 (ttm) REVERT: U 120 MET cc_start: 0.9438 (mmt) cc_final: 0.9045 (tmm) REVERT: U 138 ARG cc_start: 0.7114 (tpt90) cc_final: 0.6729 (mmp80) REVERT: V 20 LEU cc_start: 0.8372 (tt) cc_final: 0.8128 (mt) REVERT: V 122 SER cc_start: 0.7939 (m) cc_final: 0.7480 (t) REVERT: W 97 LEU cc_start: 0.6784 (tp) cc_final: 0.6520 (tp) REVERT: W 139 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7405 (tm) outliers start: 149 outliers final: 63 residues processed: 499 average time/residue: 0.5499 time to fit residues: 342.2672 Evaluate side-chains 433 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 356 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain T residue 230 PHE Chi-restraints excluded: chain T residue 240 LEU Chi-restraints excluded: chain U residue 69 ILE Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 139 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 467 optimal weight: 50.0000 chunk 130 optimal weight: 0.6980 chunk 351 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 184 optimal weight: 0.0030 chunk 319 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 352 optimal weight: 5.9990 chunk 349 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 chunk 181 optimal weight: 0.0570 overall best weight: 1.9512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 ASN O 43 ASN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 ASN T 97 ASN ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 137 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.139123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.082856 restraints weight = 67490.608| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.62 r_work: 0.2819 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 39063 Z= 0.227 Angle : 0.678 17.679 53071 Z= 0.348 Chirality : 0.047 0.338 6298 Planarity : 0.005 0.074 6999 Dihedral : 6.081 86.115 5739 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.82 % Allowed : 23.69 % Favored : 73.49 % 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: 0.52 (0.12), residues: 5181 helix: 1.38 (0.10), residues: 2794 sheet: -0.65 (0.23), residues: 568 loop : -0.91 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 297 TYR 0.022 0.002 TYR T 296 PHE 0.030 0.001 PHE J 62 TRP 0.010 0.001 TRP T 208 HIS 0.006 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00543 (39063) covalent geometry : angle 0.67828 (53071) hydrogen bonds : bond 0.04316 ( 2424) hydrogen bonds : angle 4.38555 ( 7056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 391 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8577 (mp0) cc_final: 0.8276 (pt0) REVERT: A 342 SER cc_start: 0.9443 (m) cc_final: 0.9075 (p) REVERT: A 422 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8115 (mmtp) REVERT: B 47 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8268 (pp30) REVERT: B 403 GLN cc_start: 0.8736 (tt0) cc_final: 0.8116 (tp40) REVERT: B 407 LEU cc_start: 0.8186 (mt) cc_final: 0.7770 (mp) REVERT: B 519 SER cc_start: 0.8970 (t) cc_final: 0.8521 (p) REVERT: C 85 ASP cc_start: 0.8539 (p0) cc_final: 0.8291 (p0) REVERT: C 335 GLU cc_start: 0.9203 (tt0) cc_final: 0.8959 (tt0) REVERT: D 59 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8272 (mmt) REVERT: D 404 ARG cc_start: 0.8325 (ttm110) cc_final: 0.7820 (mtp85) REVERT: D 411 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8694 (p) REVERT: E 37 ASN cc_start: 0.8531 (t0) cc_final: 0.7948 (m-40) REVERT: E 197 MET cc_start: 0.8776 (mtt) cc_final: 0.8543 (mtp) REVERT: E 382 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8276 (p0) REVERT: E 390 GLU cc_start: 0.9333 (tp30) cc_final: 0.9057 (pm20) REVERT: F 271 MET cc_start: 0.9201 (mtp) cc_final: 0.8995 (mtt) REVERT: F 389 MET cc_start: 0.8813 (mmm) cc_final: 0.8410 (mmm) REVERT: F 390 GLU cc_start: 0.8673 (mp0) cc_final: 0.8409 (mm-30) REVERT: G 26 MET cc_start: 0.9194 (ttm) cc_final: 0.8859 (mtp) REVERT: G 169 ASP cc_start: 0.8391 (m-30) cc_final: 0.7308 (p0) REVERT: G 214 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7199 (pp20) REVERT: H 37 ARG cc_start: 0.7867 (mtp-110) cc_final: 0.7378 (mtt-85) REVERT: J 33 GLN cc_start: 0.7329 (mm110) cc_final: 0.6936 (mm110) REVERT: J 37 ARG cc_start: 0.8460 (ttm110) cc_final: 0.8130 (ttm110) REVERT: J 38 ASN cc_start: 0.7100 (OUTLIER) cc_final: 0.6850 (p0) REVERT: J 49 MET cc_start: 0.6965 (ttp) cc_final: 0.6717 (tmm) REVERT: K 35 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7544 (tp) REVERT: N 38 ASN cc_start: 0.7325 (t0) cc_final: 0.6932 (t0) REVERT: N 56 THR cc_start: 0.7486 (OUTLIER) cc_final: 0.7260 (t) REVERT: R 11 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: R 18 ASP cc_start: 0.7582 (m-30) cc_final: 0.7099 (m-30) REVERT: R 21 MET cc_start: 0.8396 (tpt) cc_final: 0.7890 (tpt) REVERT: R 91 ARG cc_start: 0.5839 (OUTLIER) cc_final: 0.5570 (ptt-90) REVERT: S 93 SER cc_start: 0.6689 (m) cc_final: 0.6228 (p) REVERT: S 104 ARG cc_start: 0.9370 (tpp80) cc_final: 0.8726 (tpm-80) REVERT: S 108 GLU cc_start: 0.8625 (tp30) cc_final: 0.7463 (pt0) REVERT: T 208 TRP cc_start: 0.7850 (m100) cc_final: 0.7153 (m100) REVERT: T 230 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6690 (p90) REVERT: U 34 MET cc_start: 0.7772 (mmt) cc_final: 0.7128 (ttm) REVERT: U 120 MET cc_start: 0.9433 (mmt) cc_final: 0.9052 (tmm) REVERT: U 138 ARG cc_start: 0.7115 (tpt90) cc_final: 0.6760 (mmp80) REVERT: V 20 LEU cc_start: 0.8369 (tt) cc_final: 0.8125 (mt) REVERT: V 122 SER cc_start: 0.8038 (m) cc_final: 0.7622 (t) REVERT: V 128 ILE cc_start: 0.7713 (mm) cc_final: 0.7134 (pp) REVERT: W 97 LEU cc_start: 0.7003 (tp) cc_final: 0.6746 (tp) REVERT: W 102 LYS cc_start: 0.7050 (tppt) cc_final: 0.6825 (mptt) REVERT: W 139 LEU cc_start: 0.7822 (tm) cc_final: 0.7324 (tp) REVERT: W 146 ARG cc_start: 0.8673 (tmm160) cc_final: 0.8445 (tmm160) outliers start: 105 outliers final: 59 residues processed: 470 average time/residue: 0.5284 time to fit residues: 314.0102 Evaluate side-chains 442 residues out of total 4171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 372 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain T residue 230 PHE Chi-restraints excluded: chain U residue 69 ILE Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.2378 > 50: distance: 15 - 20: 9.502 distance: 21 - 22: 6.255 distance: 22 - 23: 12.423 distance: 22 - 24: 29.574 distance: 24 - 25: 16.703 distance: 25 - 26: 12.899 distance: 25 - 28: 19.487 distance: 26 - 27: 17.827 distance: 26 - 30: 35.085 distance: 28 - 29: 34.935 distance: 30 - 31: 16.138 distance: 31 - 32: 12.981 distance: 31 - 34: 13.022 distance: 32 - 33: 17.578 distance: 32 - 38: 27.952 distance: 34 - 35: 15.966 distance: 34 - 36: 37.903 distance: 35 - 37: 23.294 distance: 39 - 40: 20.622 distance: 40 - 41: 24.338 distance: 40 - 42: 28.717 distance: 42 - 43: 13.922 distance: 43 - 44: 9.034 distance: 43 - 46: 28.017 distance: 44 - 45: 21.866 distance: 44 - 49: 15.877 distance: 46 - 47: 20.005 distance: 46 - 48: 16.670 distance: 49 - 50: 14.749 distance: 50 - 51: 24.477 distance: 50 - 53: 17.691 distance: 51 - 52: 18.514 distance: 54 - 55: 17.494 distance: 55 - 56: 11.496 distance: 56 - 57: 7.357 distance: 56 - 58: 6.223 distance: 58 - 59: 21.357 distance: 59 - 60: 16.212 distance: 59 - 62: 10.153 distance: 60 - 61: 8.976 distance: 60 - 67: 36.265 distance: 62 - 63: 24.469 distance: 63 - 64: 7.023 distance: 64 - 65: 8.320 distance: 65 - 66: 29.163 distance: 67 - 68: 27.421 distance: 68 - 69: 5.285 distance: 68 - 71: 9.907 distance: 69 - 70: 8.290 distance: 69 - 76: 20.962 distance: 71 - 72: 15.348 distance: 72 - 73: 10.812 distance: 73 - 74: 33.781 distance: 74 - 75: 26.390 distance: 76 - 77: 14.164 distance: 77 - 78: 8.641 distance: 77 - 80: 10.690 distance: 78 - 79: 11.154 distance: 78 - 84: 10.234 distance: 80 - 81: 5.612 distance: 81 - 82: 12.894 distance: 81 - 83: 9.055